Structural Classification of Proteins

Class: Alpha and beta proteins (a/b)

: Mainly parallel beta sheets (beta-alpha-beta units)

Lineage:

Root: scop
Class: Alpha and beta proteins (a/b) [51349]
Mainly parallel beta sheets (beta-alpha-beta units)

Folds:

TIM beta/alpha-barrel [51350] (33)
contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678
the first seven superfamilies have similar phosphate-binding sites
1. Triosephosphate isomerase (TIM) [51351] (1)
  uperfamily
  1. Triosephosphate isomerase (TIM) [51352] (18)
2. Ribulose-phoshate binding barrel [51366] (6)
  uperfamily
  1. Histidine biosynthesis enzymes [51367] (6)
    structural evidence for the gene duplication within the barrel fold
  2. D-ribulose-5-phosphate 3-epimerase [51372] (5)
  3. Decarboxylase [51375] (13)
  4. Tryptophan biosynthesis enzymes [51381] (12)
  5. NanE-like [117362] (2)
    Pfam 04131
  6. PdxS-like [141755] (1)
    Pfam 01680; SOR/SNZ
3. Thiamin phosphate synthase [51391] (1)
  uperfamily
  1. Thiamin phosphate synthase [51392] (2)
4. Pyridoxine 5'-phosphate synthase [63892] (1)
  uperfamily
  1. Pyridoxine 5'-phosphate synthase [63893] (1)
5. FMN-linked oxidoreductases [51395] (1)
  uperfamily
  1. FMN-linked oxidoreductases [51396] (30)
6. Inosine monophosphate dehydrogenase (IMPDH) [51412] (1)
  The phosphate moiety of substrate binds in the 'common' phosphate-binding site
  uperfamily
  1. Inosine monophosphate dehydrogenase (IMPDH) [51413] (8)
7. PLP-binding barrel [51419] (2)
  circular permutation of the canonical fold: begins with an alpha helix and ends with a beta-strand
  uperfamily
  1. Alanine racemase-like, N-terminal domain [51420] (9)
  2. "Hypothetical" protein ybl036c [51427] (1)
8. NAD(P)-linked oxidoreductase [51430] (1)
  uperfamily
  1. Aldo-keto reductases (NADP) [51431] (20)
    Common fold covers whole protein structure
9. (Trans)glycosidases [51445] (14)
  uperfamily
  1. Amylase, catalytic domain [51446] (54)
    members of the family may contain various insert subdomains
    in alpha-amylases and closer relatives this domain is usually followed by a common all-beta domain
  2. beta-glycanases [51487] (54)
    consist of a number of sequence families
  3. Putative alpha-L-fucosidase, catalytic domain [102079] (1)
    glycosyl hydrolase family 29; contains additional beta-barrel with a topological similarity to the C-terminal domain of alpha amylases
  4. Family 1 of glycosyl hydrolase [51521] (15)
  5. Type II chitinase [51534] (22)
    glycosylase family 18
  6. 1,4-beta-N-acetylmuraminidase [63912] (3)
    Glycosyl hydrolase family 25; probably have evolved from a type II chitinase ancestor
    permutation of the common fold; strand 8 is antiparallel to the rest of the barrel
  7. beta-N-acetylhexosaminidase catalytic domain [51550] (5)
    Glycosyl hydrolase family 20, GH20
  8. alpha-D-glucuronidase/Hyaluronidase catalytic domain [82253] (4)
    Glycosyl hydrolase family 67, GH67; structurally related to GH20; contains extra C-terminal alpha-helical subdomain
  9. NagZ-like [51553] (2)
    Pfam 00933; Glycosyl hydrolase family 3 domain
  10. Bee venom hyaluronidase [69387] (1)
    distorted barrel lacks the second strand
  11. Outer surface protein, N-terminal domain [110354] (1)
    corresponds to the N-terminal part of Pfam 05913
  12. YicI catalytic domain-like [117372] (2)
  13. Glycosyl hydrolases family 35 catalytic domain [117375] (1)
    Pfam 01301
  14. TM1410-like [141796] (1)
    Pfam 03537
10. Metallo-dependent hydrolases [51556] (18)
  the beta-sheet barrel is similarly distorted and capped by a C-terminal helix
  has transition metal ions bound inside the barrel
  uperfamily
  1. Adenosine/AMP deaminase [51557] (4)
  2. Dihydroorotase [63917] (1)
  3. Cytosine deaminase catalytic domain [69390] (1)
  4. alpha-subunit of urease, catalytic domain [51560] (3)
  5. Hydantoinase (dihydropyrimidinase), catalytic domain [75073] (9)
  6. SAH/MTA deaminase-like [82258] (5)
  7. Isoaspartyl dipeptidase, catalytic domain [89489] (1)
  8. N-acetylglucosamine-6-phosphate deacetylase, NagA, catalytic domain [82261] (3)
  9. D-aminoacylase, catalytic domain [82264] (1)
  10. TatD Mg-dependent DNase-like [82267] (4)
  11. Phosphotriesterase-like [51564] (4)
  12. Renal dipeptidase [75079] (1)
  13. Uronate isomerase-like [75082] (2)
    contains all-alpha subdomain inserted after the first strand
  14. Adenine deaminase-like [141816] (1)
  15. PP1699/LP2961-like [141819] (5)
    Pfam 04909; Amidohydrolase; stand-alone domain
  16. DR0824-like [159397] (1)
  17. Imidazolonepropionase-like [159400] (4)
  18. Zn-dependent arginine carboxypeptidase-like [159408] (3)
11. Aldolase [51569] (8)
  Common fold covers whole protein structure
  uperfamily
  1. Class I aldolase [51570] (37)
    the catalytic lysine forms schiff-base intermediate with substrate
    possible link between the aldolase superfamily and the phosphate-binding beta/alpha barrels
  2. Class II FBP aldolase [51591] (3)
    metal-dependent
  3. 5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase) [51594] (5)
    hybrid of classes I and II aldolase
  4. Class I DAHP synthetase [51599] (6)
  5. HMGL-like [89494] (3)
    Pfam 00682
  6. NeuB-like [110368] (2)
    Pfam 03102
  7. GatZ-like [141837] (1)
    Pfam 08013
  8. Class-II DAHP synthetase [141840] (1)
    Pfam 01474
12. Enolase C-terminal domain-like [51604] (2)
  binds metal ion (magnesium or manganese) in conserved site inside barrel
  N-terminal alpha+beta domain is common to this superfamily
  uperfamily
  1. Enolase [51605] (8)
  2. D-glucarate dehydratase-like [51609] (20)
13. Phosphoenolpyruvate/pyruvate domain [51621] (7)
  uperfamily
  1. Pyruvate kinase [51622] (6)
  2. Pyruvate phosphate dikinase, C-terminal domain [51629] (3)
  3. Phosphoenolpyruvate carboxylase [51632] (1)
  4. Phosphoenolpyruvate mutase/Isocitrate lyase-like [88704] (6)
    forms a swapped dimer
  5. HpcH/HpaI aldolase [51638] (4)
    forms a swapped dimer; contains a PK-type metal-binding site
  6. Ketopantoate hydroxymethyltransferase PanB [89503] (3)
  7. Mll9387-like [159416] (1)
    Pfam 09370; TIM-barrel signal transduction protein; forms a swapped dimer similar to the Phosphoenolpyruvate mutase/Isocitrate lyase-like and HpcH/HpaI aldolase families
14. Malate synthase G [51645] (1)
  uperfamily
  1. Malate synthase G [51646] (2)
15. RuBisCo, C-terminal domain [51649] (1)
  uperfamily
  1. RuBisCo, large subunit, C-terminal domain [51650] (12)
    N-terminal domain is alpha+beta
16. Xylose isomerase-like [51658] (7)
  different families share similar but non-identical metal-binding sites
  uperfamily
  1. Endonuclease IV [51659] (2)
  2. IolI-like [75090] (3)
  3. Hypothetical protein YgbM (EC1530) [75093] (1)
  4. L-rhamnose isomerase [51662] (1)
  5. Xylose isomerase [51665] (12)
  6. UxuA-like [110377] (1)
    Pfam 03786
  7. KguE-like [141854] (1)
    part of Pfam 01261
17. Bacterial luciferase-like [51679] (4)
  consists of clearly related families of somewhat different folds
  uperfamily
  1. Bacterial luciferase (alkanal monooxygenase) [51680] (2)
    typical (beta/alpha)8-barrel fold
    heterodimer of two similar chains
  2. Non-fluorescent flavoprotein (luxF, FP390) [51683] (2)
    incomplete beta/alpha barrel with mixed beta-sheet of 7 strands
  3. F420 dependent oxidoreductases [51687] (3)
  4. Ssud-like monoxygenases [82275] (2)
18. Nicotinate/Quinolinate PRTase C-terminal domain-like [51690] (2)
  incomplete beta/alpha barrel with parallel beta-sheet of 7 strands
  uperfamily
  1. NadC C-terminal domain-like [51691] (6)
  2. Monomeric nicotinate phosphoribosyltransferase C-terminal domain [110910] (3)
19. PLC-like phosphodiesterases [51695] (3)
  uperfamily
  1. Mammalian PLC [51696] (2)
  2. Bacterial PLC [51699] (2)
  3. Glycerophosphoryl diester phosphodiesterase [89508] (4)
    Pfam 03009
20. Cobalamin (vitamin B12)-dependent enzymes [51703] (4)
  uperfamily
  1. Methylmalonyl-CoA mutase, N-terminal (CoA-binding) domain [51704] (2)
    the subunits are clearly related but only one (alpha) is active
  2. Glutamate mutase, large subunit [51707] (1)
  3. Diol dehydratase, alpha subunit [51710] (2)
  4. D-lysine 5,6-aminomutase alpha subunit, KamD [117392] (1)
    most similar to the glutamate mutase subunit; contains second cofactor, PLP
21. tRNA-guanine transglycosylase [51713] (1)
  uperfamily
  1. tRNA-guanine transglycosylase [51714] (2)
22. Dihydropteroate synthetase-like [51717] (2)
  uperfamily
  1. Dihydropteroate synthetase [51718] (4)
  2. Methyltetrahydrofolate-utiluzing methyltransferases [51723] (2)
23. UROD/MetE-like [51726] (2)
  uperfamily
  1. Uroporphyrinogen decarboxylase, UROD [51727] (2)
  2. Cobalamin-independent methionine synthase [110384] (1)
    Pfam 01717; duplication; consists of two related domains
24. FAD-linked oxidoreductase [51730] (2)
  distinct cofactor-binding mode from both FMN- and NAD(P)-linked TIM-barrel oxidoreductases; families are related by a circular permutation
  uperfamily
  1. Methylenetetrahydrofolate reductase [51731] (2)
  2. Proline dehydrohenase domain of bifunctional PutA protein [82279] (1)
25. Monomethylamine methyltransferase MtmB [75098] (1)
  uperfamily
  1. Monomethylamine methyltransferase MtmB [75099] (1)
26. Homocysteine S-methyltransferase [82282] (1)
  uperfamily
  1. Homocysteine S-methyltransferase [82283] (3)
    Pfam 02574
27. (2r)-phospho-3-sulfolactate synthase ComA [102110] (1)
  uperfamily
  1. (2r)-phospho-3-sulfolactate synthase ComA [102111] (2)
28. Radical SAM enzymes [102114] (3)
  common Fe-S cluster and SAM binding sites are embedded into complete or incomplete beta/alpha-barrel
  uperfamily
  1. Biotin synthase [102115] (1)
    regular (beta/alpha)8 barrel
  2. Oxygen-independent coproporphyrinogen III oxidase HemN [102118] (1)
    open beta/alpha barrel decorated with additional structures
  3. MoCo biosynthesis proteins [110388] (1)
    open alpha/beta-barrel with a specific second FeS cluster-binding region corresponding to Pfam 06463
29. GlpP-like [110391] (1)
  uperfamily
  1. GlpP-like [110392] (1)
    Pfam 04309
30. CutC-like [110395] (1)
  uperfamily
  1. CutC-like [110396] (1)
    Pfam 03932
31. ThiG-like [110399] (1)
  shares the common phosphate-binding site with other superfamilies
  uperfamily
  1. ThiG-like [110400] (2)
    Pfam 05690
32. TM1631-like [117396] (1)
  uperfamily
  1. TM1631-like [117397] (2)
    Pfam 01904; DUF72
33. EAL domain-like [141868] (1)
  variant of the beta/alpha-barrel fold with strand 1 being antiparallel to the rest
  uperfamily
  1. EAL domain [141869] (1)
    Pfam 00563
NAD(P)-binding Rossmann-fold domains [51734] (1)
core: 3 layers, a/b/a; parallel beta-sheet of 6 strands, order 321456
The nucleotide-binding modes of this and the next two folds/superfamilies are similar
1. NAD(P)-binding Rossmann-fold domains [51735] (12)
  uperfamily
  1. Alcohol dehydrogenase-like, C-terminal domain [51736] (28)
    N-terminal all-beta domain defines family
  2. Tyrosine-dependent oxidoreductases [51751] (108)
    also known as short-chain dehydrogenases and SDR family
    parallel beta-sheet is extended by 7th strand, order 3214567; left-handed crossover connection between strands 6 and 7
  3. Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain [51800] (52)
    family members also share a common alpha+beta fold in C-terminal domain
  4. Formate/glycerate dehydrogenases, NAD-domain [51830] (14)
    this domain interrupts the other domain which defines family
  5. Siroheme synthase N-terminal domain-like [75110] (2)
  6. LDH N-terminal domain-like [51848] (33)
  7. 6-phosphogluconate dehydrogenase-like, N-terminal domain [51868] (26)
    the beta-sheet is extended to 8 strands, order 32145678; strands 7 & 8 are antiparallel to the rest
    C-terminal domains also show some similarity
  8. Aminoacid dehydrogenase-like, C-terminal domain [51883] (24)
    extra N-terminal helix displaces the C-terminal helix (following strand 6) from its usual position creating a family nicotineamide-binding site
  9. Potassium channel NAD-binding domain [63944] (4)
  10. Transcriptional repressor Rex, C-terminal domain [102174] (1)
  11. CoA-binding domain [51900] (7)
  12. Ornithine cyclodeaminase-like [110436] (2)
    Pfam 02423; contains additional alpha+beta dimerisation subdomain mostly formed by the N-terminal meander beta-sheet
FAD/NAD(P)-binding domain [51904] (1)
core: 3 layers, b/b/a; central parallel beta-sheet of 5 strands, order 32145; top antiparallel beta-sheet of 3 strands, meander
1. FAD/NAD(P)-binding domain [51905] (8)
  uperfamily
  1. C-terminal domain of adrenodoxin reductase-like [51906] (5)
  2. FAD-linked reductases, N-terminal domain [51913] (25)
    C-terminal domain is alpha+beta is common for the family
  3. GDI-like N domain [51931] (3)
    Similar to FAD-linked reductases in both domains but does not bind FAD
  4. Succinate dehydrogenase/fumarate reductase flavoprotein N-terminal domain [51934] (7)
  5. FAD/NAD-linked reductases, N-terminal and central domains [51943] (28)
    duplication: both domains have similar folds and functions
    most members of the family contain common C-terminal alpha+beta domain
  6. Thi4-like [141942] (2)
    Pfam 01946; stand-alone, moderately decorated domain
  7. GidA-like [141946] (1)
    part of Pfam 01266
  8. HI0933 N-terminal domain-like [159436] (2)
    N-terminal part of Pfam 03486
Nucleotide-binding domain [51970] (1)
3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32145; Rossmann-like
1. Nucleotide-binding domain [51971] (3)
  this superfamily shares the common nucleotide-binding site with and provides a link between the Rossmann-fold NAD(P)-binding and FAD/NAD(P)-binding domains
  uperfamily
  1. N-terminal domain of adrenodoxin reductase-like [51972] (5)
  2. D-aminoacid oxidase, N-terminal domain [51979] (2)
    This family is probably related to the FAD-linked reductases and shares with them the C-terminal domain fold
  3. UDP-galactopyranose mutase, N-terminal domain [69427] (2)
    domain structure is similar to that of D-aminoacid oxidase
MurCD N-terminal domain [51983] (1)
3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32145; incomplete Rossmann-like fold; binds UDP group
1. MurCD N-terminal domain [51984] (1)
  uperfamily
  1. MurCD N-terminal domain [51985] (3)
7-stranded beta/alpha barrel [51988] (3)
variant of beta/alpha barrel; parallel beta-sheet barrel, closed, n=7, S=8; strand order 1234567; some members may have fewer strands
1. Glycosyl hydrolases family 6, cellulases [51989] (1)
  uperfamily
  1. Glycosyl hydrolases family 6, cellulases [51990] (5)
    Pfam 01341
2. PHP domain-like [89550] (2)
  uperfamily
  1. PHP domain [89551] (2)
    putative phosphoesterase domain; contains trinuclear metal-binding site; some similarity to the metallohydrolases of TIM-barrel fold
  2. RNase P subunit p30 [110442] (1)
    Pfam 01876
3. Glycoside hydrolase/deacetylase [88713] (8)
  in the different families beta-barrels are similarly distorted but may vary in the number of strands
  uperfamily
  1. 4-alpha-glucanotransferase, N-terminal domain [89554] (1)
    family 57 glycoside hydrolase; overall domain organization is similar to that of the alpha-mannosidase family
  2. alpha-mannosidase [88714] (2)
    family 38 glycoside hydrolase; overall domain organization is similar to that of the 4-alpha-glucanotransferase family
  3. AmyC N-terminal domain-like [102189] (2)
  4. NodB-like polysaccharide deacetylase [89559] (6)
    variant of beta/alpha barrel; parallel beta-sheet barrel, closed, n=6, S=8; strand order 123456
  5. LamB/YcsF-like [117449] (3)
    Pfam 03746
  6. PA1517-like [141965] (1)
    seven-stranded barrel with a detectable sequence similarity to the six-stranded barrel NodB-like family; member of the same Pfam family (Pfam 01522)
  7. Divergent polysaccharide deacetylase [141968] (1)
    Pfam 04748
  8. YdjC-like [159441] (1)
    Pfam 04794
PFL-like glycyl radical enzymes [51997] (1)
contains: barrel, closed; n=10, S=10; accommodates a hairpin loop inside the barrel
1. PFL-like glycyl radical enzymes [51998] (5)
  duplication: the N- and C-terminal halves have similar topologies
  uperfamily
  1. PFL-like [51999] (2)
    Pfam 02901; except the C-terminal ~100 residues covered by Pfam 01228
  2. R1 subunit of ribonucleotide reductase, C-terminal domain [52002] (2)
  3. B12-dependent (class II) ribonucleotide reductase [75131] (1)
  4. Class III anaerobic ribonucleotide reductase NRDD subunit [52005] (1)
  5. SP0239-like [159444] (1)
    Pfam 05167; DUF771
The "swivelling" beta/beta/alpha domain [52008] (10)
3 layers: b/b/a; the central sheet is parallel, and the other one is antiparallel; there are some variations in topology
this domain is thought to be mobile in most multi-domain proteins known to contain it
1. Phosphohistidine domain [52009] (2)
  contains barrel, closed, n=7, S=10
  uperfamily
  1. Pyruvate phosphate dikinase, central domain [52010] (3)
  2. N-terminal domain of enzyme I of the PEP:sugar phosphotransferase system [52013] (1)
2. RraA-like [89562] (1)
  structural similarity and possible distant homology to the phosphohistidine domain of pyruvate phosphate dikinase
  uperfamily
  1. RraA-like [89563] (4)
    aka MenG-like; characterized as regulator of RNase E activity A (RraA) that globally modulates RNA abundance in E. coli
3. Putative cyclase [102198] (1)
  contains mixed beta-sheet barrel, closed n=7, S=10
  uperfamily
  1. Putative cyclase [102199] (2)
    Pfam 04199; COG1878: predicted metal-dependent hydrolase
4. LeuD/IlvD-like [52016] (3)
  contains mixed beta-sheet barrel, closed n=7, S=10
  uperfamily
  1. LeuD-like [52017] (5)
    Pfam 00694; permutation of the domain order in the proteins containing this family domain
  2. IlvD/EDD C-terminal domain-like [141976] (1)
    C-terminal part of Pfam 00920
  3. AF0055-like [141979] (1)
    PF01989; DUF126; probable link between the LeuD-like and Phosphohistidine domain superfamilies (sequence similarity crosshits)
5. Carbamoyl phosphate synthetase, small subunit N-terminal domain [52021] (1)
  uperfamily
  1. Carbamoyl phosphate synthetase, small subunit N-terminal domain [52022] (1)
6. Swiveling domain of dehydratase reactivase alpha subunit [82317] (1)
  uperfamily
  1. Swiveling domain of dehydratase reactivase alpha subunit [82318] (2)
7. PA domain [52025] (1)
  uperfamily
  1. PA domain [52026] (2)
8. GroEL apical domain-like [52029] (2)
  uperfamily
  1. GroEL-like chaperone, apical domain [52030] (4)
  2. Group II chaperonin (CCT, TRIC), apical domain [52034] (4)
9. FumA C-terminal domain-like [117457] (1)
  uperfamily
  1. FumA C-terminal domain-like [117458] (1)
    Pfam 05683
10. LD-carboxypeptidase A C-terminal domain-like [141986] (1)
  uperfamily
  1. LD-carboxypeptidase A C-terminal domain-like [141987] (1)
    C-terminal half of Pfam 02016
Barstar-like [52037] (2)
2 layers, a/b; parallel beta-sheet of 3 strands, order 123
1. Barstar-related [52038] (1)
  uperfamily
  1. Barstar-related [52039] (2)
2. Ribosomal protein L32e [52042] (1)
  uperfamily
  1. Ribosomal protein L32e [52043] (1)
    contains irregular N-terminal extension to the common fold
MurF and HprK N-domain-like [63417] (2)
core: 3 layers, a/b/a; parallel beta-sheet of 4 strands, order 1234; structural similarity of the MurF and HprK extends beyond the core.
1. MurE/MurF N-terminal domain [63418] (1)
  binds UDP group
  uperfamily
  1. MurE/MurF N-terminal domain [63419] (2)
2. HprK N-terminal domain-like [75138] (2)
  probable phosphatase
  uperfamily
  1. HPr kinase/phoshatase HprK N-terminal domain [75139] (2)
  2. DRTGG domain [159447] (1)
    Pfam 07085
Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) [52046] (3)
2 curved layers, a/b; parallel beta-sheet; order 1234...N; there are sequence similarities between different superfamilies
1. RNI-like [52047] (3)
  regular structure consisting of similar repeats
  uperfamily
  1. 28-residue LRR [52048] (4)
  2. Rna1p (RanGAP1), N-terminal domain [52052] (1)
  3. Cyclin A/CDK2-associated p19, Skp2 [52055] (1)
2. L domain-like [52058] (8)
  less regular structure consisting of variable repeats
  uperfamily
  1. Internalin LRR domain [52059] (3)
    capped at the N-end with a truncated EF-hand subdomain
  2. Leucine rich effector protein YopM [69433] (1)
  3. Ngr ectodomain-like [75142] (6)
  4. Polygalacturonase inhibiting protein PGIP [89569] (1)
  5. Rab geranylgeranyltransferase alpha-subunit, C-terminal domain [52062] (1)
  6. mRNA export factor tap [52065] (1)
  7. U2A'-like [52068] (1)
    duplication: consists of 5-6 partly irregular repeats
  8. L domain [52071] (6)
3. Outer arm dynein light chain 1 [52075] (1)
  (beta-beta-alpha)n superhelix
  uperfamily
  1. Outer arm dynein light chain 1 [52076] (1)
Ribosomal proteins L15p and L18e [52079] (1)
core: three turns of irregular (beta-beta-alpha)n superhelix
1. Ribosomal proteins L15p and L18e [52080] (1)
  uperfamily
  1. Ribosomal proteins L15p and L18e [52081] (5)
SpoIIaa-like [52086] (2)
core: 4 turns of a (beta-alpha)n superhelix
1. CRAL/TRIO domain [52087] (1)
  uperfamily
  1. CRAL/TRIO domain [52088] (3)
    Pfam 00650
2. SpoIIaa-like [52091] (2)
  uperfamily
  1. Anti-sigma factor antagonist SpoIIaa [52092] (4)
  2. Sfri0576-like [159456] (2)
    significant structural variability despite high sequence similarity
ClpP/crotonase [52095] (1)
core: 4 turns of (beta-beta-alpha)n superhelix
1. ClpP/crotonase [52096] (4)
  uperfamily
  1. Clp protease, ClpP subunit [52097] (5)
  2. Tail specific protease, catalytic domain [52100] (3)
    includes N-terminal all-alpha subdomain
  3. Crotonase-like [52103] (17)
  4. Biotin dependent carboxylase carboxyltransferase domain [89572] (8)
    Pfam 01039
    the active site is formed by two different homologous subunits or domains of this fold
BRCT domain [52112] (1)
3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134
1. BRCT domain [52113] (5)
  Pfam 00533
  uperfamily
  1. BRCT domain [63955] (2)
  2. 53BP1 [75148] (1)
  3. DNA-repair protein XRCC1 [52114] (1)
  4. DNA ligase [52117] (2)
  5. DNA topoisomerase II binding protein 1, TopBP1 [117468] (1)
Lumazine synthase [52120] (1)
3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134
1. Lumazine synthase [52121] (1)
  uperfamily
  1. Lumazine synthase [52122] (7)
Uracil-DNA glycosylase-like [52140] (1)
3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134
1. Uracil-DNA glycosylase-like [52141] (4)
  uperfamily
  1. Uracil-DNA glycosylase [52142] (5)
  2. Mug-like [52147] (4)
  3. Single-strand selective monofunctional uracil-DNA glycosylase SMUG1 [89579] (1)
  4. AF0587 domain-like [159464] (1)
    a middle domain in the founder protein
Creatininase [102214] (1)
3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134
1. Creatininase [102215] (1)
  uperfamily
  1. Creatininase [102216] (1)
DNA polymerase III psi subunit [102219] (1)
3 layers, a/b/a; parallel beta-sheet of 4 strands, order 2134
1. DNA polymerase III psi subunit [102220] (1)
  uperfamily
  1. DNA polymerase III psi subunit [102221] (1)
Initiation factor IF2/eIF5b, domain 3 [52155] (1)
3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134
1. Initiation factor IF2/eIF5b, domain 3 [52156] (1)
  uperfamily
  1. Initiation factor IF2/eIF5b, domain 3 [52157] (1)
Aminoacid dehydrogenase-like, N-terminal domain [53222] (1)
core: 3 layers: a/b/a; parallel beta-sheet of 4 strands; 2134
1. Aminoacid dehydrogenase-like, N-terminal domain [53223] (5)
  uperfamily
  1. Aminoacid dehydrogenases [53224] (10)
    dimerisation domain; contains additional structures including two extra N-terminal strands in the beta-sheet
  2. Tetrahydrofolate dehydrogenase/cyclohydrolase [53235] (3)
  3. Methylene-tetrahydromethanopterin dehydrogenase [82333] (1)
  4. Shikimate dehydrogenase-like [82336] (5)
  5. Malic enzyme N-domain [53240] (4)
    Pfam 00390; decorated with additional structures; includes N-terminal additional subdomains and extra N-terminal strand
Toprim domain [110454] (1)
3 layers, a/b/a; parallel beta-sheet of 4 strands, order 2134
1. Toprim domain [110455] (1)
  this domain is also present in several multidomain proteins that are not split in scop yet: scop_sf 56712, scop_sf 56719, scop_sf 56726, scop_sf 56731
  uperfamily
  1. Toprim domain [110456] (2)
    Pfam 01751
AtpF-like [159467] (1)
3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 2134
1. AtpF-like [159468] (1)
  1. AtpF-like [159469] (2)
    Pfam 01990; segment-swapping in some members
Ribosomal protein L13 [52160] (1)
3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 3214
1. Ribosomal protein L13 [52161] (1)
  uperfamily
  1. Ribosomal protein L13 [52162] (5)
Ribosomal protein L4 [52165] (1)
3 layers, a/b/a; core: parallel beta-sheet of 4 strands, order 1423
1. Ribosomal protein L4 [52166] (1)
  uperfamily
  1. Ribosomal protein L4 [52167] (5)
Nqo1 FMN-binding domain-like [142018] (1)
3 layers, a/b/a; parallel beta-sheet of 4 strands, order 3214
1. Nqo1 FMN-binding domain-like [142019] (1)
  uperfamily
  1. Nqo1 FMN-binding domain-like [142020] (1)
    N-terminal part of Pfam 01512
Flavodoxin-like [52171] (15)
3 layers, a/b/a; parallel beta-sheet of 5 strand, order 21345
1. CheY-like [52172] (7)
  uperfamily
  1. CheY-related [52173] (32)
  2. Receiver domain of the ethylene receptor [52194] (1)
  3. Positive regulator of the amidase operon AmiR [52197] (1)
  4. Ornithine decarboxylase N-terminal "wing" domain [52252] (1)
  5. N-terminal domain of the circadian clock protein KaiA [82344] (1)
    lacks canonical receiver domains features
  6. RcsC linker domain-like [142037] (1)
    PfamB 016190; probable rudiment CheY-like domain; precedes the C-terminal CheY-related domain of similar structure
  7. AF1403 C-terminal domain-like [142040] (1)
2. Toll/Interleukin receptor TIR domain [52200] (1)
  uperfamily
  1. Toll/Interleukin receptor TIR domain [52201] (2)
3. Hypothetical protein MTH538 [52206] (1)
  uperfamily
  1. Hypothetical protein MTH538 [52207] (1)
4. Succinyl-CoA synthetase domains [52210] (1)
  uperfamily
  1. Succinyl-CoA synthetase domains [52211] (6)
    contain additional N-terminal strand "0", antiparallel to strand 2
5. Flavoproteins [52218] (8)
  uperfamily
  1. Flavodoxin-related [52219] (13)
    binds FMN
  2. Cytochrome p450 reductase N-terminal domain-like [52231] (4)
  3. Quinone reductase [52235] (6)
    binds FAD
  4. Hypothetical protein SP1951 [102234] (1)
  5. Hypothetical protein YwqN [102237] (1)
  6. NADPH-dependent FMN reductase [89590] (4)
    Pfam 03358
  7. Flavoprotein NrdI [110477] (1)
  8. WrbA-like [117474] (3)
6. Cobalamin (vitamin B12)-binding domain [52242] (1)
  uperfamily
  1. Cobalamin (vitamin B12)-binding domain [52243] (6)
7. N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) [52255] (1)
  uperfamily
  1. N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) [52256] (4)
8. SGNH hydrolase [52266] (9)
  uperfamily
  1. Esterase [52267] (1)
  2. Esterase domain of haemagglutinin-esterase-fusion glycoprotein HEF1 [52270] (1)
  3. Acetylhydrolase [52273] (3)
  4. Rhamnogalacturonan acetylesterase [52276] (1)
  5. TAP-like [89594] (2)
  6. Hypothetical protein alr1529 [102240] (1)
  7. Putative acetylxylan esterase-like [142058] (2)
    Pfam 03629 (DUF303); contains a characteristic zinc(less) finger-like insertion after strand 1; lacks the conserved in other families Asn residue
  8. YxiM C-terminal domain-like [159482] (1)
    subfamily of Pfam 00657
  9. BT2961-like [159485] (2)
    PfamB 005894;homotrimeric assembly
9. Beta-D-glucan exohydrolase, C-terminal domain [52279] (1)
  uperfamily
  1. Beta-D-glucan exohydrolase, C-terminal domain [52280] (1)
10. Formate/glycerate dehydrogenase catalytic domain-like [52283] (3)
  uperfamily
  1. Formate/glycerate dehydrogenases, substrate-binding domain [52284] (9)
    this domain is interrupted by the Rossmann-fold domain
  2. L-alanine dehydrogenase-like [52297] (2)
  3. S-adenosylhomocystein hydrolase [52300] (3)
11. Type II 3-dehydroquinate dehydratase [52304] (1)
  uperfamily
  1. Type II 3-dehydroquinate dehydratase [52305] (5)
12. N-(deoxy)ribosyltransferase-like [52309] (3)
  there are similar active site architectures as well as the catalytic mechanisms of functionally characterised members
  uperfamily
  1. N-deoxyribosyltransferase [52310] (3)
  2. Hypothetical protein PA1492 [110461] (1)
    lacks the last strand; monomer; predicted deoxyribosyltransferase activity
  3. ADP ribosyl cyclase-like [56630] (3)
    contains extra N-terminal all-alpha subdomain
13. Ribosomal protein S2 [52313] (1)
  fold elaborated with additional structures
  uperfamily
  1. Ribosomal protein S2 [52314] (3)
14. Precorrin-8X methylmutase CbiC/CobH [63965] (1)
  fold elaborated with additional structures
  uperfamily
  1. Precorrin-8X methylmutase CbiC/CobH [63966] (3)
15. Class I glutamine amidotransferase-like [52317] (9)
  conserved positions of the oxyanion hole and catalytic nucleophile; different constituent families contain different additional structures
  uperfamily
  1. Class I glutamine amidotransferases (GAT) [52318] (18)
    contains a catalytic Cys-His-Glu triad
  2. A4 beta-galactosidase middle domain [82351] (1)
    probable non-catalytic branch of the class I GAT family; overall fold is very similar but the active site is not conserved
  3. DJ-1/PfpI [52325] (9)
    contains a catalytic triad or dyad different from the class I GAT triad
  4. Catalase, C-terminal domain [52328] (2)
  5. Aspartyl dipeptidase PepE [52331] (1)
    probable circular permutation in the common core; contains a catalytic Ser-His-Glu triad
  6. ThuA-like [110486] (1)
    Pfam 06283; overall fold is very similar the class I GAT family but the putative active site has a different structure
  7. LD-carboxypeptidase A N-terminal domain-like [142074] (1)
    N-terminal half of Pfam 02016
  8. HTS-like [142077] (1)
    Pfam 04204
  9. STM3548-like [159492] (1)
    Pfam 07090; DUF1355
Methylglyoxal synthase-like [52334] (1)
3 layers, a/b/a; parallel beta-sheet of 5 strands, order 32145
1. Methylglyoxal synthase-like [52335] (3)
  contains a common phosphate-binding site
  uperfamily
  1. Carbamoyl phosphate synthetase, large subunit allosteric, C-terminal domain [52336] (1)
  2. Methylglyoxal synthase, MgsA [52339] (3)
  3. Inosicase [63971] (3)
Ferredoxin reductase-like, C-terminal NADP-linked domain [52342] (1)
3 layers, a/b/a; parallel beta-sheet of 5 strands, order 32145
1. Ferredoxin reductase-like, C-terminal NADP-linked domain [52343] (5)
  binds NADP differently than classical Rossmann-fold
  N-terminal FAD-linked domain contains (6,10) barrel
  uperfamily
  1. Reductases [52344] (13)
  2. Aromatic dioxygenase reductase-like [52359] (3)
    contains additional 2Fe-2S ferredoxin domain at one of the termini
  3. Dihydroorotate dehydrogenase B, PyrK subunit [52362] (1)
    contains 2Fe-2S cluster in the C-terminal extension
  4. NADPH-cytochrome p450 reductase-like [52365] (3)
  5. Flavohemoglobin, C-terminal domain [52370] (2)
    contains additional globin domain
Adenine nucleotide alpha hydrolase-like [52373] (3)
core: 3 layers, a/b/a ; parallel beta-sheet of 5 strands, order 32145
1. Nucleotidylyl transferase [52374] (5)
  uperfamily
  1. Class I aminoacyl-tRNA synthetases (RS), catalytic domain [52375] (22)
    contains a conserved all-alpha subdomain at the C-terminal extension
  2. Cytidylyltransferase [52394] (1)
  3. Adenylyltransferase [52397] (13)
  4. Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC) [63976] (3)
    contains C-terminal subdomain similar to one structural repeat of the Creatinase/aminopeptidase family
  5. ATP sulfurylase catalytic domain [63979] (5)
2. Adenine nucleotide alpha hydrolases-like [52402] (6)
  share similar mode of ligand (Adenosine group) binding
  can be subdivided into two group with closer relationships within each group than between the groups; the first three families form one group whereas the last two families form the other group
  uperfamily
  1. N-type ATP pyrophosphatases [52403] (13)
  2. PP-loop ATPase [82359] (2)
  3. PAPS reductase-like [52410] (2)
  4. ETFP subunits [52432] (6)
    alpha/beta heterodimer of homologous subunits; contains additional strands on both edges of the core sheet
  5. Universal stress protein-like [52436] (7)
    Pfam 00582
  6. ThiI-like [142093] (2)
    Pfam 02568
3. UDP-glucose/GDP-mannose dehydrogenase C-terminal domain [52413] (1)
  uperfamily
  1. UDP-glucose/GDP-mannose dehydrogenase C-terminal domain [52414] (2)
Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain [52417] (1)
3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32145; Rossmann-like
1. Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain [52418] (1)
  uperfamily
  1. Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain [52419] (6)
Cryptochrome/photolyase, N-terminal domain [52424] (1)
3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32145; Rossmann-like
1. Cryptochrome/photolyase, N-terminal domain [52425] (1)
  uperfamily
  1. Cryptochrome/photolyase, N-terminal domain [52426] (5)
DsrEFH-like [75168] (1)
3 layers: a/b/a, core: parallel beta-sheet of 5 strands, order 43215
1. DsrEFH-like [75169] (2)
  uperfamily
  1. DsrEF-like [75170] (6)
    Pfam 02635
  2. DsrH-like [117489] (3)
    Pfam 04077
PIN domain-like [88722] (1)
3 layers, a/b/a; core: parallel beta-sheet of 5 strands, order 32145
1. PIN domain-like [88723] (2)
  uperfamily
  1. PIN domain [89619] (7)
    Pfam 01850
  2. 5' to 3' exonuclease catalytic domain [53045] (8)
    contains an alpha-helical arch and additional strand 6 antiparallel to the rest; strand order 321456; similarity to the resolvase-like fold
Ribose/Galactose isomerase RpiB/AlsB [89622] (1)
3 layers: a/b/a, core: parallel beta-sheet of 5 strands, order 21354; topological similarity to a part of the arginase/deacetylase fold
1. Ribose/Galactose isomerase RpiB/AlsB [89623] (1)
  uperfamily
  1. Ribose/Galactose isomerase RpiB/AlsB [89624] (3)
EreA/ChaN-like [159500] (1)
Core: 3 layers: a/b/a; parallel beta-sheet of 5 strands, order:51423;
1. EreA/ChaN-like [159501] (3)
  there are four conserved residues in the putative active site: two His and two Glu
  1. ChaN-like [159502] (1)
    Pfam 04187; DUF399; Ferric uptake regulator CjrA
  2. PMT domain-like [159505] (1)
    This is the second from the PMT C-terminus; it retains the superfamily fold and the active site mainchain conformation but lacks the conserved in the other two families His and Glu residues
  3. EreA-like [159508] (2)
    Pfam 05139; Erythromycin esterase-like; the superfamily core is decorated with insertion of a four-helical bundle and a C-terminal alpha+beta extension
alpha/beta knot [75216] (1)
core: 3 layers: a/b/a, parallel beta-sheet of 5 strands, order 21435; contains a deep trefoil knot
1. alpha/beta knot [75217] (8)
  known or predicted SAM-dependent methytransferases including the SPOUT 'sequence' superfamily
  all known members have dimeric structures
  uperfamily
  1. YbeA-like [82371] (4)
    Pfam 02590
  2. tRNA(m1G37)-methyltransferase TrmD [89629] (3)
    fold and dimerisation mode are similar to those of the YbeA-like family; contains additional C-terminal all-alpha subdomain
  3. SpoU-like RNA 2'-O ribose methyltransferase [75218] (4)
    contains extra strand (3) in the parallel beta-sheet, order 321546
  4. Hypothetical protein MTH1 (MT0001), dimerisation domain [75221] (1)
    contains extra strand (3) in the parallel beta-sheet, order 321546; interrupted by an insert OB-fold domain
  5. YggJ C-terminal domain-like [89632] (3)
    contains extra strand (3) in the parallel beta-sheet, order 321546; similar dimerisation to the MTH1 domain
  6. EMG1/NEP1-like [159513] (2)
    Pfam 03587; structurally most similar to the AF1056-like family, but more decorated
  7. AF1056-like [159518] (2)
    Pfam 04013; DUF358
  8. AF0751-like [159523] (1)
    Pfam 01994; DUF127
PreATP-grasp domain [52439] (1)
3 layers: a/b/a; parallel or mixed beta-sheet of 4 to 6 strands
possible rudiment form of Rossmann-fold domain
1. PreATP-grasp domain [52440] (8)
  precedes the ATP-grasp domain common to all superfamily members, can contain a substrate-binding function
  uperfamily
  1. BC N-terminal domain-like [52441] (8)
  2. D-Alanine ligase N-terminal domain [52452] (3)
  3. Lysine biosynthesis enzyme LysX, N-terminal domain [102284] (1)
  4. Prokaryotic glutathione synthetase, N-terminal domain [52457] (1)
  5. Eukaryotic glutathione synthetase, substrate-binding domain [52460] (2)
    circularly permuted version of prokaryotic enzyme
  6. Synapsin domain [52463] (3)
  7. Glutathionylspermidine synthase substrate-binding domain-like [142119] (1)
    central part of Pfam 03738; GSP; overal similarity of the Pfam domain to the Eukaryotic glutathione synthetase
  8. PurP N-terminal domain-like [159526] (3)
    Pfam 06849; DUF1246
DHS-like NAD/FAD-binding domain [52466] (1)
3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456; Rossmann-like
1. DHS-like NAD/FAD-binding domain [52467] (6)
  binds cofactor molecules in the opposite direction than classical Rossmann fold
  uperfamily
  1. Deoxyhypusine synthase, DHS [52468] (1)
  2. C-terminal domain of the electron transfer flavoprotein alpha subunit [52471] (3)
    lacks strand 3; shares the FAD-binding mode with the pyruvate oxidase domain
  3. Pyruvate oxidase and decarboxylase, middle domain [52475] (12)
    N-terminal domain is Pyr module, and C-terminal domain is PP module of thiamin diphosphate-binding fold
  4. Transhydrogenase domain III (dIII) [52484] (3)
    binds NADP, shares with the pyruvate oxidase FAD-binding domain a common ADP-binding mode
  5. Sir2 family of transcriptional regulators [63984] (7)
    silent information regulator 2; contains insertion of a rubredoxin-like zinc finger domain
  6. ACDE2-like [142130] (1)
    Pfam 02552
Tubulin nucleotide-binding domain-like [52489] (1)
3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456
1. Tubulin nucleotide-binding domain-like [52490] (1)
  uperfamily
  1. Tubulin, GTPase domain [52491] (9)
Isochorismatase-like hydrolases [52498] (1)
3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456
1. Isochorismatase-like hydrolases [52499] (1)
  uperfamily
  1. Isochorismatase-like hydrolases [100948] (7)
Dipeptide transport protein [63991] (1)
3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456; also contains a C-terminal alpha+beta subdomain
1. Dipeptide transport protein [63992] (1)
  uperfamily
  1. Dipeptide transport protein [63993] (1)
Homo-oligomeric flavin-containing Cys decarboxylases, HFCD [52506] (1)
3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456
1. Homo-oligomeric flavin-containing Cys decarboxylases, HFCD [52507] (1)
  uperfamily
  1. Homo-oligomeric flavin-containing Cys decarboxylases, HFCD [52508] (5)
    Pfam 02441; formerly DFP, DNA/pantothenate metabolism flavoprotein family
HAD-like [56783] (1)
3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456
1. HAD-like [56784] (25)
  usually contains an insertion (sub)domain after strand 1
  uperfamily
  1. Probable phosphatase YrbI [69467] (1)
    the insertion subdomain is a beta-hairpin involved into tetramerisation
  2. HAD-related [56785] (3)
    the insertion subdomain is a 4-helical bundle
  3. beta-Phosphoglucomutase-like [75173] (9)
    the insertion subdomain is a 4-helical bundle
  4. YihX-like [56789] (3)
    the insertion subdomain is a 4-helical bundle
  5. Phosphonoacetaldehyde hydrolase-like [56792] (2)
    the insertion subdomain is a 4-helical bundle
  6. Phosphoserine phosphatase [64511] (2)
    the insertion subdomain is a 4-helical bundle
  7. 5'(3')-deoxyribonucleotidase (dNT-2) [82382] (1)
    the insertion subdomain is a 4-helical bundle; dephosphorylates dUMP and dTMP
  8. Homoserine kinase ThrH [102304] (1)
    the insertion subdomain is a rudiment 4-helical bundle
  9. Class B acid phosphatase, AphA [102307] (2)
    the insertion subdomain is a helical hairpin
  10. Hypothetical protein MW1667 (SA1546) [102310] (1)
    the insertion subdomain is multi-helical
  11. phosphatase domain of polynucleotide kinase [82385] (2)
    no insertion subdomains
  12. Predicted hydrolases Cof [82388] (13)
    contains an alpha+beta subdomain inserted into a new site after strand 3
  13. NagD-like [102317] (6)
    duplication: consists of two segment-swapped domains of this fold; this results in the insertion of a circularly permuted domain after strand 3, analogously to the Cof family
  14. Meta-cation ATPase, catalytic domain P [81656] (2)
    interrupted by a large insertion, domain N
  15. Trehalose-phosphatase [110506] (1)
    Pfam 02358; contains an insert alpha+beta subdomain; similar overall fold to the Cof family
  16. NLI interacting factor-like phosphatase [110509] (1)
    Pfam 03031; NIF; the insertion subdomain is a 3-stranded beta-sheet;
  17. Magnesium-dependent phosphatase-1, Mdp1 [117509] (1)
    the insertion subdomain is a 3-stranded beta-sheet different from the NIF family
  18. Hypothetical protein VC0232 [117512] (1)
    contains a deletion in the common fold; segment-swapped tetramer
  19. Histidinol phosphatase-like [142177] (3)
    no insertion subdomains
  20. MtnX-like [142180] (1)
    Pfam 06888; the insertion subdomain is a rudiment 4-helical bundle
  21. Pyrimidine 5'-nucleotidase (UMPH-1) [142183] (2)
    Pfam 05822; the insertion subdomain is a rudiment 4-helical bundle
  22. Enolase-phosphatase E1 [142186] (2)
    the insertion subdomain is a 4-helical bundle
  23. 5' nucleotidase-like [142191] (1)
    Pfam 05761; the insertion domain cosists of 3-helical bundle and a pseudo beta-barrel; contains extra C-terminal long alpha hairpin subdomain (scop_cf 46556)
  24. AF1437-like [159537] (1)
    the insertion subdomain is a rudiment 4-helical bundle; extra alpha-hairpin insertion after strand 3
  25. BT0820-like [159540] (1)
    PfamB 073209; deletion in the common fold; segment-swapped dimer
NagB/RpiA/CoA transferase-like [100949] (1)
core: 3 layers: a/b/a; parallel or mixed beta-sheet of 6 strands, order 321456
1. NagB/RpiA/CoA transferase-like [100950] (8)
  uperfamily
  1. NagB-like [52513] (3)
    share a common phosphate-binding site with the RpiA family
  2. D-ribose-5-phosphate isomerase (RpiA), catalytic domain [75176] (4)
    share a common phosphate-binding site with the NagB-like family; part of sheet is folded upon itself and forms a barrel-like structure like the CoA transferase subunits
  3. CoA transferase beta subunit-like [74657] (3)
    catalytic subunit: similar active site structure to the NagB and RpiA families; mixed beta-sheet of 7 strands, order 4321567; strand 3 is antiparallel to the rest
  4. CoA transferase alpha subunit-like [74656] (6)
    parallel beta-sheet of 7 strands, order 4321567
  5. IF2B-like [110513] (5)
    Pfam 01008; contains extra N-terminal alpha+beta domain (1-126); beta(3)-alpha(5); 3 layers: b/a/a
  6. Methenyltetrahydrofolate synthetase [110520] (3)
    Pfam 01812; 5-FTHF cyclo-ligase
  7. YkgG-like [142200] (1)
    Pfam 02589; DUF162
  8. SorC sugar-binding domain-like [159545] (5)
    Pfam 04198
Hypothetical protein MTH777 (MT0777) [75180] (1)
3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456
1. Hypothetical protein MTH777 (MT0777) [75181] (1)
  uperfamily
  1. Hypothetical protein MTH777 (MT0777) [75182] (1)
Thiamin pyrophosphokinase, catalytic domain [63998] (1)
3 layers: a/b/a; parallel beta-sheet of 6 strands, order 432156
1. Thiamin pyrophosphokinase, catalytic domain [63999] (1)
  uperfamily
  1. Thiamin pyrophosphokinase, catalytic domain [64000] (2)
Undecaprenyl diphosphate synthase [64004] (1)
3 layers: a/b/a; parallel beta-sheet of 6 strands, order 342156
1. Undecaprenyl diphosphate synthase [64005] (1)
  the sheet topology is similar to those of the N-terminal domain of phosphoglycerate kinase and carbamate kinase
  uperfamily
  1. Undecaprenyl diphosphate synthase [64006] (2)
F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD) [102323] (1)
3 layers: a/b/a; parallel beta-sheet of 6 strands, order 213456
1. F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD) [102324] (1)
  the sheet topology is similar to those of the Periplasmic binding protein-like I domains
  uperfamily
  1. F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD) [102325] (1)
Thiamin diphosphate-binding fold (THDP-binding) [52517] (1)
3 layers: a/b/a; parallel beta-sheet of 6 strands, order 213465
1. Thiamin diphosphate-binding fold (THDP-binding) [52518] (8)
  there are two different functional modules of this fold: pyridine-binding (Pyr) and pyrophosphate-binding (PP) modules
  two Pyr and two PP modules assemble together in a conserved heterotetrameric core that binds two THDP coenzyme molecules
  uperfamily
  1. Pyruvate oxidase and decarboxylase Pyr module [88724] (12)
    the N-terminal, Pyr module is separated from the C-terminal, PP module by an alpha/beta domain of Rossmann-like topology
  2. TK-like Pyr module [88735] (5)
    different order of the modules, PP module is N-terminal, Pyr module is next to it followed by a Rossmann-like domain
  3. Branched-chain alpha-keto acid dehydrogenase Pyr module [88741] (6)
    parent family to TK and PFOR
    heterodimeric protein related to TK; alpha-subunit is the PP module and the N-terminal domain of beta-subunit is the Pyr module
  4. PFOR Pyr module [88746] (1)
    domains VI, I and II are arranged in the same way as the TK PP, Pyr and C domains
  5. Pyruvate oxidase and decarboxylase PP module [88749] (12)
    the N-terminal, Pyr module is separated from the C-terminal, PP module by an alpa/beta domain of Rossmann-like topology
  6. TK-like PP module [88760] (5)
    different order of the modules, PP module is N-terminal, Pyr module is next to it followed by a Rossmann-like domain
  7. Branched-chain alpha-keto acid dehydrogenase PP module [88766] (5)
    parent family to TK and PFOR
    heterodimeric protein related to TK; alpha-subunit is the PP module and the N-terminal domain of beta-subunit is the Pyr module
  8. PFOR PP module [88771] (1)
    domains VI, I and II are arranged in the same way as the TK PP, Pyr and C domains
P-loop containing nucleoside triphosphate hydrolases [52539] (1)
3 layers: a/b/a, parallel or mixed beta-sheets of variable sizes
1. P-loop containing nucleoside triphosphate hydrolases [52540] (24)
  division into families based on beta-sheet topologies
  uperfamily
  1. Nucleotide and nucleoside kinases [52541] (46)
    parallel beta-sheet of 5 strands, order 23145
  2. Shikimate kinase (AroK) [52566] (4)
    similar to the nucleotide/nucleoside kinases but acts on different substrate
  3. Chloramphenicol phosphotransferase [52569] (1)
    similar to the nucleotide/nucleoside kinases but acts on different substrate
  4. Gluconate kinase [75195] (1)
    similar to the nucleotide/nucleoside kinases
  5. Plasmid maintenance system epsilon/zeta, toxin zeta subunit [82395] (1)
    similar to the nucleotide/nucleoside kinases; extra N- and C-terminal structures
  6. Adenosine-5'phosphosulfate kinase (APS kinase) [52572] (2)
  7. ATP sulfurylase C-terminal domain [64011] (2)
  8. PAPS sulfotransferase [52575] (15)
    Pfam 00685
    similar to the nucleotide/nucleoside kinases but transfer sulphate group
  9. Phosphoribulokinase/pantothenate kinase [52584] (5)
  10. 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain [52589] (2)
  11. G proteins [52592] (118)
    core: mixed beta-sheet of 6 strands, order 231456; strand 2 is antiparallel to the rest
  12. Motor proteins [52641] (15)
  13. Nitrogenase iron protein-like [52652] (29)
    core: parallel beta-sheet of 7 strands; order 3241567
  14. RecA protein-like (ATPase-domain) [52670] (29)
    core: mixed beta-sheet of 8 strands, order 32451678; strand 7 is antiparallel to the rest
  15. Bacterial cell division inhibitor SulA [89678] (1)
    homologous to RecA but lacks its P-loop motif; the fold is C-terminally truncated; 5-stranded parallel beta-sheet, order: 15423
  16. ABC transporter ATPase domain-like [52686] (29)
    there are two additional subdomains inserted into the central core that has a RecA-like topology
  17. Tandem AAA-ATPase domain [81268] (27)
    duplication: tandem repeat of two RecA-like (AAA) domains
  18. Extended AAA-ATPase domain [81269] (34)
    fold is similar to that of RecA, but lacks the last two strands, followed by a family-specific Arg-finger domain
  19. RNA helicase [52724] (3)
    duplication: consists of two similar domains, one binds NTP and the other binds RNA; also contains an all-alpha subdomain in the C-terminal extension
  20. Helicase-like "domain" of reverse gyrase [69496] (1)
  21. DNA helicase UvsW [102396] (1)
    contains extra N-terminal alpha+beta subdomain
  22. YjeE-like [75213] (1)
    mixed beta-sheet; order 234156(0), strands 2 and 6 are antiparallel to the rest
  23. Type II thymidine kinase [117558] (3)
    N-terminal part of Pfam 00265; parallel beta-sheet of 6 strands, order 324516; topological similarity to the RecA-like proteins, especially CobA (scop_pr 52684)
  24. Atu3015-like [142332] (2)
    unknown function; similar to the nucleotide/nucleoside kinases
PTS IIb component [52727] (1)
3 layers: a/b/a, parallel beta-sheet of 6 strands, order 324156
1. PTS IIb component [52728] (1)
  uperfamily
  1. PTS IIb component [52729] (2)
DNA polymerase III chi subunit [102399] (1)
3 layers, a/b/a; parallel beta-sheet of 7 strands, order 7165243
1. DNA polymerase III chi subunit [102400] (1)
  structural similarity and possible evolutionary relationship to the AAA domain; lacks the P-loop motif
  uperfamily
  1. DNA polymerase III chi subunit [102401] (1)
Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT) [52732] (1)
3 layers: a/b/a, parallel beta-sheet of 7 strands, order 3214567
1. Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT) [52733] (1)
  uperfamily
  1. Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT) [52734] (2)
CofD-like [142337] (1)
3 layers: a/b/a, parallel beta-sheet of 7 strands, order 3214567; topological similarity to the CobT-like fold (scop_cf 52732)
1. CofD-like [142338] (1)
  uperfamily
  1. CofD-like [142339] (2)
    Pfam 01933; UPF0052
MCP/YpsA-like [102404] (1)
3 layers: a/b/a, parallel beta-sheet of 7 strands, order 4321567
1. MCP/YpsA-like [102405] (2)
  uperfamily
  1. MoCo carrier protein-like [102406] (6)
    Pfam 03641
  2. YpsA-like [159579] (1)
    Pfam 06908; DUF1273; lacking the last strand 7; different set of conserved residues in the putative active site than in the MoCo carrier protein-like family
Methylesterase CheB, C-terminal domain [52737] (1)
3 layers: a/b/a, parallel beta-sheet of 7 strands, order 3421567
1. Methylesterase CheB, C-terminal domain [52738] (1)
  uperfamily
  1. Methylesterase CheB, C-terminal domain [52739] (1)
Subtilisin-like [52742] (1)
3 layers: a/b/a, parallel beta-sheet of 7 strands, order 2314567; left-handed crossover connection between strands 2 & 3
1. Subtilisin-like [52743] (2)
  uperfamily
  1. Subtilases [52744] (18)
  2. Serine-carboxyl proteinase, SCP [52764] (3)
    elaborated with additional structures
Indigoidine synthase A-like [110580] (1)
core: 3 layers, a/b/a; parallel beta-sheet of 7 strands, order 2134756
1. Indigoidine synthase A-like [110581] (1)
  uperfamily
  1. Indigoidine synthase A-like [110582] (1)
    Pfam 04227
Arginase/deacetylase [52767] (1)
3 layers: a/b/a, parallel beta-sheet of 8 strands, order 21387456
1. Arginase/deacetylase [52768] (2)
  uperfamily
  1. Arginase-like amidino hydrolases [52769] (8)
    Pfam 00491
  2. Histone deacetylase, HDAC [52773] (3)
Alpha-2,3/8-sialyltransferase CstII [102413] (1)
3 layers: a/b/a; parallel beta-sheet of 8 strands, order 54321678
1. Alpha-2,3/8-sialyltransferase CstII [102414] (1)
  uperfamily
  1. Alpha-2,3/8-sialyltransferase CstII [102415] (1)
Cell-division inhibitor MinC, N-terminal domain [64042] (1)
beta(2)-(alpha-beta)2-beta; 2 layers, a/b; mixed beta-sheet of 5 strands, order 12345; strands 1 & 5 are antiparallel to the rest
1. Cell-division inhibitor MinC, N-terminal domain [64043] (1)
  uperfamily
  1. Cell-division inhibitor MinC, N-terminal domain [64044] (1)
DTD-like [69499] (1)
beta(2)-(alpha-beta)2-beta(3); 3 layers, a/b/b; some topological similarity to the N-terminal domain of MinC
1. DTD-like [69500] (1)
  active form is a dimer
  uperfamily
  1. DTD-like [69501] (3)
    Pfam 02580
CoA-dependent acyltransferases [52776] (1)
core: 2 layers, a/b; mixed beta-sheet of 6 strands, order 324561; strands 3 & 6 are antiparallel to the rest
1. CoA-dependent acyltransferases [52777] (3)
  uperfamily
  1. CAT-like [52778] (5)
    trimeric enzymes with the active sites being located in between subunits
  2. Choline/Carnitine O-acyltransferase [82424] (4)
    Pfam 00755; monomeric enzyme containing tandem repeat of two CAT subunit-like domains
  3. NRPS condensation domain (amide synthase) [75229] (2)
    Pfam 00668; functional domain of multifunctional enzyme containing tandem repeat of two CAT subunit-like domains
Phosphotyrosine protein phosphatases I-like [52787] (2)
3 layers: a/b/a; parallel beta-sheet of 4 strands, order 2134
1. Phosphotyrosine protein phosphatases I [52788] (1)
  share the common active site structure with the family II
  uperfamily
  1. Low-molecular-weight phosphotyrosine protein phosphatases [52789] (7)
2. PTS system IIB component-like [52794] (2)
  uperfamily
  1. PTS system, Lactose/Cellobiose specific IIB subunit [52795] (2)
    Pfam 02302
  2. PTS system, Fructose specific IIB subunit-like [159584] (2)
    Pfam 02379
(Phosphotyrosine protein) phosphatases II [52798] (1)
core: 3 layers, a/b/a; parallel beta-sheet of 4 strands, order 1423
1. (Phosphotyrosine protein) phosphatases II [52799] (5)
  share with the family I the common active site structure with a circularly permuted topology
  uperfamily
  1. Dual specificity phosphatase-like [52800] (10)
  2. Higher-molecular-weight phosphotyrosine protein phosphatases [52805] (12)
    has an extension to the beta-sheet of 3 antiparallel strands before strand 4
  3. Myotubularin-like phosphatases [102422] (1)
    common fold is decorated with additional structures
  4. Myo-inositol hexaphosphate phosphohydrolase (phytase) PhyA [117583] (1)
  5. Mycobacterial PtpB-like [142348] (1)
Rhodanese/Cell cycle control phosphatase [52820] (1)
3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32451
1. Rhodanese/Cell cycle control phosphatase [52821] (4)
  Pfam 00581
  the active site structure is similar to those of the families I and II protein phosphatases; the topology can be related by a different circular permutation to the family I topology
  uperfamily
  1. Cell cycle control phosphatase, catalytic domain [52822] (4)
  2. Single-domain sulfurtransferase [69509] (3)
  3. Multidomain sulfurtransferase (rhodanese) [52827] (6)
    duplication: consists of two domains of this fold
  4. Ubiquitin carboxyl-terminal hydrolase 8, USP8 [117586] (1)
Thioredoxin fold [52832] (2)
core: 3 layers, a/b/a; mixed beta-sheet of 4 strands, order 4312; strand 3 is antiparallel to the rest
1. Thioredoxin-like [52833] (23)
  uperfamily
  1. Thioltransferase [52834] (31)
  2. PDI-like [52849] (6)
    duplication: contains two tandem repeats of this fold
  3. Calsequestrin [52855] (1)
    duplication: contains three tandem repeats of this fold
  4. DsbA-like [100953] (4)
    contains an all-alpha subdomain insertion
  5. Glutathione S-transferase (GST), N-terminal domain [52862] (44)
  6. Phosducin [52888] (2)
  7. ERP29 N domain-like [52892] (2)
  8. spliceosomal protein U5-15Kd [52895] (1)
  9. SH3BGR (SH3-binding, glutamic acid-rich protein-like) [102446] (1)
    related to glutaredoxin 1 (GRX1) but lacks both conserved cysteine residues
  10. KaiB-like [102449] (2)
    Pfam 07689; contains members with alternative folds
  11. DsbC/DsbG C-terminal domain-like [52898] (3)
    elaborated common fold
  12. Glutathione peroxidase-like [52901] (42)
  13. Thioredoxin-like 2Fe-2S ferredoxin [52918] (1)
  14. ArsC-like [69518] (3)
    Pfam 03960
  15. Txnl5-like [110612] (2)
    Pfam 06110
  16. YuzD-like [117605] (1)
    Pfam 07315
  17. YKR049C-like [142395] (1)
    Pfam 07955; DUF1687; contains an all-alpha insert subdomain
  18. Atu2684-like [142398] (1)
    Pfam 06764; DUF1223; contains extra C-terminal domain of Immunoglobulin-like fold (scop_cf 48725), intimately associated with the N-terminal thioredixin-like domain and contributing to the active site
  19. HyaE-like [142401] (2)
    Pfam 07449; have evolved a different function; contains no conserved cysteine residues
  20. NQO2-like [142405] (1)
    complex I 24 kDa subunit; contains 2Fe-2S cluster in the active site; includes extra N-terminal four-helical bundle
  21. Mitochondrial ribosomal protein L51/S25/CI-B8 domain [142408] (1)
    Pfam 05047; "minimalized" version of the thioredoxin-like fold; variable positions for cysteine residues in the putative active site
  22. Selenoprotein W-related [142411] (3)
    Pfam 05169; "minimalized" version of the thioredoxin-like fold
  23. UAS domain [159589] (1)
    SMART 00594
2. RNA 3'-terminal phosphate cyclase, RPTC, insert domain [52913] (1)
  uperfamily
  1. RNA 3'-terminal phosphate cyclase, RPTC, insert domain [52914] (1)
Peptidyl-tRNA hydrolase II [102461] (1)
3 layers: a/b/a; mixed beta-sheet of 4 strands, order 2143, strand 4 is antiparallel to the rest
1. Peptidyl-tRNA hydrolase II [102462] (1)
  uperfamily
  1. Peptidyl-tRNA hydrolase II [102463] (4)
    Pfam 01981; UPF0099
TK C-terminal domain-like [52921] (1)
3 layers: a/b/a; mixed beta-sheet of 5 strands, order 13245, strand 1 is antiparallel to the rest
1. TK C-terminal domain-like [52922] (3)
  uperfamily
  1. Transketolase C-terminal domain-like [52923] (5)
  2. Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain [52926] (6)
  3. Pyruvate-ferredoxin oxidoreductase, PFOR, domain II [52931] (1)
Pyruvate kinase C-terminal domain-like [52934] (2)
3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32145, strand 5 is antiparallel to the rest
1. PK C-terminal domain-like [52935] (2)
  uperfamily
  1. Pyruvate kinase, C-terminal domain [52936] (6)
  2. MTH1675-like [110616] (2)
    PfamB 019040; probable flavoenzyme, binds FMN; the phosphoribityl group binds in the equivalent site to the binding site of the PK allosteric regulator FBP
2. ATP synthase (F1-ATPase), gamma subunit [52943] (1)
  contains an antiparallel coiled coil formed by N- and C-terminal extensions to the common fold
  uperfamily
  1. ATP synthase (F1-ATPase), gamma subunit [52944] (3)
Anticodon-binding domain-like [52953] (6)
3 layers: a/b/a; mixed beta-sheet of five strands, order 21345; strand 4 is antiparallel to the rest
1. Class II aaRS ABD-related [52954] (2)
  uperfamily
  1. Anticodon-binding domain of Class II aaRS [52955] (13)
  2. Brix domain [142420] (2)
    Pfam 04427; tandem repeat of two ABD-like structural repeats, which are associated together with the formation of single beta-sheet, folded into half-barrel
2. TolB, N-terminal domain [52964] (1)
  uperfamily
  1. TolB, N-terminal domain [52965] (1)
3. B12-dependent dehydatase associated subunit [52968] (2)
  uperfamily
  1. Diol dehydratase, beta subunit [52969] (2)
    contains additional structures in the C-terminal extension
  2. Dehydratase-reactivating factor beta subunit [82433] (2)
4. ITPase-like [52972] (3)
  formerly Maf/Ham1; elaborated with additional structures inserted in the common fold
  uperfamily
  1. ITPase (Ham1) [52973] (5)
    Pfam 01725
  2. Maf-like [52976] (2)
  3. YjjX-like [110621] (3)
    Pfam 01931
5. CinA-like [142433] (1)
  uperfamily
  1. CinA-like [142434] (1)
    Pfam 02464
6. XCC0632-like [159594] (2)
  short crossover loop between strands 2 and 3; the antiparallel part of the beta-sheet (strands 3, 4 and 5) and the C-terminal helix are quite long
  1. NLBH-like [159595] (1)
    Pfam 05211; Neuraminyllactose-binding hemagglutinin
  2. XCC0632-like [159598] (1)
    Pfam 03886; DUF330
MTH938-like [64075] (1)
core: 3 layers, b+a/b/a ; the central mixed sheet of 5 strands: order 21534; strand 2 is antiparallel to the rest
1. MTH938-like [64076] (1)
  uperfamily
  1. MTH938-like [64077] (5)
Restriction endonuclease-like [52979] (4)
core: 3 layers, a/b/a; mixed beta-sheet of 5 strands, order 12345; strands 2 &, in some families, 5 are antiparallel to the rest
1. Restriction endonuclease-like [52980] (33)
  uperfamily
  1. Restriction endonuclease EcoRI [52981] (1)
  2. Restriction endonuclease EcoRV [52984] (1)
  3. Restriction endonuclease BamHI [52987] (1)
  4. Restriction endonuclease BglI [52990] (1)
  5. Restriction endonuclease BglII [52993] (1)
  6. Restriction endonuclease BstyI [102471] (1)
  7. Restriction endonuclease PvuII [52996] (1)
  8. Cfr10I/Bse634I [52999] (2)
  9. Restriction endonuclease MunI [53002] (1)
  10. Restriction endonuclease NaeI [53005] (1)
  11. Restriction endonuclease NgoIV [53008] (1)
  12. Restriction endonuclease BsobI [53011] (1)
  13. Restriction endonuclease HincII [69525] (1)
  14. Restriction endonuclease FokI, C-terminal (catalytic) domain [53014] (1)
  15. Type II restriction endonuclease catalytic domain [102474] (1)
  16. lambda exonuclease [53017] (1)
  17. DNA mismatch repair protein MutH from [53020] (1)
  18. Very short patch repair (VSR) endonuclease [53023] (1)
  19. TnsA endonuclease, N-terminal domain [53026] (1)
  20. Endonuclease I (Holliday junction resolvase) [53029] (1)
  21. Hjc-like [64080] (3)
    Pfam 01870
  22. XPF/Rad1/Mus81 nuclease [89716] (3)
  23. Restriction endonuclease MspI [110624] (1)
  24. Exodeoxyribonuclease V beta chain (RecB), C-terminal domain [117619] (1)
    related to the RecC domain
  25. Exodeoxyribonuclease V beta chain (RecC), C-terminal domain [117622] (1)
    related to the RecB domain
  26. Hypothetical protein VC1899 [117625] (1)
    contains 2 extra N-terminal domains; d1: [alpha/beta; 3 layers: a/b/a; mixed beta-sheet of 7 strands, order 3214567; strand 6 is antiparallel to the rest; topological similarity to the Formyltransferase fold (scop_cf 53327)]; d2: [distorted "winged helix" fold (scop_sf 46785)]
  27. Hypothetical protein TT1808 (TTHA1514) [117628] (1)
    Pfam 05685; DUF820
  28. RecU-like [117631] (2)
    Pfam 03838
  29. Restriction endonuclease EcoO109IR [117635] (1)
  30. MRR-like [117638] (1)
    Pfam 04471
  31. PA4535-like [142449] (1)
    contains the PD motif at the beginning of strand 2 and putative catalytic glutamate in strand 3, whereas the putative catalytic lysine is migrated to an alpha-helix
  32. XisH-like [159601] (2)
    Pfam 08814
  33. YaeQ-like [159605] (2)
    Pfam 07152; contains extra N- and C-terminal beta-structures forming additional five-stranded beta-sheet; retains the PD motif in the putative active site
2. tRNA-intron endonuclease catalytic domain-like [53032] (1)
  uperfamily
  1. tRNA-intron endonuclease catalytic domain-like [53033] (3)
3. Eukaryotic RPB5 N-terminal domain [53036] (1)
  uperfamily
  1. Eukaryotic RPB5 N-terminal domain [53037] (1)
4. TBP-interacting protein-like [159612] (1)
  contains extra C-terminal alpha+beta domain of complex fold with an embeded C2H2 zinc-finger
  1. TBP-interacting protein-like [159613] (1)
    PfamB 059845 (N-terminal domain) and Pfam B059846 (C-terminal region)
Resolvase-like [53040] (2)
Core: 3 layers: a/b/a; mixed beta-sheet of 5 strands, order 21345; strand 5 is antiparallel to the rest
1. Resolvase-like [53041] (1)
  uperfamily
  1. gamma,delta resolvase, catalytic domain [53042] (1)
2. beta-carbonic anhydrase, cab [53056] (1)
  uperfamily
  1. beta-carbonic anhydrase, cab [53057] (4)
PTS system fructose IIA component-like [53061] (1)
3 layers: a/b/a; mixed beta-sheet of 5 strands, order 21345; strand 5 is antiparallel to the rest
1. PTS system fructose IIA component-like [53062] (2)
  active dimer is formed by strand 5 swapping
  uperfamily
  1. EIIA-man component-like [53063] (2)
  2. DhaM-like [159618] (2)
    probable link between the PTS system fructose IIA component-like superfamily and the DAK1/DegV-like superfamily (scop_sf 82549)
Ribonuclease H-like motif [53066] (7)
3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32145; strand 2 is antiparallel to the rest
1. Actin-like ATPase domain [53067] (14)
  duplication contains two domains of this fold
  uperfamily
  1. Actin/HSP70 [53068] (14)
  2. BadF/BadG/BcrA/BcrD-like [64089] (5)
  3. Acetokinase-like [53080] (3)
  4. ATPase domain of dehydratase reactivase alpha subunit [82440] (2)
  5. Hexokinase [53083] (5)
  6. Glycerol kinase [53089] (2)
  7. Glucokinase [110627] (1)
    Pfam 02685
  8. Ppx/GppA phosphatase [110630] (2)
    Pfam 02541
  9. YeaZ-like [110633] (2)
    Pfam 00814; ubiquitous cytoplasmic protein; annotated as Glycoprotease (Peptidase_M22 family) on the basis of one member's known extracellular activity
  10. ROK [110636] (8)
    Pfam 00480
  11. Cyto-EpsL domain [117644] (1)
    N-terminal part of Pfam 05134
  12. Ta0583-like [142481] (1)
  13. CoaX-like [142484] (3)
    Pfam 03309; Bordetella pertussis Bvg accessory factor family, Baf
  14. Fumble-like [159623] (3)
    Pfam 03630; type II pantothenate kinase-like
2. Creatinase/prolidase N-terminal domain [53092] (1)
  uperfamily
  1. Creatinase/prolidase N-terminal domain [53093] (4)
3. Ribonuclease H-like [53098] (14)
  consists of one domain of this fold
  uperfamily
  1. Ribonuclease H [53099] (11)
  2. Retroviral integrase, catalytic domain [53107] (3)
  3. mu transposase, core domain [53112] (1)
  4. Transposase inhibitor (Tn5 transposase) [53115] (1)
  5. DnaQ-like 3'-5' exonuclease [53118] (26)
    contains Pfam 00929
  6. RuvC resolvase [53134] (1)
  7. Mitochondrial resolvase ydc2 catalytic domain [69533] (1)
  8. Putative Holliday junction resolvase RuvX [102485] (3)
  9. CAF1-like ribonuclease [102492] (2)
  10. PIWI domain [110640] (3)
    Pfam 02171
  11. TM1739-like [142505] (1)
    Pfam 04251; DUF430; particular similarity to the PIWI domain family
  12. Hermes transposase-like [142508] (1)
  13. Tex RuvX-like domain-like [159635] (1)
  14. Prp8 beta-finger domain-like [159638] (2)
4. Translational machinery components [53137] (2)
  uperfamily
  1. Ribosomal protein L18 and S11 [53138] (7)
  2. ERF1/Dom34 middle domain-like [53143] (3)
5. Nitrogenase accessory factor-like [53146] (2)
  uperfamily
  1. MTH1175-like [53147] (3)
  2. Nitrogenase accessory factor [102496] (1)
    capable of binding the iron molybdenum cofactor, FeMo-co
6. DNA repair protein MutS, domain II [53150] (1)
  uperfamily
  1. DNA repair protein MutS, domain II [53151] (2)
7. Methylated DNA-protein cysteine methyltransferase domain [53155] (1)
  uperfamily
  1. Methylated DNA-protein cysteine methyltransferase domain [53156] (3)
Phosphorylase/hydrolase-like [53162] (8)
core: 3 layers, a/b/a ; mixed sheet of 5 strands: order 21354; strand 4 is antiparallel to the rest; contains crossover loops
1. HybD-like [53163] (2)
  the HybD fold coincides with the consensus core structure
  uperfamily
  1. Hydrogenase maturating endopeptidase HybD [53164] (1)
  2. Germination protease [64095] (1)
    elaborated with the N-terminal alpha+beta subdomain and the insertion all-alpha dimerisation subdomain
2. Purine and uridine phosphorylases [53167] (1)
  complex architecture; contains mixed beta-sheet of 8 strands, order 23415867, strands 3, 6 & 7 are antiparallel to the rest; and barrel, closed; n=5, S=8
  uperfamily
  1. Purine and uridine phosphorylases [53168] (18)
3. Peptidyl-tRNA hydrolase-like [53178] (1)
  uperfamily
  1. Peptidyl-tRNA hydrolase-like [53179] (2)
4. Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase) [53182] (1)
  uperfamily
  1. Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase) [53183] (4)
5. Zn-dependent exopeptidases [53187] (9)
  core: mixed beta-sheet of 8 strands, order 12435867; strands 2, 6 & 7 are antiparallel to the rest
  uperfamily
  1. Pancreatic carboxypeptidases [53188] (10)
  2. Carboxypeptidase T [53198] (1)
  3. Leucine aminopeptidase, C-terminal domain [53201] (2)
  4. Bacterial dinuclear zinc exopeptidases [53204] (19)
  5. FolH catalytic domain-like [53210] (2)
  6. N-acetylmuramoyl-L-alanine amidase-like [102517] (2)
  7. AstE/AspA-like [142526] (6)
    Pfam 04952; Succinylglutamate desuccinylase / Aspartoacylase family; contains extra C-terminal domain, new variant of the Barrel-sandwich hybrid fold (scop_cf 51229)
  8. Glutaminyl-peptide cyclotransferase-like [142532] (1)
    part of Pfam 04389
  9. FGase-like [159652] (2)
    Pfam 05013; N-formylglutamate amidohydrolase
6. LigB-like [53213] (1)
  circular permutation of the common fold, most similar to the PNP fold
  uperfamily
  1. LigB-like [53214] (2)
7. AF0625-like [142535] (1)
  contains extra C-terminal alpha/beta domain: 3 layers, a/b/a; parallel beta-sheet of 4 strands, order 2134
  uperfamily
  1. AF0625-like [142536] (2)
    Pfam 04414; DUF516, binds magnesium ion and pyrophosphate in the putative active site
8. Cgl1923-like [159659] (1)
  1. Cgl1923-like [159660] (1)
    Pfam 01908; DUF75
Molybdenum cofactor biosynthesis proteins [53217] (1)
3 layers: a/b/a; mixed beta-sheet of 5 strands; order: 21354, strand 5 is antiparallel to the rest; permutation of the Phosphorylase/hydrolase-like fold
1. Molybdenum cofactor biosynthesis proteins [53218] (2)
  uperfamily
  1. MogA-like [53219] (8)
  2. MoeA central domain-like [64103] (5)
CobE/GbiG C-terminal domain-like [159663] (1)
3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32154; strand 5 is antiparallel to the rest
1. CobE/GbiG C-terminal domain-like [159664] (1)
  probably involved in deacylation steps in both anaerobic and aerobic pathways of cobalamin biosynthesis
  1. CobE/GbiG C-terminal domain-like [159665] (3)
    C-terminal part of Pfam 01890 (CbiG); corresponds to standalone protein CobE in the aerobic pathway; also includes resent structure 3BY5
CbiG N-terminal domain-like [159671] (1)
3 layers: a/b/a; mixed beta-sheet of 6 strands, order 213456, strand 5 is antiparallel to the rest
1. CbiG N-terminal domain-like [159672] (1)
  probable biological unit is a homodimer; putative active site is formed by residues from both subunits
  1. CbiG N-terminal domain-like [159673] (1)
    N-terminal part of Pfam 01890; also includes variable linker domain to CobE-like C-terminal domain; the linker domain may be in a rudimentary form or missing
Bacterial fluorinating enzyme, N-terminal domain [102521] (1)
3 layers: a/b/a; mixed beta-sheet of 6 strands; order: 213546, strand 5 is antiparallel to the rest; topological similarity to the MogA-like family fold
1. Bacterial fluorinating enzyme, N-terminal domain [102522] (1)
  uperfamily
  1. Bacterial fluorinating enzyme, N-terminal domain [102523] (1)
Caspase-like [52128] (1)
3 layers, a/b/a; core: mixed beta-sheet of 6 strands, order 213456, strand 6 is antiparallel to the rest
1. Caspase-like [52129] (2)
  mature protein may be composed of two chains folded in a single domain
  uperfamily
  1. Caspase catalytic domain [52130] (7)
  2. Gingipain R (RgpB), N-terminal domain [52137] (1)
    contains extra N-terminal alpha/beta subdomain
Macro domain-like [52948] (1)
3 layers: a/b/a; mixed beta-sheet of 6 strands, order 165243, strand 3 is antiparallel to the rest
1. Macro domain-like [52949] (2)
  uperfamily
  1. Leucine aminopeptidase (Aminopeptidase A), N-terminal domain [52950] (2)
  2. Macro domain [89724] (7)
    found in different proteins, including macro-H2a histone and the Appr-1"-p processing enzyme
MurD-like peptide ligases, peptide-binding domain [53243] (1)
3 layers: a/b/a; mixed beta-sheet of 6 strands, order 126345; strand 1 is antiparallel to the rest
1. MurD-like peptide ligases, peptide-binding domain [53244] (2)
  uperfamily
  1. MurCDEF C-terminal domain [53245] (5)
  2. Folylpolyglutamate synthetase, C-terminal domain [53250] (2)
Phosphoglycerate mutase-like [53253] (1)
core: 3 layers, a/b/a; mixed beta-sheet of 6 strands, order 324156; strand 5 is antiparallel to the rest
1. Phosphoglycerate mutase-like [53254] (3)
  uperfamily
  1. Cofactor-dependent phosphoglycerate mutase [53255] (8)
  2. Histidine acid phosphatase [53258] (7)
  3. 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, phosphatase domain [53267] (2)
PRTase-like [53270] (1)
core: 3 layers, a/b/a; mixed beta-sheet of 6 strands, order 321456; strand 3 is antiparallel to the rest
1. PRTase-like [53271] (2)
  uperfamily
  1. Phosphoribosyltransferases (PRTases) [53272] (36)
  2. Phosphoribosylpyrophosphate synthetase-like [53296] (3)
    duplication: consists of two domains of this fold
vWA-like [53299] (1)
core: 3 layers, a/b/a; mixed beta-sheet of 6 strands, order 321456; strand 3 is antiparallel to the rest
1. vWA-like [53300] (5)
  uperfamily
  1. Integrin A (or I) domain [53301] (12)
  2. Trunk domain of Sec23/24 [82458] (2)
  3. Ku70 subunit N-terminal domain [100959] (1)
  4. Ku80 subunit N-terminal domain [100962] (1)
  5. RoRNP C-terminal domain-like [142565] (1)
Pyruvate-ferredoxin oxidoreductase, PFOR, domain III [53322] (1)
3 layers: a/b/a; mixed beta-sheet of 6 strands, order 231456; strand 3 is antiparallel to the rest
1. Pyruvate-ferredoxin oxidoreductase, PFOR, domain III [53323] (1)
  uperfamily
  1. Pyruvate-ferredoxin oxidoreductase, PFOR, domain III [53324] (1)
RbsD-like [102545] (1)
3 layers: a/b/a; mixed beta-sheet of 6 strands, order 251634; strand 6 is antiparallel to the rest
1. RbsD-like [102546] (1)
  uperfamily
  1. RbsD-like [102547] (2)
FabD/lysophospholipase-like [52150] (1)
core: 3 layers, a/b/a; mixed beta-sheet of 6 strands, order 432156; strand 4 is antiparallel to the rest
1. FabD/lysophospholipase-like [52151] (3)
  uperfamily
  1. FabD-like [52152] (2)
    the superfamily common core covers almost all of the family fold
  2. Lysophospholipase [53645] (1)
    common core is decorated with many additional structures; mixed beta-sheet of 9 strands, order 654321798; strands 4, 6 and 8 are antiparallel to the rest
  3. Patatin [89729] (1)
    plant proteins; structurally and functionally related to animal cytosolic phospholipase A2
L-sulfolactate dehydrogenase-like [89732] (1)
core: 3 layers, a/b/a; mixed sheet of 7 strands, order 1237456; strands 1, 6 and 7 are antiparallel to the rest
1. L-sulfolactate dehydrogenase-like [89733] (1)
  topological similarity to the domain 2 of TM1585
  uperfamily
  1. L-sulfolactate dehydrogenase-like [89734] (3)
    Pfam 02615; type II malate/L-lactate dehydrogenase;
Formyltransferase [53327] (1)
3 layers: a/b/a; mixed beta-sheet of 7 strands, order 3214567; strand 6 is antiparallel to the rest
1. Formyltransferase [53328] (1)
  uperfamily
  1. Formyltransferase [53329] (7)
S-adenosyl-L-methionine-dependent methyltransferases [53334] (1)
core: 3 layers, a/b/a; mixed beta-sheet of 7 strands, order 3214576; strand 7 is antiparallel to the rest
1. S-adenosyl-L-methionine-dependent methyltransferases [53335] (57)
  uperfamily
  1. COMT-like [53336] (3)
  2. Plant O-methyltransferase, C-terminal domain [64111] (5)
  3. RNA methyltransferase FtsJ [53339] (1)
  4. Fibrillarin homologue [53342] (3)
  5. rRNA methyltransferase RlmA [102557] (1)
  6. rRNA methyltransferase AviRa [89738] (1)
  7. rRNA adenine dimethylase-like [88784] (5)
  8. mRNA cap methylase [88785] (3)
  9. mRNA cap (Guanine N-7) methyltransferase [102560] (1)
    mRNA capping enzyme
  10. Hypothetical protein MJ0882 [53345] (1)
  11. Hypothetical protein HI0319 (YecO) [69544] (1)
  12. Glycine N-methyltransferase [53348] (3)
  13. Arylamine N-methyltransferase [69547] (2)
  14. Histamine methyltransferase [75261] (1)
  15. Hypothetical Protein YjhP [82469] (1)
  16. Salicylic acid carboxyl methyltransferase (SAMT) [102563] (1)
  17. Thiopurine S-methyltransferase [102566] (2)
  18. Leucine carboxy methyltransferase Ppm1 [102569] (1)
  19. Precorrin-6Y methyltransferase (CbiT) [82472] (1)
  20. MraW-like putative methyltransferases [82475] (2)
  21. N5-glutamine methyltransferase, HemK [89743] (2)
  22. Catalytic, N-terminal domain of histone methyltransferase Dot1l [89746] (2)
  23. Guanidinoacetate methyltransferase [69550] (2)
  24. Arginine methyltransferase [53351] (4)
    lacks the last two strands of the common fold replaced with a beta-sandwich oligomerisation subdomain
  25. Protein-L-isoaspartyl O-methyltransferase [53354] (5)
    topological variant; strand order 3214567; strand 6 is antiparallel to the rest
  26. Glucose-inhibited division protein B (GidB) [75264] (2)
  27. tRNA(1-methyladenosine) methyltransferase-like [64117] (4)
    contains additional N-terminal beta-sandwich domain
  28. NOL1/NOP2/sun [102575] (3)
    Pfam 01189; contains additional N-terminal 3-helical and ferredoxin-like domains
  29. Ribosomal protein L11 methyltransferase PrmA [102578] (1)
    contains additional N-terminal ferredoxin-like domain
  30. (Uracil-5-)-methyltransferase [102581] (1)
    Pfam 05958
  31. Chemotaxis receptor methyltransferase CheR, C-terminal domain [53357] (1)
    contains additional N-terminal all-alpha domain, res. 11-91
  32. C5 cytosine-specific DNA methylase, DCM [88786] (3)
  33. DNA methylase TaqI, N-terminal domain [88787] (1)
  34. N6 adenine-specific DNA methylase, DAM [88788] (2)
  35. Type II DNA methylase [53377] (3)
    circularly permuted version of the common fold
  36. Spermidine synthase [69557] (7)
    contains additional N-terminal tetramerisation all-beta domain, res. 1-71
  37. Mycolic acid cyclopropane synthase [69560] (6)
  38. Ta1320-like [89751] (2)
  39. UbiE/COQ5-like [110671] (5)
    Pfam 01209
  40. AD-003 protein-like [117685] (2)
    Pfam 05891; DUF858
  41. CAC2371-like [117688] (3)
    similar overall fold to the Glycine N-methyltransferase (scop_fa 53348) and mRNA cap (Guanine N-7) methyltransferase (scop_fa 102560) families
  42. TehB-like [142603] (1)
    Pfam 03848; overall structural similarity to Thiopurine S-methyltransferase (Pfam 05724)
  43. N-6 DNA Methylase-like [142606] (3)
    Pfam 02384; contains C-terminal extension to the canonical fold and extra N-terminal all-alpha domain similar to the insert domain of the DAM family (scop_fa 88788)
  44. YhhF-like [142611] (5)
    Pfam 03602
  45. Met-10+ protein-like [142622] (1)
    Pfam 02475; contains extra N-terminal alpha+beta domain: beta(2)-alpha-beta(2); mixed beta-sheet; order: 1234; cf scop_fold 102740
  46. Nsp15 N-terminal domain-like [142625] (2)
    rudiment methyltransferase fold that probably has lost the enzymatic activity; contains extra N-terminal alpha+beta subdomain
  47. BC2162-like [142629] (1)
    contains extra helical regions inserted after strands 5 and 6 of the canonical fold
  48. CmcI-like [142632] (1)
    Pfam 04989; may have evolved different enzymatic activity
  49. hypothetical RNA methyltransferase [142635] (4)
    C-terminal part of Pfam 03602; similar to (Uracil-5-)-methyltransferase (Pfam 05958)
  50. RPA4359-like [142644] (1)
    Pfam 02636; DUF185
  51. TrmB-like [142647] (2)
    Pfam 02390
  52. Methyltransferase 10 domain [142651] (1)
    Pfam 05971; DUF890
  53. YhiQ-like [159686] (3)
    Pfam 04445; DUF548; contains extra N-terminal alpha+beta subdomain [beta-alpha-beta(4)]
  54. FkbM-like [159691] (1)
    contains extra N-terminal alpha/beta and all-alpha subdomains
  55. ML2640-like [159694] (1)
    Pfam 02409; O-methyltransferase N-terminus (DUF142); most similar structure to the Leucine carboxy methyltransferase Ppm1 family
  56. TRM1-like [159697] (1)
    Pfam 02005; contains extra C-terminal alpha+beta subdomain
  57. LPG1296-like [159700] (1)
    Pfam 04378; DUF519
LmbE-like [102587] (1)
3 layers, a/b/a; mixed beta-sheet of 7 strands, order 3214576; strand 7 is antiparallel to the rest; topological similarity to SAM-dependent methyltransferases
1. LmbE-like [102588] (1)
  uperfamily
  1. LmbE-like [102589] (2)
    putative deacetylases
PLP-dependent transferase-like [53382] (3)
main domain: 3 layers: a/b/a, mixed beta-sheet of 7 strands, order 3245671; strand 7 is antiparallel to the rest
1. PLP-dependent transferases [53383] (9)
  uperfamily
  1. AAT-like [53384] (28)
  2. Beta-eliminating lyases [53397] (4)
  3. Pyridoxal-dependent decarboxylase [69565] (3)
  4. Cystathionine synthase-like [53402] (24)
  5. GABA-aminotransferase-like [53417] (27)
    formerly omega-Aminoacid:pyruvate aminotransferase-like
  6. Ornithine decarboxylase major domain [53444] (1)
  7. Glycine dehydrogenase subunits (GDC-P) [142678] (2)
    Pfam 02347
  8. SelA-like [142683] (1)
    Pfam 03841
  9. SepSecS-like [159704] (3)
    Pfam 05889
2. PhnH-like [159709] (1)
  single domain protein of similar topology to the core domain of PLP-transferases
  1. PhnH-like [159710] (1)
    Pfam 05845; Bacterial phosphonate metabolism protein (PhnH)
3. Dhaf3308-like [159713] (1)
  not known to bind PLP cofactor; the extra N-terminal subdomain has a enolase N-terminal domain-like fold (scop_cf 54825)
  1. Dhaf3308-like [159714] (1)
    Pfam 04016; DUF364
Nucleotide-diphospho-sugar transferases [53447] (1)
3 layers: a/b/a; mixed beta-sheet of 7 strands, order 3214657; strand 6 is antiparallel to the rest
1. Nucleotide-diphospho-sugar transferases [53448] (19)
  uperfamily
  1. Spore coat polysaccharide biosynthesis protein SpsA [53449] (1)
  2. beta 1,4 galactosyltransferase (b4GalT1) [53452] (1)
  3. Galactosyltransferase LgtC [53458] (1)
  4. Glycogenin [75273] (1)
  5. alpha-1,3-galactosyltransferase-like [64131] (3)
  6. UDP-glucose pyrophosphorylase [53461] (6)
  7. glucose-1-phosphate thymidylyltransferase [53464] (6)
  8. 1,3-glucuronyltransferase [53467] (2)
  9. N-acetylglucosaminyltransferase I [64136] (1)
  10. Exostosin [89760] (1)
  11. Molybdenum cofactor biosynthesis protein MobA [53470] (1)
  12. Cytidylytransferase [68901] (12)
  13. Glycolipid 2-alpha-mannosyltransferase [102609] (1)
  14. Polypeptide N-acetylgalactosaminyltransferase 1, N-terminal domain [117702] (1)
  15. MGS-like [142691] (1)
    contains extra C-terminal all-alpha subdomain: 5 helices, orthogonal array
  16. TTHA0179-like [159717] (1)
  17. mannose-1-phosphate guanylyl transferase [159720] (1)
  18. MM2497-like [159723] (1)
    Pfam 01983; DUF121
  19. Glycosylating toxin catalytic domain-like [159726] (3)
    contains Glycosyltransferase sugar-binding region containing DXD motif, Pfam 04488
RibA-like [142694] (1)
3 layers: a/b/a; mixed beta-sheet of 7 strands, order 1235467, strands 1 and 3 are antiparallel to the rest; partial topological similarity to some alpha/beta hydrolases (scop_cf 53473)
1. RibA-like [142695] (1)
  uperfamily
  1. RibA-like [142696] (1)
    Pfam 00925; GTP cyclohydrolase II
Activating enzymes of the ubiquitin-like proteins [69571] (1)
3 layers: a/b/a; mixed beta-sheet of 8 strands, order 32145678; strands 6 and 8 are antiparallel to the rest
1. Activating enzymes of the ubiquitin-like proteins [69572] (2)
  transfer adenylyl group to the C-terminal carboxyl group of the ubiquitin and MoaD/ThiS-related proteins
  the ATP nucleotide-binding site is similar to that of the NAD-binding Rossmann-folds
  uperfamily
  1. Molybdenum cofactor biosynthesis protein MoeB [69573] (1)
  2. Ubiquitin activating enzymes (UBA) [89763] (2)
    the common fold is elaborated with additional (sub)domains
alpha/beta-Hydrolases [53473] (1)
core: 3 layers, a/b/a; mixed beta-sheet of 8 strands, order 12435678, strand 2 is antiparallel to the rest
1. alpha/beta-Hydrolases [53474] (41)
  many members have left-handed crossover connection between strand 8 and additional strand 9
  uperfamily
  1. Acetylcholinesterase-like [53475] (11)
  2. Carboxylesterase [53487] (9)
  3. Mycobacterial antigens [53491] (4)
  4. Hypothetical protein TT1662 [102616] (1)
  5. PepX catalytic domain-like [69581] (4)
  6. Prolyl oligopeptidase, C-terminal domain [53496] (1)
    N-terminal domain is a 7-bladed beta-propeller
  7. DPP6 catalytic domain-like [82497] (3)
    N-terminal domain is a 8-bladed beta-propeller
  8. Serine carboxypeptidase-like [53499] (5)
  9. Gastric lipase [53506] (2)
  10. Proline iminopeptidase-like [53509] (3)
  11. Acetyl xylan esterase-like [82504] (2)
    Pfam 05448; AXE1
  12. Haloalkane dehalogenase [53513] (3)
  13. Dienelactone hydrolase [53518] (2)
  14. Carbon-carbon bond hydrolase [53522] (4)
    closely related to the Proline iminopeptidase-like family
  15. Biotin biosynthesis protein BioH [82509] (1)
  16. Aclacinomycin methylesterase RdmC [102620] (1)
  17. Carboxylesterase/lipase [102623] (1)
  18. Epoxide hydrolase [53525] (4)
  19. Haloperoxidase [53531] (7)
  20. Thioesterases [53542] (3)
  21. Carboxylesterase/thioesterase 1 [53547] (5)
  22. Ccg1/TafII250-interacting factor B (Cib) [75285] (1)
  23. A novel bacterial esterase [53552] (1)
  24. Lipase [53555] (1)
  25. Fungal lipases [53558] (12)
  26. Bacterial lipase [53570] (7)
    lack the first two strands of the common fold
  27. Pancreatic lipase, N-terminal domain [53577] (6)
  28. Hydroxynitrile lyase-like [53585] (3)
  29. Thioesterase domain of polypeptide, polyketide and fatty acid synthases [69584] (4)
    Pfam 00975
  30. Cutinase-like [52260] (3)
    minimal alpha/beta hydrolase lacking peripheral secondary structures; similar to a flavodoxin-like fold
  31. YdeN-like [110699] (1)
    Pfam 06821; DUF1234; lack the first two strands of the common fold
  32. Putative serine hydrolase Ydr428c [110702] (1)
  33. Acylamino-acid-releasing enzyme, C-terminal donain [117711] (1)
    closely related to the prolyl peptidase and DPP6 domains (scop_fa 53496 and 82497)
  34. Hypothetical esterase YJL068C [117714] (1)
    part of Pfam 00756
  35. Hypothetical protein VC1974 [117717] (1)
  36. Atu1826-like [159742] (2)
  37. PHB depolymerase-like [159747] (1)
  38. IroE-like [159750] (1)
  39. TTHA1544-like [159753] (1)
    minimal hydrolase fold (one strand less than the cutinase-like family); there is neither catalytic triad, nor nucleopilic residue in the elbow motif
  40. O-acetyltransferase [159756] (3)
  41. 2,6-dihydropseudooxynicotine hydrolase-like [159762] (1)
    Pfam 06500; DUF1100
Nucleoside hydrolase [53589] (1)
core: 3 layers, a/b/a ; mixed beta-sheet of 8 strands, order 32145687; strand 7 is antiparallel to the rest
1. Nucleoside hydrolase [53590] (1)
  uperfamily
  1. Nucleoside hydrolase [53591] (4)
Dihydrofolate reductase-like [53596] (1)
3 layers: a/b/a; mixed beta-sheet of 8 strands, order 34251687; strand 8 is antiparallel to the rest
1. Dihydrofolate reductase-like [53597] (2)
  uperfamily
  1. Dihydrofolate reductases [53598] (12)
  2. RibD C-terminal domain-like [142701] (3)
    Pfam 01872
Ribokinase-like [53612] (3)
core: 3 layers: a/b/a; mixed beta-sheet of 8 strands, order 21345678, strand 7 is antiparallel to the rest
potential superfamily: members of this fold have similar functions but different ATP-binding sites
1. Ribokinase-like [53613] (5)
  has extra strand located between strands 2 and 3
  uperfamily
  1. Thiamin biosynthesis kinases [53620] (4)
  2. YjeF C-terminal domain-like [75292] (2)
  3. PfkB-like kinase [82515] (2)
    includes a variety of carbohydrate and pyrimidine kinases
  4. Ribokinase-like [53614] (13)
  5. ADP-specific Phosphofructokinase/Glucokinase [64147] (3)
    Pfam 04587
2. MurD-like peptide ligases, catalytic domain [53623] (2)
  has extra strand located between strands 1 and 2
  uperfamily
  1. MurCDEF [53624] (5)
  2. Folylpolyglutamate synthetase [53629] (2)
3. CoaB-like [102645] (1)
  combination of the Rossmann-like and Ribokinase-like topologies; mixed beta-sheet of 8 strands, order 32145678, strand 7 is antiparallel to the rest
  uperfamily
  1. CoaB-like [102646] (2)
    Pfam 04127
YjeF N-terminal domain-like [64152] (1)
3 layers: a/b/a; mixed (mainly parallel) beta-sheet of 8 strands, order 32145678; strand 8 is antiparallel to the rest
1. YjeF N-terminal domain-like [64153] (1)
  possible circular permutation of the ribokinase-like fold (of the YjeF C-terminal domain)
  uperfamily
  1. YjeF N-terminal domain-like [64154] (2)
Carbamate kinase-like [53632] (1)
3 layers: a/b/a; mixed (mainly parallel) beta-sheet of 8 strands, order 34215786; strand 8 is antiparallel to the rest
1. Carbamate kinase-like [53633] (3)
  the sheet topology is similar to those of undecaprenyl diphosphate synthase and the N-terminal domain of phosphoglycerate kinase
  uperfamily
  1. Carbamate kinase [53634] (2)
  2. N-acetyl-l-glutamate kinase [75297] (4)
  3. PyrH-like [142721] (10)
    part of Pfam 00696
2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain [64157] (1)
core:3 layers: a/b/a; mixed beta-sheet of 8 strands, order 45321678, strands 4 and 5 are antiparallel to the rest
1. 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain [64158] (1)
  uperfamily
  1. 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain [64159] (1)
Alkaline phosphatase-like [53648] (1)
core:3 layers: a/b/a; mixed beta-sheet of 8 strands, order 43516728, strand 7 is antiparallel to the rest
1. Alkaline phosphatase-like [53649] (5)
  uperfamily
  1. 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, catalytic domain [64162] (1)
  2. Alkaline phosphatase [53650] (3)
    common fold is decorated with several large insertions
  3. Arylsulfatase [53653] (4)
    includes additional C-terminal alpha+beta (sub)domain
  4. Phosphonoacetate hydrolase [102651] (1)
    contains alpha+beta subdomain inserted near C-terminus
  5. DeoB catalytic domain-like [142735] (1)
    Pfam 08342 in the N-terminal part; Pfam 01676 in the C-terminal part; there is an alpha+beta domain between the two parts, inserted in the same location as the substrate-binding domain of 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase
TTHA0583/YokD-like [110709] (1)
3 layers: a/b/a; mixed beta-sheet of 8 strands, order 78612354; strands 3, 4 and 8 are antiparallel to the rest
1. TTHA0583/YokD-like [110710] (2)
  uperfamily
  1. Hypothetical protein TT1679 [110711] (1)
    Pfam 04260, DUF436
  2. Aminoglycoside 3-N-acetyltransferase-like [159765] (1)
    Pfam 02522; CoA-dependent enzymes
Glycerol-3-phosphate (1)-acyltransferase [69592] (1)
3 layers: a/b/a; mixed beta-sheet of 9 strands, order 918736452; strands 1, 2 and 8 are antiparallel to the rest
1. Glycerol-3-phosphate (1)-acyltransferase [69593] (1)
  some topological similarity to the dihydrofolate reductase fold
  uperfamily
  1. Glycerol-3-phosphate (1)-acyltransferase [69594] (1)
AraD/HMP-PK domain-like [53638] (1)
3 layers: a/b/a; mixed (mostly antiparallel) beta-sheet of 9 strands, order 432159876; left-handed crossover between strands 4 and 5
1. AraD/HMP-PK domain-like [53639] (2)
  uperfamily
  1. AraD-like aldolase/epimerase [53640] (4)
    metal (zinc)-ion dependent
  2. Phosphomethylpyrimidine kinase C-terminal domain-like [159768] (2)
SurE-like [64166] (1)
3 layers: a/b/a; mixed beta-sheet of 9 strands, order 342156798; strands 3, 8 and 9 are antiparallel to the rest; left-handed crossover connection between strands 6 and 7
1. SurE-like [64167] (1)
  some topological similarity to the N-terminal domain of Glutaminase/Asparaginase family
  uperfamily
  1. SurE-like [64168] (2)
YerB-like [159773] (1)
3 layers: b/b/a; central mixed beta-sheet of 9 strands, order 541329678; strands 3 and 7 are antiparallel to the rest; an unusual "over the other end" connection between strands 3 and 4
1. YerB-like [159774] (1)
  1. YerB-like [159775] (1)
    PfamB 028118
CdCA1 repeat-like [159778] (1)
contains two parallel beta-strands of four strands each; the sheets contact each other with edges at a right angle
1. CdCA1 repeat-like [159779] (1)
  1. CdCA1 repeat-like [159780] (1)
    Pfam 10563
Isocitrate/Isopropylmalate dehydrogenase-like [53658] (1)
consists of two intertwined (sub)domains related by pseudo dyad; duplication
3 layers: a/b/a; single mixed beta-sheet of 10 strands, order 213A945867 (A=10); strands from 5 to 9 are antiparallel to the rest
1. Isocitrate/Isopropylmalate dehydrogenase-like [53659] (5)
  the constituent families form similar dimers
  uperfamily
  1. Dimeric isocitrate & isopropylmalate dehydrogenases [53660] (13)
    the active site is between the two identical subunits
  2. PdxA-like [102656] (2)
    Pfam 04166; contains extra beta-alpha unit between strands 2 and 3; closer relationships to the PlsX-like and phosphotransacetylase families
  3. PlsX-like [102660] (2)
    Pfam 02504; contains extra beta-alpha unit between strands 2 and 3; closer relationships to the PdxA-like and phosphotransacetylase families
  4. Phosphotransacetylase [102663] (4)
    Pfam 01515; contains extra beta-alpha unit between strands 2 and 3; closer relationships to the PdxA-like and PlsX-like families
  5. Monomeric isocitrate dehydrogenase [82526] (1)
    the active site is contained within one subunit between the canonical ICDH fold and a large insert domain that itself is a probable rudiment form of ICDH fold resulted from duplication, domain swapping and deletion
Amidase signature (AS) enzymes [75303] (1)
possible duplication: the topologies of N- and C-terminal halves are similar; 3 layers: a/b/a; single mixed beta-sheet of 10 strands, order 213549A867 (A=10); strands from 5 to 9 are antiparallel to the rest
1. Amidase signature (AS) enzymes [75304] (1)
  uperfamily
  1. Amidase signature (AS) enzymes [75305] (5)
ATC-like [53670] (2)
consists of two similar domains related by pseudo dyad; duplication
core: 3 layers, a/b/a, parallel beta-sheet of 4 strands, order 2134
1. Aspartate/ornithine carbamoyltransferase [53671] (1)
  uperfamily
  1. Aspartate/ornithine carbamoyltransferase [53672] (11)
2. Aspartate/glutamate racemase [53681] (1)
  uperfamily
  1. Aspartate/glutamate racemase [53682] (3)
    C-terminal extension is added to the N-terminal domain
Tryptophan synthase beta subunit-like PLP-dependent enzymes [53685] (1)
consists of two similar domains related by pseudo dyad; duplication
core: 3 layers, a/b/a; parallel beta-sheet of 4 strands, order 3214
1. Tryptophan synthase beta subunit-like PLP-dependent enzymes [53686] (1)
  uperfamily
  1. Tryptophan synthase beta subunit-like PLP-dependent enzymes [53687] (22)
SIS domain [53696] (1)
3 layers: a/b/a; parallel beta-sheet of 5 strands, order 21345
1. SIS domain [53697] (3)
  uperfamily
  1. mono-SIS domain [69599] (8)
    dimer of mono-domain subunits
  2. double-SIS domain [53698] (4)
    duplication: consists of two SIS domains related by pseudo dyad
  3. Phosphoglucose isomerase, PGI [53701] (6)
    permutation of the double-SIS domain fold
Formate dehydrogenase/DMSO reductase, domains 1-3 [53705] (1)
contains of two similar intertwined domains related by pseudo dyad; duplication
core: 3 layers: a/b/a; parallel beta-sheet of 5 strands, order 32451
1. Formate dehydrogenase/DMSO reductase, domains 1-3 [53706] (1)
  molybdopterine enzyme
  uperfamily
  1. Formate dehydrogenase/DMSO reductase, domains 1-3 [53707] (12)
    domain 1 (residues 1-55) binds Fe4S4 cluster in FDH but not DMSO reductase
ALDH-like [53719] (1)
consists of two similar domains with 3 layers (a/b/a) each; duplication
core: parallel beta-sheet of 5 strands, order 32145
1. ALDH-like [53720] (2)
  binds NAD differently from other NAD(P)-dependent oxidoreductases
  uperfamily
  1. ALDH-like [53721] (14)
  2. L-histidinol dehydrogenase HisD [69602] (1)
NadA-like [142753] (1)
duplication; consists of three similar domains related by pseudo threefold symmetry; 3 layers, a/b/a; parallel beta sheet, order: 2134
1. NadA-like [142754] (1)
  uperfamily
  1. NadA-like [142755] (1)
    Pfam 02445
Aconitase iron-sulfur domain [53731] (1)
consists of three similar domains with 3 layers (a/b/a) each; duplication
core: parallel beta-sheet of 5 strands, order 32145
1. Aconitase iron-sulfur domain [53732] (1)
  uperfamily
  1. Aconitase iron-sulfur domain [53733] (4)
    duplication: consists of three structurally similar subdomains with subdomains 1 and 3 being related by pseudo twofold symmetry
Phosphoglucomutase, first 3 domains [53737] (1)
consists of three similar domains with 3 layers (a/b/a) each; duplication
core: mixed beta-sheet of 4 strands, order 2134, strand 4 is antiparallel to the rest
1. Phosphoglucomutase, first 3 domains [53738] (1)
  uperfamily
  1. Phosphoglucomutase, first 3 domains [53739] (3)
FucI/AraA N-terminal and middle domains [53742] (1)
consists of two domains of similar topology, 3 layers (a/b/a) each
Domain 1 (1-173) has parallel beta-sheet of 5 strands, order 21345
Domain 2 (174-355) has parallel beta-sheet of 4 strands, order 2134
1. FucI/AraA N-terminal and middle domains [53743] (2)
  uperfamily
  1. L-fucose isomerase, N-terminal and second domains [53744] (1)
  2. AraA N-terminal and middle domain-like [142760] (1)
    N-terminal part of Pfam 02610
YgbK-like [142763] (1)
consists of two domains with partial topological similarity to the P-loop kinases but without the P-loop motif; the domain association results in the formation of a single mixed beta-sheet of 15 strands
1. YgbK-like [142764] (1)
  uperfamily
  1. YgbK-like [142765] (1)
    Pfam 07005; DUF1537; the B-fam model-covered region is non-compact in structure and distributed between the two domains
Phosphoglycerate kinase [53747] (1)
consists of two non-similar domains, 3 layers (a/b/a) each
Domain 1 has parallel beta-sheet of 6 strands, order 342156
Domain 2 has parallel beta-sheet of 6 strands, order 321456
1. Phosphoglycerate kinase [53748] (1)
  uperfamily
  1. Phosphoglycerate kinase [53749] (7)
    Domain 2 binds ATP
UDP-Glycosyltransferase/glycogen phosphorylase [53755] (1)
consists of two non-similar domains with 3 layers (a/b/a) each
domain 1: parallel beta-sheet of 7 strands, order 3214567
domain 2: parallel beta-sheet of 6 strands, order 321456
1. UDP-Glycosyltransferase/glycogen phosphorylase [53756] (11)
  uperfamily
  1. beta-Glucosyltransferase (DNA-modifying) [53757] (1)
  2. Peptidoglycan biosynthesis glycosyltransferase MurG [53760] (1)
  3. UDP-N-acetylglucosamine 2-epimerase [53763] (3)
  4. Gtf glycosyltransferase [64178] (3)
    Glycosyltransferase family 28
  5. ADP-heptose LPS heptosyltransferase II [89784] (1)
  6. Trehalose-6-phosphate synthase, OtsA [82540] (1)
    family 20 glycosyltransferase; good structural similarity in the active site to the Oligosaccharide phosphorylases
  7. Oligosaccharide phosphorylase [53766] (4)
  8. Glycosyl transferases group 1 [110734] (4)
    Pfam 00534
  9. Sialyltransferase-like [142773] (1)
  10. UDPGT-like [159785] (4)
    Pfam 00201
  11. FucT-like [159794] (1)
    Pfam 00852; Glycosyltransferase family 10 (fucosyltransferase)
Glutaminase/Asparaginase [53773] (1)
consists of two non-similar alpha/beta domains, 3 layers (a/b/a) each
Domain 1 has mixed beta-sheet of 6 strands, order 213456, strand 6 is antiparallel to the rest; left-handed crossover connection between strands 4 and 5
Domain 2 has parallel beta-sheet of 4 strands, order 1234
1. Glutaminase/Asparaginase [53774] (1)
  uperfamily
  1. Glutaminase/Asparaginase [53775] (8)
Phosphofructokinase [53783] (1)
consists of two non-similar domains, 3 layers (a/b/a) each
Domain 1 has mixed sheet of 7 strands, order 3214567; strands 3 & 7 are antiparallel to the rest
Domain 2 has parallel sheet of 4 strands, order 2314
1. Phosphofructokinase [53784] (1)
  uperfamily
  1. Phosphofructokinase [53785] (3)
Tetrapyrrole methylase [53789] (1)
consists of two non-similar domains
Domain 1 has parallel sheet of 5 strands, order 32415
Domain 2 has mixed sheet of 5 strands, order 12534; strands 4 & 5 are antiparallel to the rest
1. Tetrapyrrole methylase [53790] (1)
  uperfamily
  1. Tetrapyrrole methylase [53791] (10)
    Pfam 00590
GckA/TtuD-like [82543] (1)
consists of two non-similar domains
Domain 1 has parallel sheet of 6 strands, order 321456, Rossmann-like topology
Domain 2 has mixed sheet of 6 strands, order 126345; strands 5 and 6 are antiparallel to the rest; some similarity to CbiF Domain 2
1. GckA/TtuD-like [82544] (1)
  uperfamily
  1. GckA/TtuD-like [82545] (1)
DAK1/DegV-like [82548] (1)
2 different domains; d1: [core: 3 layers, a/b/a; parallel sheet of 5 strands, order: 2134]; D2: [2 layers, a/b; mixed sheet of 6 strands, order 321645; strands 2 and 6 are antiparallel to the rest]
1. DAK1/DegV-like [82549] (2)
  domain folds and architecture show some similarity to the tubulin-like GTPases; the nucleotide-binding sites of the Dihydroxyacetone kinase and tubulin families are different
  uperfamily
  1. DegV-like [82550] (2)
    Pfam 02645, DUF194
  2. DAK1 [109613] (2)
    Pfam 02733
DHH phosphoesterases [64181] (1)
consists of two non-similar domains
Domain 1 has parallel sheet of 6 strands, order 321456
Domain 2 has mixed sheet of 5 strands, order 12345; strands 1 & 4 are antiparallel to the rest
1. DHH phosphoesterases [64182] (2)
  constituent families have similar domain organization with variable interdomain linker and spatial arrangement of the domains
  uperfamily
  1. Manganese-dependent inorganic pyrophosphatase (family II) [64183] (3)
  2. Exonuclease RecJ [75323] (1)
Glycerate kinase I [110737] (1)
consists of two different alpha/beta domains; (1) of the Flavodoxin-like fold (scop_cf 52171); (2) similar to the Restriction endonuclease-like fold (scop_cf 52979), inserted into domain 1
1. Glycerate kinase I [110738] (1)
  uperfamily
  1. Glycerate kinase I [110739] (1)
    Pfam 02595
PEP carboxykinase-like [53794] (1)
contains a P-loop NTP-binding motif; mixed beta-sheet folds into a barrel-like structure with helices packed on one side
1. PEP carboxykinase-like [53795] (2)
  uperfamily
  1. PEP carboxykinase C-terminal domain [53796] (4)
  2. HPr kinase HprK C-terminal domain [64186] (3)
PEP carboxykinase N-terminal domain [68922] (1)
contains mixed beta-sheets; topology is partly similar to that of the catalytic C-terminal domain
1. PEP carboxykinase N-terminal domain [68923] (1)
  uperfamily
  1. PEP carboxykinase N-terminal domain [68924] (4)
Chelatase-like [53799] (3)
duplication: tandem repeat of two domains; 3 layers (a/b/a); parallel beta-sheet of 4 strands, order 2134
1. Chelatase [53800] (3)
  interdomain linker is short; swapping of C-terminal helices between the two domains
  uperfamily
  1. Ferrochelatase [53801] (3)
  2. Cobalt chelatase CbiK [53804] (1)
  3. CbiX-like [110742] (1)
    Pfam 01903; single-domain protein; forms the C-terminal helix-swapped dimer similar to the CbiK subunit
2. "Helical backbone" metal receptor [53807] (4)
  contains a long alpha helical insertion in the interdomain linker
  uperfamily
  1. Periplasmic ferric siderophore binding protein FhuD [53808] (1)
  2. TroA-like [53811] (5)
  3. Nitrogenase iron-molybdenum protein [53816] (6)
    contains three domains of this fold; "Helical backbone" holds domains 2 and 3
    both chains are homologous; the inter-chain arrangement of domains 1 is similar to the intra-chain arrangement of domains 2 and 3
  4. TM0189-like [142789] (3)
    Part of Pfam 01497 that include some other superfamily members
3. PrpR receptor domain-like [159800] (1)
  recent PDB entry 2q5c belongs to this superfamily
  1. PrpR receptor domain-like [159801] (1)
    N-terminal domain corresponds to Pfam 06506; C-terminal domain, assigned to Pfam 00158, is distinct from other structures of this Pfam family
HemD-like [69617] (1)
duplication: consists of two similar 'swapped' domain with 3 layers (a/b/a) each; parallel beta-sheet of 5 strands, order 21345
1. HemD-like [69618] (1)
  uperfamily
  1. HemD-like [69619] (2)
    Pfam 02602
CAC2185-like [142794] (1)
consists of two non-similar domains, 3 layers (a/b/a) each; d1 has parallel sheet of 4 strands, order 2134; d2 has parallel sheet of 5 strands, order 21345, and antiparallel meander sheet of 3 strands
1. CAC2185-like [142795] (1)
  uperfamily
  1. CAC2185-like [142796] (1)
Periplasmic binding protein-like I [53821] (1)
consists of two similar intertwined domain with 3 layers (a/b/a) each: duplication
parallel beta-sheet of 6 strands, order 213456
1. Periplasmic binding protein-like I [53822] (1)
  Similar in architecture to the superfamily II but partly differs in topology
  uperfamily
  1. L-arabinose binding protein-like [53823] (18)
Periplasmic binding protein-like II [53849] (1)
consists of two similar intertwined domain with 3 layers (a/b/a) each: duplication
mixed beta-sheet of 5 strands, order 21354; strand 5 is antiparallel to the rest
1. Periplasmic binding protein-like II [53850] (3)
  Similar in architecture to the superfamily I but partly differs in topology
  uperfamily
  1. Phosphate binding protein-like [53851] (65)
  2. Transferrin [53888] (11)
    further duplication: composed of two two-domain lobes
  3. PG0945 N-terminal domain-like [159818] (1)
    truncated to one domain; extra C-terminal region provides dimerisation interface
Thiolase-like [53900] (1)
consists of two similar domains related by pseudo dyad; duplication
3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32451; strand 5 is antiparallel to the rest
1. Thiolase-like [53901] (2)
  uperfamily
  1. Thiolase-related [53902] (12)
  2. Chalcone synthase-like [53914] (10)
NIF3 (NGG1p interacting factor 3)-like [102704] (1)
consist of two intertwined domains; duplication: contains two structural repeats of alpha-beta-(beta-alpha)3 motif with mixed beta-sheet, order: 1432, strand 1 is antiparallel to the rest
1. NIF3 (NGG1p interacting factor 3)-like [102705] (1)
  di-iron binding protein
  uperfamily
  1. NIF3 (NGG1p interacting factor 3)-like [102706] (3)
    Pfam 01784
Fe-only hydrogenase [53919] (1)
consist of two intertwined domains; contains partial duplication
1. Fe-only hydrogenase [53920] (1)
  uperfamily
  1. Fe-only hydrogenase [53921] (2)
ComB-like [142822] (1)
contains of two similar intertwined domains related by pseudo dyad; duplication; core: 3 layers: a/b/a; parallel beta-sheet of 4 strands, order 1423
1. ComB-like [142823] (1)
  uperfamily
  1. ComB-like [142824] (1)
    Pfam 04029; 2-phosphosulpholactate phosphatase
CoA-transferase family III (CaiB/BaiF) [89795] (1)
consist of two different alpha/beta domains; N-terminal domain has a SurE-like topology with a left-handed beta-alpha-beta unit
1. CoA-transferase family III (CaiB/BaiF) [89796] (1)
  uperfamily
  1. CoA-transferase family III (CaiB/BaiF) [89797] (4)
    forms interlocked homodimer of two ring-like subunits
Cytidine deaminase-like [53926] (2)
core: alpha-beta(2)-(alpha-beta)2; 3 layers (a/b/a); mixed beta-sheet of 4 strands, order 2134; strand 1 is antiparallel to the rest
1. Cytidine deaminase-like [53927] (5)
  contains extra C-terminal strand 5, order 21345
  uperfamily
  1. Cytidine deaminase [53928] (7)
    strand 5 is antiparallel to strand 4
  2. Deoxycytidylate deaminase-like [89800] (10)
    strand 5 is parallel to strand 4
  3. Hypothetical protein TM1506 [110651] (1)
    strand 5 is parallel to strand 4
  4. AICAR transformylase domain of bifunctional purine biosynthesis enzyme ATIC [64198] (3)
    duplication: consists of two domains of this fold with extra secondary structures within and in between the two core motifs
  5. FdhD/NarQ [159821] (1)
    Pfam 02634; contains extra N-terminal beta-hairpin arm, involved in dimerization, and an alpha+beta subdomain of beta-grasp fold (scop_cf 54235)
2. JAB1/MPN domain [102712] (1)
  uperfamily
  1. JAB1/MPN domain [102713] (1)
    Pfam 01398; synonyms Mov34, PAD-1;