Lineage for Fold d.58: Ferredoxin-like

  1. Root: SCOPe 2.02
  2. 1190016Class d: Alpha and beta proteins (a+b) [53931] (376 folds)
  3. 1203810Fold d.58: Ferredoxin-like [54861] (59 superfamilies)
    alpha+beta sandwich with antiparallel beta-sheet; (beta-alpha-beta)x2

Superfamilies:

  1. 1203811d.58.1: 4Fe-4S ferredoxins [54862] (6 families) (S)
  2. 1204103d.58.2: Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain [54893] (1 family) (S)
  3. 1204208d.58.3: Protease propeptides/inhibitors [54897] (3 families) (S)
  4. 1204251d.58.4: Dimeric alpha+beta barrel [54909] (24 families) (S)
    dimerizes through the beta-sheet; forms beta-sheet barrel, closed (n=8, S=12); dimers may assemble in higher oligomers
  5. 1204632d.58.5: GlnB-like [54913] (6 families) (S)
    form timeric structures with the orthogonally packed beta-sheets
  6. 1204903d.58.6: Nucleoside diphosphate kinase, NDK [54919] (2 families) (S)
  7. 1205320d.58.7: RNA-binding domain, RBD [54928] (6 families) (S)
  8. 1205808d.58.8: Viral DNA-binding domain [54957] (1 family) (S)
  9. 1205860d.58.9: RuBisCO, large subunit, small (N-terminal) domain [54966] (1 family) (S)
    C-terminal domain is beta/alpha barrel
  10. 1206080d.58.10: Acylphosphatase/BLUF domain-like [54975] (3 families) (S)
  11. 1206180d.58.11: EF-G C-terminal domain-like [54980] (3 families) (S)
  12. 1206263d.58.12: eEF-1beta-like [54984] (1 family) (S)
  13. 1206278d.58.13: Anticodon-binding domain of PheRS [54991] (1 family) (S)
  14. 1206291d.58.14: Ribosomal protein S6 [54995] (1 family) (S)
  15. 1206381d.58.15: Ribosomal protein S10 [54999] (1 family) (S)
  16. 1206455d.58.16: PAP/Archaeal CCA-adding enzyme, C-terminal domain [55003] (2 families) (S)
  17. 1206509d.58.17: HMA, heavy metal-associated domain [55008] (2 families) (S)
  18. 1206627d.58.18: ACT-like [55021] (14 families) (S)
    regulatory domain linked to a wide range of metabolic enzymes
  19. 1206822d.58.19: Bacterial exopeptidase dimerisation domain [55031] (1 family) (S)
  20. 1206869d.58.20: NAD-binding domain of HMG-CoA reductase [55035] (1 family) (S)
  21. 1206920d.58.21: Molybdenum cofactor biosynthesis protein C, MoaC [55040] (2 families) (S)
  22. 1206966d.58.22: TRADD, N-terminal domain [55044] (1 family) (S)
  23. 1206972d.58.23: Probable ACP-binding domain of malonyl-CoA ACP transacylase [55048] (1 family) (S)
  24. 1206979d.58.24: CheY-binding domain of CheA [55052] (1 family) (S)
  25. 1206998d.58.25: Killer toxin KP6 alpha-subunit [55056] (1 family) (S)
  26. 1207005d.58.26: GHMP Kinase, C-terminal domain [55060] (7 families) (S)
    common fold is elaborated with additional secondary structures
  27. 1207075d.58.27: Translational regulator protein regA [55064] (1 family) (S)
    common fold is elaborated with additional secondary structures
  28. 1207081d.58.28: Peptide methionine sulfoxide reductase [55068] (1 family) (S)
    common fold is elaborated with additional secondary structures
  29. 1207098d.58.29: Nucleotide cyclase [55073] (3 families) (S)
    common fold is elaborated with additional secondary structures
  30. 1207177d.58.30: 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK [55083] (1 family) (S)
    common fold is elaborated with additional secondary structures
  31. 1207232d.58.31: Methyl-coenzyme M reductase subunits [55088] (2 families) (S)
    each of the three different subunits, alpha, beta and gamma, contains this fold decorated with additional secondary structures
  32. 1207303d.58.32: FAD-linked oxidases, C-terminal domain [55103] (4 families) (S)
    duplication: contains two subdomains of this fold
  33. 1207366d.58.33: Formylmethanofuran:tetrahydromethanopterin formyltransferase [55112] (1 family) (S)
    duplication: contains two subdomains of this fold
  34. 1207420d.58.34: Formiminotransferase domain of formiminotransferase-cyclodeaminase. [55116] (1 family) (S)
    duplication: contains two subdomains of this fold
  35. 1207428d.58.36: Nitrite/Sulfite reductase N-terminal domain-like [55124] (2 families) (S)
    duplication: contains two subdomains of this fold
  36. 1207485d.58.38: Urease metallochaperone UreE, C-terminal domain [69737] (1 family) (S)
  37. 1207502d.58.39: Glutamyl tRNA-reductase catalytic, N-terminal domain [69742] (1 family) (S)
    common fold is elaborated with additional secondary structures
  38. 1207507d.58.40: D-ribose-5-phosphate isomerase (RpiA), lid domain [75445] (1 family) (S)
  39. 1207533d.58.41: SEA domain [82671] (1 family) (S)
  40. 1207538d.58.42: N-utilization substance G protein NusG, N-terminal domain [82679] (1 family) (S)
  41. 1207554d.58.43: Mechanosensitive channel protein MscS (YggB), C-terminal domain [82689] (1 family) (S)
    the last strand of the fold is flipped away and involved in oligomerisation
  42. 1207572d.58.44: Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains [82693] (1 family) (S)
    duplication: the N- and C-terminal halves of the whole proteins are structurally similar; each half contains two domains of this fold
  43. 1207600d.58.46: eEF1-gamma domain [89942] (1 family) (S)
    elaborated with additional structures
  44. 1207605d.58.47: Hypothetical protein VC0424 [89946] (1 family) (S)
  45. 1207610d.58.48: MTH1187/YkoF-like [89957] (3 families) (S)
  46. 1207664d.58.49: YajQ-like [89963] (1 family) (S)
    duplication: consists of two domains of this fold swapped with their N-terminal strands
  47. 1207672d.58.50: Hypothetical protein TT1725 [103007] (1 family) (S)
  48. 1207677d.58.51: eIF-2-alpha, C-terminal domain [110993] (1 family) (S)
  49. 1207686d.58.52: Sporulation related repeat [110997] (1 family) (S)
    duplication: one domain contains two repeats of similar sequence and structure
  50. 1207691d.58.53: CRISPR-associated protein [117987] (1 family) (S)
    duplication: contains two subdomains of this fold
  51. 1207697d.58.54: YbeD/HP0495-like [117991] (2 families) (S)
  52. 1207707d.58.55: DOPA-like [143410] (2 families) (S)
    probable biological unit is homodimer; the extra C-terminal strand, adjacent and antiparallel to strand 4, contributes to the dimerisation interface
  53. 1207722d.58.56: CcmK-like [143414] (2 families) (S)
    contains extra C-terminal helix; forms compact hexameric 'tiles' of hexagonal shape
  54. 1207771d.58.57: Transposase IS200-like [143422] (1 family) (S)
    contains extra N-terminal hairpin and C-terminal helix, both are involved in dimerization; there can be helix-swapping in the dimer
  55. 1207808d.58.58: TTP0101/SSO1404-like [143430] (2 families) (S)
    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
  56. 1207826d.58.59: Rnp2-like [160350] (1 family) (S)
    contains extra C-terminal helix
  57. 1207838d.58.60: Bacterial polysaccharide co-polymerase-like [160355] (1 family) (S)
    Decorated common fold with extra helical regions, which facilitate oligomerization
  58. 1207881d.58.61: MTH889-like [160363] (2 families) (S)
    assembles into hexameric ring-like structures with the formation of a singe beta-barrel sheet of 24 strands
  59. 1207919d.58.62: Ribosomal protein L10-like [160369] (1 family) (S)
    consists of globular N-terminal domain, structurally similar to NDK, and the L7/L12-binding C-terminal alpha-helical tail

More info for Fold d.58: Ferredoxin-like

Timeline for Fold d.58: Ferredoxin-like: