Fold: Ferredoxin-like

alpha+beta sandwich with antiparallel beta-sheet; (beta-alpha-beta)x2

Lineage:

1. Root: scop
2. Class: Alpha and beta proteins (a+b) [53931]
   Mainly antiparallel beta sheets (segregated alpha and beta regions)
3. Fold: Ferredoxin-like [54861]
   alpha+beta sandwich with antiparallel beta-sheet; (beta-alpha-beta)x2

Superfamilies:

1. 4Fe-4S ferredoxins [54862] (6)
   uperfamily
   1. Short-chain ferredoxins [54863] (5)
      contains two 4Fe-4S clusters
   2. 7-Fe ferredoxin [54870] (5)
      has C-terminal extension to the common fold
   3. Archaeal ferredoxins [54874] (1)
   4. Single 4Fe-4S cluster ferredoxin [54877] (5)
      contains only one 4Fe-4S cluster
   5. Ferredoxin domains from multidomain proteins [54884] (15)
      members of this "family" may be more closely related to other ferredoxins than to each other
   6. ETF-QO domain-like [143256] (1)
      Pfam 05187; Electron transfer flavoprotein-ubiquinone oxidoreductase; contains single Fe4-S4 cluster
2. Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain [54893] (1)
   uperfamily
   1. Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain [54894] (2)
3. Protease propeptides/inhibitors [54897] (3)
   uperfamily
   1. Pancreatic carboxypeptidase, activation domain [54898] (6)
   2. Subtilase propeptides/inhibitors [54905] (4)
      decorated with additional structure
   3. Prohormone convertase 1 pro-domain [75431] (1)
4. Dimeric alpha+beta barrel [54909] (23)
   dimerizes through the beta-sheet; forms beta-sheet barrel, closed (n=8, S=12); dimers may assemble in higher oligomers
   uperfamily
   1. Actinorhodin biosynthesis monooxygenase ActVa-Orf6 [82666] (1)
   2. Plant stress-induced protein [89927] (3)
   3. PG130-like [102959] (5)
      subfamily of Pfam 03992
   4. Hypothetical protein YjcS [102962] (1)
   5. YciI-like [102965] (1)
      structural similarity to MLI extends to the active site cavity location
   6. Muconalactone isomerase, MLI [54910] (1)
      decamer: pentamer of dimers
   7. Lrp/AsnC-like transcriptional regulator C-terminal domain [69733] (4)
      octamer: tetramer of dimers
   8. Polyketide synthesis cyclase [110959] (1)
      Pfam 04673
   9. DGPF domain (Pfam 04946) [110962] (1)
      there is the putative active site cavity in the equivalent location location to the MLI and YciI active sites
   10. Chlorite dismutase-like [110965] (2)
       Pfam 06778; duplication: consists of two similar domains; forms a pentamer similar to the MLI decamer
   11. PA3566-like [110970] (5)
       subfamily of Pfam 03992
   12. Hypothetical protein YdhR [117940] (1)
   13. NIPSNAP [117943] (2)
       Pfam 07978
   14. Dyp-type peroxidase-like [143265] (3)
       Pfam 04261
   15. EthD-like [143272] (1)
       Pfam 07110
   16. Atu0297-like [143275] (1)
       Pfam 07045; DUF1330
   17. SOR-like [143278] (1)
       Pfam 07682; duplication: consists of two similar domains
   18. YbaA-like [160289] (1)
       Pfam 07237; DUF1428
   19. MmlI-like [160292] (1)
       Pfam 09448; Methylmuconolactone methyl-isomerase
   20. Marine metagenome family DABB2 [160295] (1)
   21. YiiL-like [160298] (1)
       Pfam 05336; DUF718
   22. Marine metagenome family DABB1 [160301] (2)
   23. Marine metagenome family DABB3 [160306] (1)
       duplication: consists of two similar domains; forms a pentamer similar to the Chlorite dismutase-like pentamer and the MLI decamer
5. GlnB-like [54913] (5)
   form timeric structures with the orthogonally packed beta-sheets
   uperfamily
   1. Prokaryotic signal transducing protein [54914] (8)
   2. Divalent ion tolerance proteins CutA (CutA1) [75434] (7)
   3. DUF190/COG1993 [89934] (1)
   4. ATP phosphoribosyltransferase (ATP-PRTase, HisG), regulatory C-terminal domain [88851] (2)
   5. RPA1041-like [160310] (1)
      PF09413; DUF2007; provisional superfamily assignment based on a single monomeric solution structure
6. SEA domain [82671] (1)
   uperfamily
   1. SEA domain [82672] (1)
7. Nucleoside diphosphate kinase, NDK [54919] (1)
   uperfamily
   1. Nucleoside diphosphate kinase, NDK [54920] (20)
8. RNA-binding domain, RBD [54928] (5)
   uperfamily
   1. Canonical RBD [54929] (71)
   2. Non-canonical RBD domain [54954] (1)
   3. Splicing factor U2AF subunits [64276] (1)
   4. Smg-4/UPF3 [102987] (1)
      Pfam 03467
   5. GUCT domain [160314] (1)
      Pfam 08152
9. Viral DNA-binding domain [54957] (1)
   uperfamily
   1. Viral DNA-binding domain [54958] (6)
10. RuBisCO, large subunit, small (N-terminal) domain [54966] (1)
    C-terminal domain is beta/alpha barrel
    uperfamily
    1. Ribulose 1,5-bisphosphate carboxylase-oxygenase [54967] (12)
11. Acylphosphatase/BLUF domain-like [54975] (2)
    uperfamily
    1. Acylphosphatase-like [54976] (6)
    2. BLUF domain [143364] (3)
       Pfam 04940; sensors of blue-light using FAD
12. EF-G C-terminal domain-like [54980] (3)
    uperfamily
    1. EF-G/eEF-2 domains III and V [54981] (3)
       domain III structure is lacking some of the superfamily characters and is often disordered in crystals
    2. YigZ C-terminal domain-like [102991] (2)
       similar to EF-G domain V; N-terminal domain shares structural similarity with the EF-G domain IV
    3. Hypothetical protein AF0491, C-terminal domain [110976] (1)
13. eEF-1beta-like [54984] (1)
    uperfamily
    1. eEF-1beta-like [54985] (3)
14. eEF1-gamma domain [89942] (1)
    elaborated with additional structures
    uperfamily
    1. eEF1-gamma domain [89943] (1)
15. Anticodon-binding domain of PheRS [54991] (1)
    uperfamily
    1. Anticodon-binding domain of PheRS [54992] (1)
16. Ribosomal protein S6 [54995] (1)
    uperfamily
    1. Ribosomal protein S6 [54996] (4)
17. Ribosomal protein S10 [54999] (1)
    uperfamily
    1. Ribosomal protein S10 [55000] (2)
18. N-utilization substance G protein NusG, N-terminal domain [82679] (1)
    uperfamily
    1. N-utilization substance G protein NusG, N-terminal domain [82680] (2)
19. PAP/Archaeal CCA-adding enzyme, C-terminal domain [55003] (2)
    uperfamily
    1. Poly(A) polymerase, PAP, C-terminal domain [55004] (2)
    2. Archaeal tRNA CCA-adding enzyme [102995] (1)
       decorated fold with a large insertion
20. HMA, heavy metal-associated domain [55008] (1)
    uperfamily
    1. HMA, heavy metal-associated domain [55009] (12)
21. Urease metallochaperone UreE, C-terminal domain [69737] (1)
    uperfamily
    1. Urease metallochaperone UreE, C-terminal domain [69738] (2)
22. ACT-like [55021] (14)
    regulatory domain linked to a wide range of metabolic enzymes
    uperfamily
    1. Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain [55022] (2)
    2. Allosteric threonine deaminase C-terminal domain [55025] (1)
    3. Phenylalanine metabolism regulatory domain [55028] (2)
    4. Nickel responsive regulator NikR, C-terminal domain [102999] (2)
    5. Glycine cleavage system transcriptional repressor [110980] (1)
       tandem repeat of two ACT-like domains; swapped domain dimer
    6. IlvH-like [143376] (3)
       Duplication: tandem repeat of two ACT-like domains; dimer, the N- and C-terminal domains have different dimerisation modes
    7. SP0238-like [143381] (1)
       stand-alone protein; dimer, the dimerization interface is formed by parallel packing of the subunit beta-sheets
    8. Atu0741-like [143384] (1)
       duplication: tandem repeat of two ACT-like domains; contains strand invasion of extra N-terminal strand into the C-terminal domain beta-sheet; dimerizes with the formation of orthogonally packed intersubunit beta-sheets
    9. VC0802-like [143387] (1)
       duplication: tandem repeat of two ACT-like domains; contains circular permutation (the C-terminal strand replacement with extra N-terminal strand); dimerizes with the formation of orthogonally packed intersubunit beta-sheets
    10. Aspartokinase allosteric domain-like [143390] (3)
        duplication: tandem repeat of two ACT-like domains; similar subunit and oligomeric structures to the VC0802-like family
    11. BT0572-like [143395] (1)
        duplication: tandem repeat of two ACT-like domains; dimerizes with the formation of orthogonally packed intersubunit beta-sheets
    12. AF1403 N-terminal domain-like [143398] (1)
        dimerizes with the formation of a single intersubunit beta-sheet
    13. NIL domain-like [160322] (4)
        Pfam 09383
    14. TM1266-like [160329] (1)
        PfamB 015436; stand-alone tetrameric protein; there are single beta-sheet dimers, whose beta-sheets are packed in parallel fasion in the tetramer
23. Bacterial exopeptidase dimerisation domain [55031] (1)
    uperfamily
    1. Bacterial exopeptidase dimerisation domain [55032] (9)
24. NAD-binding domain of HMG-CoA reductase [55035] (1)
    uperfamily
    1. NAD-binding domain of HMG-CoA reductase [55036] (2)
25. Molybdenum cofactor biosynthesis protein C, MoaC [55040] (1)
    uperfamily
    1. Molybdenum cofactor biosynthesis protein C, MoaC [55041] (1)
26. TRADD, N-terminal domain [55044] (1)
    uperfamily
    1. TRADD, N-terminal domain [55045] (1)
27. Probable ACP-binding domain of malonyl-CoA ACP transacylase [55048] (1)
    uperfamily
    1. Probable ACP-binding domain of malonyl-CoA ACP transacylase [55049] (2)
28. CheY-binding domain of CheA [55052] (1)
    uperfamily
    1. CheY-binding domain of CheA [55053] (2)
29. D-ribose-5-phosphate isomerase (RpiA), lid domain [75445] (1)
    uperfamily
    1. D-ribose-5-phosphate isomerase (RpiA), lid domain [75446] (4)
30. Killer toxin KP6 alpha-subunit [55056] (1)
    uperfamily
    1. Killer toxin KP6 alpha-subunit [55057] (1)
31. Hypothetical protein VC0424 [89946] (1)
    uperfamily
    1. Hypothetical protein VC0424 [89947] (1)
32. Hypothetical protein TT1725 [103007] (1)
    uperfamily
    1. Hypothetical protein TT1725 [103008] (1)
33. Mechanosensitive channel protein MscS (YggB), C-terminal domain [82689] (1)
    the last strand of the fold is flipped away and involved in oligomerisation
    uperfamily
    1. Mechanosensitive channel protein MscS (YggB), C-terminal domain [82690] (1)
34. GHMP Kinase, C-terminal domain [55060] (7)
    common fold is elaborated with additional secondary structures
    uperfamily
    1. Galactokinase [103011] (3)
    2. Homoserine kinase [55061] (1)
    3. Mevalonate kinase [75450] (2)
    4. Phosphomevalonate kinase (PMK) [75454] (1)
    5. Mevalonate 5-diphosphate decarboxylase [64281] (1)
    6. 4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE [89950] (2)
    7. Early switch protein XOL-1 [89953] (1)
       lost the ATP-binding site
35. Translational regulator protein regA [55064] (1)
    common fold is elaborated with additional secondary structures
    uperfamily
    1. Translational regulator protein regA [55065] (1)
36. Peptide methionine sulfoxide reductase [55068] (1)
    common fold is elaborated with additional secondary structures
    uperfamily
    1. Peptide methionine sulfoxide reductase [55069] (3)
37. Nucleotide cyclase [55073] (2)
    common fold is elaborated with additional secondary structures
    uperfamily
    1. Adenylyl and guanylyl cyclase catalytic domain [55074] (5)
       Pfam 00211
       structurally similar to the "palm" domain of DNA/RNA polymerase superfamily
    2. GGDEF domain [117984] (1)
       Pfam 00990; less decorated than the adenylyl/guanylyl cyclase domain
38. 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK [55083] (1)
    common fold is elaborated with additional secondary structures
    uperfamily
    1. 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK [55084] (2)
39. Glutamyl tRNA-reductase catalytic, N-terminal domain [69742] (1)
    common fold is elaborated with additional secondary structures
    uperfamily
    1. Glutamyl tRNA-reductase catalytic, N-terminal domain [69743] (1)
40. MTH1187/YkoF-like [89957] (2)
    uperfamily
    1. MTH1187-like [89958] (5)
       Pfam 01910; two domains form a single beta-sheet dimer; two dimers pack sheet-to-sheet in a tetramer; contains extra C-terminal helix
    2. Putative thiamin/HMP-binding protein YkoF [110987] (1)
       duplication: one subunit consists of two domains assembled as in the MHT1178-like dimer
41. Methyl-coenzyme M reductase subunits [55088] (2)
    each of the three different subunits, alpha, beta and gamma, contains this fold decorated with additional secondary structures
    uperfamily
    1. Methyl-coenzyme M reductase gamma chain [55089] (3)
    2. Methyl-coenzyme M reductase alpha and beta chain N-terminal domain [55094] (6)
       C-terminal domain is all-alpha
42. FAD-linked oxidases, C-terminal domain [55103] (4)
    duplication: contains two subdomains of this fold
    uperfamily
    1. Vanillyl-alcohol oxidase-like [55104] (2)
    2. D-lactate dehydrogenase [55109] (1)
    3. Cholesterol oxidase [64284] (1)
    4. Cytokinin dehydrogenase 1 [110990] (1)
43. Formylmethanofuran:tetrahydromethanopterin formyltransferase [55112] (1)
    duplication: contains two subdomains of this fold
    uperfamily
    1. Formylmethanofuran:tetrahydromethanopterin formyltransferase [55113] (3)
44. Formiminotransferase domain of formiminotransferase-cyclodeaminase. [55116] (1)
    duplication: contains two subdomains of this fold
    uperfamily
    1. Formiminotransferase domain of formiminotransferase-cyclodeaminase. [55117] (1)
45. Nitrite/Sulfite reductase N-terminal domain-like [55124] (2)
    duplication: contains two subdomains of this fold
    uperfamily
    1. Duplicated SiR/NiR-like domains 1 and 3 [55125] (3)
    2. DsrA/DsrB N-terminal-domain-like [160336] (4)
       Dissimilatory sulfite reductase is a heterodimer of homologous DsrA and DsrB subunits, the assembly of which is similar to the architecture of duplicated sulfite reductase CysI
46. Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains [82693] (1)
    duplication: the N- and C-terminal halves of the whole proteins are structurally similar; each half contains two domains of this fold
    uperfamily
    1. Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains [82694] (1)
47. YajQ-like [89963] (1)
    duplication: consists of two domains of this fold swapped with their N-terminal strands
    uperfamily
    1. YajQ-like [89964] (1)
48. eIF-2-alpha, C-terminal domain [110993] (1)
    uperfamily
    1. eIF-2-alpha, C-terminal domain [110994] (2)
49. Sporulation related repeat [110997] (1)
    duplication: one domain contains two repeats of similar sequence and structure
    uperfamily
    1. Sporulation related repeat [110998] (1)
       Pfam 05036; SPOR
50. CRISPR-associated protein [117987] (1)
    duplication: contains two subdomains of this fold
    uperfamily
    1. CRISPR-associated protein [117988] (1)
51. YbeD/HP0495-like [117991] (2)
    uperfamily
    1. YbeD-like [117992] (1)
       Pfam 04359; DUF493
    2. HP0495-like [160343] (1)
       PfamB 045675
52. DOPA-like [143410] (1)
    probable biological unit is homodimer; the extra C-terminal strand, adjacent and antiparallel to strand 4, contributes to the dimerisation interface
    uperfamily
    1. DOPA dioxygenase-like [143411] (1)
       Pfam 08883
53. CcmK-like [143414] (1)
    contains extra C-terminal helix; forms compact hexameric 'tiles' of hexagonal shape
    uperfamily
    1. CcmK-like [143415] (3)
       Pfam 00936; BMC domain
54. Transposase IS200-like [143422] (1)
    contains extra N-terminal hairpin and C-terminal helix, both are involved in dimerization; there can be helix-swapping in the dimer
    uperfamily
    1. Transposase IS200-like [143423] (3)
       Pfam 01797
55. TTP0101/SSO1404-like [143430] (1)
    contains extra C-terminal beta-strand that integrates into the beta-sheet of the other subunit in the homodimer, a probable biological unit of this superfamily
    uperfamily
    1. TTP0101/SSO1404-like [143431] (3)
       Pfam 02647; DUF196; this family includes recent structure of SSO1404 (PDB entry 2IVY)
56. Rnp2-like [160350] (1)
    contains extra C-terminal helix
    1. Rpp14/Pop5-like [160351] (2)
       Pfam 01900
57. Bacterial polysaccharide co-polymerase-like [160355] (1)
    Decorated common fold with extra helical regions, which facilitate oligomerization
    1. FepE-like [160356] (3)
       the ferredoxin-like fold resides mainly on in the N-terminal part that corresponds to Pfam 02706 (Wzz)
58. MTH889-like [160363] (1)
    assembles into hexameric ring-like structures with the formation of a singe beta-barrel sheet of 24 strands
    1. MTH889-like [160364] (2)
       Pfam 02680; DUF211, COG1888
59. Ribosomal protein L10-like [160369] (1)
    consists of globular N-terminal domain, structurally similar to NDK, and the L7/L12-binding C-terminal alpha-helical tail
    1. Ribosomal protein L10-like [160370] (1)
       Pfam 00466; covers globular domain only

Generated from scop database 1.75 with scopm 1.101 on Wed Jun 3 10:42:06 2009 Copyright © 1994-2009 The scop authors / scop@mrc-lmb.cam.ac.uk