Lineage for Fold d.58: Ferredoxin-like

  1. Root: SCOP 1.73
  2. 713694Class d: Alpha and beta proteins (a+b) [53931] (334 folds)
  3. 723373Fold d.58: Ferredoxin-like [54861] (55 superfamilies)
    alpha+beta sandwich with antiparallel beta-sheet; (beta-alpha-beta)x2

Superfamilies:

  1. 723374d.58.1: 4Fe-4S ferredoxins [54862] (6 families) (S)
  2. 723615d.58.2: Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain [54893] (1 family) (S)
  3. 723710d.58.3: Protease propeptides/inhibitors [54897] (3 families) (S)
  4. 723747d.58.4: Dimeric alpha+beta barrel [54909] (17 families) (S)
    dimerizes through the beta-sheet; forms beta-sheet barrel, closed (n=8, S=12); dimers may assemble in higher oligomers
  5. 723963d.58.5: GlnB-like [54913] (4 families) (S)
    form timeric structures with the orthogonally packed beta-sheets
  6. 724082d.58.6: Nucleoside diphosphate kinase, NDK [54919] (1 family) (S)
  7. 724300d.58.7: RNA-binding domain, RBD [54928] (4 families) (S)
  8. 724702d.58.8: Viral DNA-binding domain [54957] (1 family) (S)
  9. 724752d.58.9: RuBisCO, large subunit, small (N-terminal) domain [54966] (1 family) (S)
    C-terminal domain is beta/alpha barrel
  10. 724932d.58.10: Acylphosphatase/BLUF domain-like [54975] (2 families) (S)
  11. 724976d.58.11: EF-G C-terminal domain-like [54980] (3 families) (S)
  12. 725057d.58.12: eEF-1beta-like [54984] (1 family) (S)
  13. 725070d.58.13: Anticodon-binding domain of PheRS [54991] (1 family) (S)
  14. 725083d.58.14: Ribosomal protein S6 [54995] (1 family) (S)
  15. 725134d.58.15: Ribosomal protein S10 [54999] (1 family) (S)
  16. 725174d.58.16: PAP/Archaeal CCA-adding enzyme, C-terminal domain [55003] (2 families) (S)
  17. 725214d.58.17: HMA, heavy metal-associated domain [55008] (1 family) (S)
  18. 725281d.58.18: ACT-like [55021] (12 families) (S)
    regulatory domain linked to a wide range of metabolic enzymes
  19. 725435d.58.19: Bacterial exopeptidase dimerisation domain [55031] (1 family) (S)
  20. 725482d.58.20: NAD-binding domain of HMG-CoA reductase [55035] (1 family) (S)
  21. 725533d.58.21: Molybdenum cofactor biosynthesis protein C, MoaC [55040] (1 family) (S)
  22. 725539d.58.22: TRADD, N-terminal domain [55044] (1 family) (S)
  23. 725545d.58.23: Probable ACP-binding domain of malonyl-CoA ACP transacylase [55048] (1 family) (S)
  24. 725552d.58.24: CheY-binding domain of CheA [55052] (1 family) (S)
  25. 725571d.58.25: Killer toxin KP6 alpha-subunit [55056] (1 family) (S)
  26. 725576d.58.26: GHMP Kinase, C-terminal domain [55060] (7 families) (S)
    common fold is elaborated with additional secondary structures
  27. 725645d.58.27: Translational regulator protein regA [55064] (1 family) (S)
    common fold is elaborated with additional secondary structures
  28. 725651d.58.28: Peptide methionine sulfoxide reductase [55068] (1 family) (S)
    common fold is elaborated with additional secondary structures
  29. 725665d.58.29: Nucleotide cyclase [55073] (2 families) (S)
    common fold is elaborated with additional secondary structures
  30. 725724d.58.30: 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK [55083] (1 family) (S)
    common fold is elaborated with additional secondary structures
  31. 725752d.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. 725809d.58.32: FAD-linked oxidases, C-terminal domain [55103] (4 families) (S)
    duplication: contains two subdomains of this fold
  33. 725871d.58.33: Formylmethanofuran:tetrahydromethanopterin formyltransferase [55112] (1 family) (S)
    duplication: contains two subdomains of this fold
  34. 725925d.58.34: Formiminotransferase domain of formiminotransferase-cyclodeaminase. [55116] (1 family) (S)
    duplication: contains two subdomains of this fold
  35. 725933d.58.36: Sulfite reductase, domains 1 and 3 [55124] (1 family) (S)
    duplication: contains two subdomains of this fold
  36. 725961d.58.38: Urease metallochaperone UreE, C-terminal domain [69737] (1 family) (S)
  37. 725978d.58.39: Glutamyl tRNA-reductase catalytic, N-terminal domain [69742] (1 family) (S)
    common fold is elaborated with additional secondary structures
  38. 725983d.58.40: D-ribose-5-phosphate isomerase (RpiA), lid domain [75445] (1 family) (S)
  39. 726009d.58.41: SEA domain [82671] (1 family) (S)
  40. 726014d.58.42: N-utilization substance G protein NusG, N-terminal domain [82679] (1 family) (S)
  41. 726030d.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. 726041d.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. 726069d.58.46: eEF1-gamma domain [89942] (1 family) (S)
    elaborated with additional structures
  44. 726074d.58.47: Hypothetical protein VC0424 [89946] (1 family) (S)
  45. 726079d.58.48: MTH1187/YkoF-like [89957] (2 families) (S)
  46. 726116d.58.49: YajQ-like [89963] (1 family) (S)
    duplication: consists of two domains of this fold swapped with their N-terminal strands
  47. 726124d.58.50: Hypothetical protein TT1725 [103007] (1 family) (S)
  48. 726129d.58.51: eIF-2-alpha, C-terminal domain [110993] (1 family) (S)
  49. 726136d.58.52: Sporulation related repeat [110997] (1 family) (S)
    duplication: one domain contains two repeats of similar sequence and structure
  50. 726141d.58.53: CRISPR-associated protein [117987] (1 family) (S)
    duplication: contains two subdomains of this fold
  51. 726147d.58.54: YbeD-like [117991] (1 family) (S)
  52. 726152d.58.55: DOPA-like [143410] (1 family) (S)
    probable biological unit is homodimer; the extra C-terminal strand, adjacent and antiparallel to strand 4, contributes to the dimerisation interface
  53. 726162d.58.56: CcmK-like [143414] (1 family) (S)
    contains extra C-terminal helix; forms compact hexameric 'tiles' of hexagonal shape
  54. 726192d.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. 726210d.58.58: TTP0101/SSO1404-like [143430] (1 family) (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

More info for Fold d.58: Ferredoxin-like

Timeline for Fold d.58: Ferredoxin-like: