Structural Classification of Proteins

Fold: Double-stranded beta-helix

: one turn of helix is made by two pairs of antiparallel strands linked with short turns
has appearance of a sandwich of distinct architecture and jelly-roll topology

Lineage:

Root: scop
Class: All beta proteins [48724]
Fold: Double-stranded beta-helix [51181]
one turn of helix is made by two pairs of antiparallel strands linked with short turns
has appearance of a sandwich of distinct architecture and jelly-roll topology

Superfamilies:

RmlC-like cupins [51182] (24)
uperfamily
1. dTDP-sugar isomerase [51183] (9)
  1. dTDP-4-dehydrorhamnose 3,5-epimerase RmlC [51184]
    synonym: dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase
    1. Salmonella typhimurium [TaxId: 90371] [51185] (2)
    2. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [51186] (2)
    3. Streptococcus suis [TaxId: 1307] [89402] (7)
    4. Mycobacterium tuberculosis [TaxId: 1773] [101971] (6)
    5. Pseudomonas aeruginosa [TaxId: 287] [101972] (4)
    6. Archaeon Sulfolobus tokodaii [TaxId: 111955] [141586] (2)
      SQ Q96Z62 1-176
  2. dTDP-4-keto-6-deoxy-glucose-5-epimerase EvaD [101973]
    1. Amycolatopsis orientalis [TaxId: 31958] [101974] (2)
      SQ O52806
  3. Novobiocin biosynthesis protein NovW [141587]
    1. Streptomyces caeruleus [TaxId: 195949] [141588] (1)
      SQ Q9L9E5 1-190
  4. dTDP-6-deoxy-3,4-keto-hexulose isomerase FdtA [159287]
    1. Aneurinibacillus thermoaerophilus [TaxId: 143495] [159288] (8)
      SQ Q6T1W8 1-136! SQ Q6T1W8 2-136
2. Glucose-6-phosphate isomerase, GPI [89403] (2)
  1. Glucose-6-phosphate isomerase, GPI [89404]
    Type II phosphoglucose isomerase
    1. Archaeon Pyrococcus furiosus [TaxId: 2261] [89405] (6)
      SQ P83194
    2. Archaeon Thermococcus litoralis [TaxId: 2265] [101975] (11)
3. Hypothetical protein TM1112 [89406] (1)
  1. Hypothetical protein TM1112 [89407]
    1. Thermotoga maritima [TaxId: 2336] [89408] (2)
4. TM1287-like [89409] (4)
  1. Hypothetical protein TM1287 [89410]
    1. Thermotoga maritima [TaxId: 2336] [89411] (1)
  2. Hypothetical protein TTHA0104 [117310]
    1. Thermus thermophilus [TaxId: 274] [117311] (3)
      SQ Q5SM39
  3. Hypothetical protein TM1010 [141589]
    1. Thermotoga maritima [TaxId: 2336] [141590] (4)
      SQ Q9X0A3 2-135
  4. Hypothetical protein SPy1581 [141591]
    1. Streptococcus pyogenes [TaxId: 1314] [141592] (1)
      SQ Q99YR1 1-112
5. TM1459-like [101976] (2)
  1. Hypothetical protein TM1459 [101977]
    1. Thermotoga maritima [TaxId: 2336] [101978] (1)
  2. Hydroxypropylphosphonic acid epoxidase Fom4, C-terminal domain [141593]
    1. Streptomyces wedmorensis [TaxId: 43759] [141594] (20)
      SQ Q56185 77-198
6. Germin/Seed storage 7S protein [51187] (9)
  1. Germin [63853]
    Metal (manganese)-binding protein with oxalate oxidase and superoxide dismutase activities; homohexamer
    1. Barley (Hordeum vulgare) [TaxId: 4513] [63854] (5)
  2. Auxin binding protein [75030]
    1. Maize (Zea mays) [TaxId: 4577] [75031] (2)
  3. Seed storage 7S protein [51188]
    duplication: consists of two germin-like domains spatially arranged as subunits in the RmlC dimer; trimer is similar to the germin hexamer
    1. French bean (Phaseolus vulgaris), phaseolin [TaxId: 3885] [51189] (2)
    2. Jack bean (Canavalia ensiformis), canavalin/vinculin [TaxId: 3823] [51190] (8)
    3. Soybean (Glycine max), proglycinin [TaxId: 3847] [69345] (3)
    4. Soybean (Glycine max), beta-conglycinin beta subunit [TaxId: 3847] [109608] (3)
      SQ P25974
    5. Soybean (Glycine max), glycinin A3B4 [TaxId: 3847] [89412] (1)
    6. Soybean (Glycine max), beta-conglycinin alpha prime subunit [TaxId: 3847] [110313] (1)
      SQ Q7XXT2 204-621
  4. Oxalate decarboxylase OxdC (YvrK) [75033]
    duplication: consists of two germin-like metal-ion binding domains
    1. Bacillus subtilis [TaxId: 1423] [75034] (3)
7. YlbA-like [101979] (4)
  Pfam 05899; formerly pfam06038; duplication: consists of two germin-like domains
  1. Hypothetical protein YlbA [101980]
    1. Escherichia coli [TaxId: 562] [101981] (1)
  2. Glyoxylate-induced protein PA1140 [101982]
    1. Pseudomonas aeruginosa [TaxId: 287] [101983] (1)
  3. Hypothetical protein EF2996 [110314]
    1. Enterococcus faecalis [TaxId: 1351] [110315] (1)
      SQ Q82ZQ3
  4. Hypothetical protein DR1152 [110316]
    1. Deinococcus radiodurans [TaxId: 1299] [110317] (1)
      SQ Q9RV77
8. Pirin-like [101984] (2)
  Share a common two-domain fold with the 7S protein; there is a metal-binding site in the N-terminal domain similar to the metal-binding site of germin
  1. Pirin [101985]
    Bcl-3 and nuclear factor I-interacting protein
    1. Human (Homo sapiens) [TaxId: 9606] [101986] (1)
  2. Hypothetical protein YhhW [141595]
    1. Escherichia coli [TaxId: 562] [141596] (1)
      SQ P46852 1-231
9. Quercetin 2,3-dioxygenase-like [75035] (2)
  Share a common two-domain fold with the 7S protein; there is a metal-binding site in the N-terminal domain similar to the metal-binding site of germin
  1. Quercetin 2,3-dioxygenase [75036]
    1. Aspergillus japonicus [TaxId: 34381] [75037] (5)
  2. Hypothetical protein YxaG [141597]
    1. Bacillus subtilis [TaxId: 1423] [141598] (2)
      SQ P42106 5-334
10. Type I phosphomannose isomerase [51191] (3)
  Share a common two-domain fold with the 7S protein; there is a metal-binding site in the N-terminal domain similar to the metal-binding site of germin
  1. Phosphomannose isomerase [51192]
    1. Yeast (Candida albicans) [TaxId: 5476] [51193] (1)
      contains insert all-alpha subdomain; residues 152-266
  2. Mannose-6-phosphate isomerase ManA [101987]
    1. Bacillus subtilis [TaxId: 1423] [101988] (1)
  3. Putative mannosephosphate isomerase AF0035 [141599]
    1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [141600] (1)
      SQ O30200 1-299
11. Homogentisate dioxygenase [51194] (1)
  Share a common two-domain fold with the 7S protein; there is a metal-binding site in the C-terminal domain similar to the metal-binding site of germin
  1. Homogentisate dioxygenase [51195]
    1. Human (Homo sapiens) [TaxId: 9606] [51196] (2)
12. Acireductone dioxygenase [82191] (2)
  1. Acireductone dioxygenase [82192]
    1. Klebsiella pneumoniae [TaxId: 573] [82193] (1)
      NMR-derived model
    2. Mouse (Mus musculus) [TaxId: 10090] [141601] (1)
      SQ Q99JT9 1-179
13. KduI-like [110318] (2)
  Pfam 04962: duplication: consists of two germin-like domains
  1. 5-keto-4-deoxyuronate isomerase KduI [110319]
    1. Escherichia coli [TaxId: 562] [110320] (3)
      SQ Q46938 1-266
    2. Enterococcus faecalis [TaxId: 1351] [141602] (6)
      SQ Q838L9 1-260
14. Ureidoglycolate hydrolase AllA [117312] (3)
  Pfam 04115; beta-hairpin-swapped dimeric protein of the germin-like fold
  1. Ureidoglycolate hydrolase AllA [117313]
    1. Shigella flexneri [TaxId: 623] [117314] (2)
      SQ P77731 ! SQ P63487
    2. Pseudomonas putida [TaxId: 303] [141603] (2)
      SQ P59285 1-166
    3. Escherichia coli [TaxId: 562] [141604] (2)
      SQ P63486 1-160
15. Probable transcriptional regulator VC1968, C-terminal domain [117315] (1)
  1. Probable transcriptional regulator VC1968, C-terminal domain [117316]
    1. Vibrio cholerae [TaxId: 666] [117317] (1)
      SQ Q9KQN0
16. YML079-like [117318] (3)
  Pfam 06172; DUF985
  1. Hypothetical protein YML079W [117319]
    1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [117320] (2)
      SQ Q03629
  2. Hypothetical protein Atu3615 [141605]
    1. Agrobacterium tumefaciens [TaxId: 358] [141606] (7)
      SQ Q8U9W0 4-143
  3. Hypothetical protein SO0799 [141607]
    1. Shewanella oneidensis [TaxId: 70863] [141608] (10)
      SQ Q8EIN8 1-158
17. PA5104-like [141609] (1)
  Pfam 05962; DUF886; duplication: consists of two germin-like domains; overall structural similarity to the YlbA-like family (scop_fa 101979) except a deletion in the interdomain linker region
  1. Hypothetical protein PA5104 [141610]
    1. Pseudomonas aeruginosa [TaxId: 287] [141611] (4)
      SQ Q9HU79 2-196
18. MJ0764-like [141612] (1)
  1. Hypothetical protein MJ0764 [141613]
    1. Archaeon Methanococcus jannaschii [TaxId: 2190] [141614] (1)
      SQ Q58174 1-108
19. Cysteine dioxygenase type I [141615] (4)
  Pfam 05995, CDO_I
  1. Cysteine dioxygenase type I [141616]
    1. Mouse (Mus musculus) [TaxId: 10090] [141617] (4)
      SQ P60334 5-190
    2. Ralstonia eutropha [TaxId: 106590] [159289] (1)
      SQ Q46R41 11-202
    3. Human (Homo sapiens) [TaxId: 9606] [159290] (1)
      SQ Q16878 6-190
    4. Rattus norvegicus [TaxId: 10116] [159291] (1)
20. 3-hydroxyanthranilic acid dioxygenase-like [141618] (2)
  Pfam 06052; 3-HAO
  1. 3-hydroxyanthranilate-3,4-dioxygenase [141619]
    1. Ralstonia metallidurans [TaxId: 119219] [141620] (4)
      SQ Q1LCS4 1-174
    2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [159292] (2)
      SQ P47096 1-175
21. Acetylacetone-cleaving enzyme-like [159293] (1)
  PfamB 026844
  1. Putative acetyl/propionyl-CoA carboxylase subunit alpha Mpe_A3659 [159294]
    1. Rubrivivax gelatinosus [TaxId: 28068] [159295] (2)
      SQ A2SM23 1-144
22. VPA0057-like [159296] (1)
  Pfam 06865; DUF1255; non-canonical dimerisation mode
  1. Uncharacterized protein VPA0057 [159297]
    1. Vibrio parahaemolyticus [TaxId: 670] [159298] (1)
      SQ Q87K41 2-94
23. Gentisate 1,2-dioxygenase-like [159299] (3)
  Share a common two-domain fold with the 7S protein; there is a metal-binding site in the N-terminal domain similar to the metal-binding site of germin; homotetramer
  1. Gentisate 1,2-dioxygenase [159300]
    Salicylate 1,2-dioxygenase
    1. Escherichia coli [TaxId: 562] [159301] (4)
      SQ Q8X655 35-342
    2. Silicibacter pomeroyi [TaxId: 89184] [159302] (2)
      SQ Q5LLB1 19-373
    3. Pseudaminobacter salicylatoxidans [TaxId: 93369] [159303] (4)
      SQ Q67FT0 17-367
24. EutQ-like [159304] (1)
  Pfam 06249
  1. Ethanolamine utilization protein EutQ [159305]
    1. Salmonella typhimurium [TaxId: 90371] [159306] (2)
      SQ Q9ZFV5 100-227
Clavaminate synthase-like [51197] (13)
Iron and ketoglutarate-dependent enzymes; elaborated version of this common fold
uperfamily
1. Penicillin synthase-like [51198] (4)
  common fold is rather distorted
  1. Isopenicillin N synthase [51199]
    1. Emericella nidulans [TaxId: 162425] [51200] (29)
      SQ P05326
  2. Deacetoxycephalosporin C synthase [51201]
    1. Streptomyces clavuligerus [TaxId: 1901] [51202] (17)
      SQ P18548
  3. Anthocyanidin synthase [69346]
    1. Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702] [69347] (4)
  4. 1-aminocyclopropane-1-carboxylate oxidase 1 [141621]
    1. Petunia hybrida [TaxId: 4102] [141622] (2)
      SQ Q08506 2-308
2. Clavaminate synthase [51203] (1)
  1. Clavaminate synthase [51204]
    1. Streptomyces clavuligerus [TaxId: 1901] [51205] (5)
3. Gab protein (hypothetical protein YgaT) [63855] (1)
  1. Gab protein (hypothetical protein YgaT) [63856]
    unknown function
    1. Escherichia coli [TaxId: 562] [63857] (1)
4. YhcH-like [89413] (1)
  1. Hypothetical protein HI0227 [89414]
    1. Haemophilus influenzae [TaxId: 727] [89415] (5)
5. Type II Proline 3-hydroxylase (proline oxidase) [63858] (1)
  1. Type II Proline 3-hydroxylase (proline oxidase) [63859]
    1. Streptomyces sp. [TaxId: 1931] [63860] (2)
6. TauD/TfdA-like [75038] (2)
  1. Taurine/alpha-ketoglutarate dioxygenase TauD [75039]
    1. Escherichia coli [TaxId: 562] [75040] (4)
  2. Putative alkylsulfatase AtsK [101989]
    1. Pseudomonas putida [TaxId: 303] [101990] (6)
      SQ Q9WWU5
7. gamma-Butyrobetaine hydroxylase [89416] (2)
  Pfam 03322
  1. Carbapenem synthase, CarC [89417]
    1. Erwinia carotovora [TaxId: 554] [89418] (2)
  2. Clavaminate synthase-like protein At3g21360 [117321]
    1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117322] (3)
      SQ Q9LIG0
8. Hypoxia-inducible factor HIF ihhibitor (FIH1) [82194] (1)
  1. Hypoxia-inducible factor HIF ihhibitor (FIH1) [82195]
    1. Human (Homo sapiens) [TaxId: 9606] [82196] (10)
9. PhyH-like [141623] (2)
  Pfam 05721
  1. Syringomycin biosynthesis enzyme 2, SyrB2 [141624]
    1. Pseudomonas syringae pv. syringae [TaxId: 321] [141625] (6)
      SQ Q9RBY6 3-310
  2. Phytanoyl-CoA dioxygenase, PhyH [141626]
    1. Human (Homo sapiens) [TaxId: 9606] [141627] (1)
      SQ O14832 43-338
10. AlkB-like [141628] (2)
  1. Alkylated DNA repair protein AlkB [141629]
    1. Escherichia coli [TaxId: 562] [141630] (7)
      SQ P05050 15-214
  2. AlkB homolog 3 [141631]
    Prostate cancer antigen 1, DEPC-1
    1. Human (Homo sapiens) [TaxId: 9606] [141632] (1)
      SQ Q96Q83 70-279
11. Asparaginyl hydroxylase-like [141633] (1)
  Pfam 08007
  1. Putative asparaginyl hydroxylase YxbC [141634]
    1. Bacillus subtilis [TaxId: 1423] [141635] (4)
      SQ P46327 8-326
12. YbiU-like [141636] (1)
  Pfam 07350; DUF1479
  1. Hypothetical protein YbiU [141637]
    1. Salmonella typhimurium [TaxId: 90371] [141638] (1)
      SQ Q8ZQM7 3-419
13. TehB-like [159307] (2)
  Pfam 09313; DUF1971
  1. Uncharacterized protein YeaR [159308]
    1. Escherichia coli [TaxId: 562] [159309] (4)
      SQ P64488 1-109
  2. Tellurite resistance protein B, TehB [159310]
    1. Vibrio fischeri [TaxId: 668] [159311] (8)
      SQ Q5E3X2 5-100
cAMP-binding domain-like [51206] (3)
uperfamily
1. CO-sensing protein CooA, N-terminal domain [51207] (1)
  heme-binding domain
  1. CO-sensing protein CooA, N-terminal domain [51208]
    1. Rhodospirillum rubrum [TaxId: 1085] [51209] (1)
2. Listeriolysin regulatory protein PrfA, N-terminal domain [89419] (1)
  1. Listeriolysin regulatory protein PrfA, N-terminal domain [89420]
    1. Bacteria (Listeria monocytogenes) [TaxId: 1639] [89421] (11)
3. cAMP-binding domain [51210] (14)
  Pfam 00027
  1. Catabolite gene activator protein, N-terminal domain [51211]
    1. Escherichia coli [TaxId: 562] [51212] (26)
  2. CRP-like transcriptional regulator TM1171, N-terminal domain [101991]
    1. Thermotoga maritima [TaxId: 2336] [101992] (1)
  3. Regulatory subunit of Protein kinase A [51213]
    duplication: consists of two similar domains
    1. Cow (Bos taurus) [TaxId: 9913] [51214] (4)
      SQ P00514 109-376
    2. Rat (Rattus norvegicus) [TaxId: 10116] [63861] (1)
  4. Regulatory domain of Epac2, domains 1 and 3 [82197]
    duplication: two homologous domains of this fold are separated in the sequence by a DEP domain
    1. Mouse (Mus musculus) [TaxId: 10090] [82198] (1)
  5. HCN pacemaker channel [101993]
    potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel
    1. Mouse (Mus musculus) [TaxId: 10090] [101994] (5)
  6. Putative ion channel CnbD [110321]
    1. Mesorhizobium loti [TaxId: 381] [110322] (4)
      SQ Q98GN8 218-350 # mll3241
  7. Probable cyclic nucleotide-gated ion channel 6 [117323]
    1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117324] (1)
      SQ O82226 509-632
  8. Probable transcription regulator BT4300, N-terminal domain [141639]
    1. Bacteroides thetaiotaomicron [TaxId: 818] [141640] (1)
      SQ Q89ZS6 1-147
  9. Transcriptional regulator TTHA1359, N-terminal domain [141641]
    1. Thermus thermophilus [TaxId: 274] [141642] (1)
      SQ Q5SIL0 6-117
  10. Transcriptional regulator PG0396, N-terminal domain [141643]
    1. Porphyromonas gingivalis [TaxId: 837] [141644] (1)
      SQ Q7MAW7 10-151
  11. Cyclic AMP receptor-like protein Vfr [159312]
    1. Pseudomonas aeruginosa [TaxId: 287] [159313] (1)
      SQ P55222 9-142
  12. Chlorophenol reduction protein CprK [159314]
    1. Desulfitobacterium hafniense [TaxId: 49338] [159315] (7)
      SQ Q18R04 3-147! SQ Q18R04 9-147
    2. Desulfitobacterium dehalogenans [TaxId: 36854] [159316] (2)
      SQ Q9LAS2 19-147
Regulatory protein AraC [51215] (1)
uperfamily
1. Regulatory protein AraC [51216] (1)
  1. Regulatory protein AraC [51217]
    contains an alpha-hairpin in the C-terminal extension
    1. Escherichia coli [TaxId: 562] [51218] (4)
      SQ P03021
Thiamin pyrophosphokinase, substrate-binding domain [63862] (1)
uperfamily
1. Thiamin pyrophosphokinase, substrate-binding domain [63863] (2)
  1. Thiamin pyrophosphokinase, substrate-binding domain [63864]
    1. Mouse (Mus musculus) [TaxId: 10090] [63865] (2)
    2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [63866] (1)
Calcium ATPase, transduction domain A [81653] (1)
a distorted variant of double-helix
uperfamily
1. Calcium ATPase, transduction domain A [81652] (1)
  1. Calcium ATPase, transduction domain A [81651]
    1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [81650] (17)
      SQ P04191
TRAP-like [51219] (2)
shorter variant of double-helix; assembles in large ring-like structures containing from 9 to 11 domains
uperfamily
1. Trp RNA-binding attenuation protein (TRAP) [51220] (2)
  oligomeric ring consists of 11 single-domain subunits
  1. Trp RNA-binding attenuation protein (TRAP) [51221]
    1. Bacillus subtilis [TaxId: 1423] [51222] (1)
    2. Bacillus stearothermophilus [TaxId: 1422] [51223] (19)
2. PA3696/SPS0176-like [101995] (2)
  duplication: there are three structural repeats per subunit; nine domains per ring-like trimer
  1. Hypothetical protein SPyM3_0169 (SPyM18_0222, SPS0176) [101996]
    1. Streptococcus pyogenes [TaxId: 1314] [101997] (1)
  2. Hypothetical protein PA3696 [141645]
    1. Pseudomonas aeruginosa [TaxId: 287] [141646] (6)
      SQ Q9HXU4 5-244