Lineage for Fold d.58: Ferredoxin-like

  1. Root: SCOPe 2.06
  2. 2152203Class d: Alpha and beta proteins (a+b) [53931] (385 folds)
  3. 2172288Fold d.58: Ferredoxin-like [54861] (59 superfamilies)
    alpha+beta sandwich with antiparallel beta-sheet; (beta-alpha-beta)x2

Superfamilies:

  1. 2172289d.58.1: 4Fe-4S ferredoxins [54862] (7 families) (S)
  2. 2172653d.58.2: Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain [54893] (2 families) (S)
    automatically mapped to Pfam PF01948
  3. 2172800d.58.3: Protease propeptides/inhibitors [54897] (4 families) (S)
  4. 2172847d.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. 2173456d.58.5: GlnB-like [54913] (6 families) (S)
    form timeric structures with the orthogonally packed beta-sheets
  6. 2173863d.58.6: Nucleoside diphosphate kinase, NDK [54919] (2 families) (S)
  7. 2174486d.58.7: RNA-binding domain, RBD [54928] (6 families) (S)
  8. 2175215d.58.8: Viral DNA-binding domain [54957] (1 family) (S)
  9. 2175267d.58.9: RuBisCO, large subunit, small (N-terminal) domain [54966] (2 families) (S)
    C-terminal domain is beta/alpha barrel
  10. 2175647d.58.10: Acylphosphatase/BLUF domain-like [54975] (3 families) (S)
  11. 2175773d.58.11: EF-G C-terminal domain-like [54980] (4 families) (S)
  12. 2175889d.58.12: eEF-1beta-like [54984] (1 family) (S)
    automatically mapped to Pfam PF00736
  13. 2175907d.58.13: Anticodon-binding domain of PheRS [54991] (1 family) (S)
    automatically mapped to Pfam PF03147
  14. 2175923d.58.14: Ribosomal protein S6 [54995] (1 family) (S)
  15. 2176013d.58.15: Ribosomal protein S10 [54999] (1 family) (S)
    automatically mapped to Pfam PF00338
  16. 2176087d.58.16: PAP/Archaeal CCA-adding enzyme, C-terminal domain [55003] (3 families) (S)
  17. 2176148d.58.17: HMA, heavy metal-associated domain [55008] (2 families) (S)
  18. 2176307d.58.18: ACT-like [55021] (15 families) (S)
    regulatory domain linked to a wide range of metabolic enzymes
  19. 2176589d.58.19: Bacterial exopeptidase dimerisation domain [55031] (1 family) (S)
  20. 2176636d.58.20: NAD-binding domain of HMG-CoA reductase [55035] (1 family) (S)
  21. 2176699d.58.21: Molybdenum cofactor biosynthesis protein C, MoaC [55040] (2 families) (S)
  22. 2176765d.58.22: TRADD, N-terminal domain [55044] (1 family) (S)
  23. 2176771d.58.23: Probable ACP-binding domain of malonyl-CoA ACP transacylase [55048] (1 family) (S)
  24. 2176786d.58.24: CheY-binding domain of CheA [55052] (1 family) (S)
  25. 2176805d.58.25: Killer toxin KP6 alpha-subunit [55056] (1 family) (S)
  26. 2176812d.58.26: GHMP Kinase, C-terminal domain [55060] (8 families) (S)
    common fold is elaborated with additional secondary structures
  27. 2176905d.58.27: Translational regulator protein regA [55064] (1 family) (S)
    common fold is elaborated with additional secondary structures
    automatically mapped to Pfam PF01818
  28. 2176911d.58.28: Peptide methionine sulfoxide reductase [55068] (2 families) (S)
    common fold is elaborated with additional secondary structures
  29. 2176945d.58.29: Nucleotide cyclase [55073] (3 families) (S)
    common fold is elaborated with additional secondary structures
  30. 2177076d.58.30: 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK [55083] (1 family) (S)
    common fold is elaborated with additional secondary structures
    automatically mapped to Pfam PF01288
  31. 2177144d.58.31: Methyl-coenzyme M reductase subunits [55088] (3 families) (S)
    each of the three different subunits, alpha, beta and gamma, contains this fold decorated with additional secondary structures
  32. 2177253d.58.32: FAD-linked oxidases, C-terminal domain [55103] (7 families) (S)
    duplication: contains two subdomains of this fold
  33. 2177370d.58.33: Formylmethanofuran:tetrahydromethanopterin formyltransferase [55112] (1 family) (S)
    duplication: contains two subdomains of this fold
  34. 2177424d.58.34: Formiminotransferase domain of formiminotransferase-cyclodeaminase. [55116] (1 family) (S)
    duplication: contains two subdomains of this fold
  35. 2177432d.58.36: Nitrite/Sulfite reductase N-terminal domain-like [55124] (3 families) (S)
    duplication: contains two subdomains of this fold
  36. 2177563d.58.38: Urease metallochaperone UreE, C-terminal domain [69737] (1 family) (S)
    automatically mapped to Pfam PF05194
  37. 2177584d.58.39: Glutamyl tRNA-reductase catalytic, N-terminal domain [69742] (1 family) (S)
    common fold is elaborated with additional secondary structures
    automatically mapped to Pfam PF05201
  38. 2177589d.58.40: D-ribose-5-phosphate isomerase (RpiA), lid domain [75445] (1 family) (S)
  39. 2177615d.58.41: SEA domain [82671] (1 family) (S)
    automatically mapped to Pfam PF01390
  40. 2177620d.58.42: N-utilization substance G protein NusG, N-terminal domain [82679] (1 family) (S)
  41. 2177638d.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. 2177656d.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. 2177696d.58.46: eEF1-gamma domain [89942] (1 family) (S)
    elaborated with additional structures
  44. 2177701d.58.47: Hypothetical protein VC0424 [89946] (1 family) (S)
    automatically mapped to Pfam PF06877
  45. 2177706d.58.48: MTH1187/YkoF-like [89957] (3 families) (S)
  46. 2177760d.58.49: YajQ-like [89963] (1 family) (S)
    duplication: consists of two domains of this fold swapped with their N-terminal strands
  47. 2177768d.58.50: Hypothetical protein TT1725 [103007] (1 family) (S)
    automatically mapped to Pfam PF04456
  48. 2177773d.58.51: eIF-2-alpha, C-terminal domain [110993] (1 family) (S)
  49. 2177786d.58.52: Sporulation related repeat [110997] (2 families) (S)
    duplication: one domain contains two repeats of similar sequence and structure
    automatically mapped to Pfam PF05036
  50. 2177795d.58.53: CRISPR-associated protein [117987] (2 families) (S)
    duplication: contains two subdomains of this fold
  51. 2177826d.58.54: YbeD/HP0495-like [117991] (2 families) (S)
  52. 2177836d.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. 2177851d.58.56: CcmK-like [143414] (2 families) (S)
    contains extra C-terminal helix; forms compact hexameric 'tiles' of hexagonal shape
  54. 2178051d.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
    automatically mapped to Pfam PF01797
  55. 2178088d.58.58: CRISPR associated protein Cas2-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. 2178130d.58.59: Rnp2-like [160350] (1 family) (S)
    contains extra C-terminal helix
    automatically mapped to Pfam PF01900
  57. 2178146d.58.60: Bacterial polysaccharide co-polymerase-like [160355] (1 family) (S)
    Decorated common fold with extra helical regions, which facilitate oligomerization
  58. 2178198d.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. 2178236d.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: