SCOPe 2.02: Superfamily a.4.5: "Winged helix" DNA-binding domain

Lineage for Superfamily a.4.5: "Winged helix" DNA-binding domain

1. Root: SCOPe 2.02

2. Class a: All alpha proteins [46456] (284 folds)

3. Fold a.4: DNA/RNA-binding 3-helical bundle [46688] (14 superfamilies)
   core: 3-helices; bundle, closed or partly opened, right-handed twist; up-and down

4. Superfamily a.4.5: "Winged helix" DNA-binding domain [46785] (85 families)
   contains a small beta-sheet (wing)

Families:

1. a.4.5.1: Biotin repressor-like [46786] (2 proteins)

2. a.4.5.2: LexA repressor, N-terminal DNA-binding domain [46789] (1 protein)

3. a.4.5.3: Arginine repressor (ArgR), N-terminal DNA-binding domain [46792] (1 protein)

4. a.4.5.4: CAP C-terminal domain-like [46796] (8 proteins)

5. a.4.5.5: ArsR-like transcriptional regulators [46801] (5 proteins)
   The N- and C-terminal helical extensions to the common fold form the dimer interface

6. a.4.5.6: GntR-like transcriptional regulators [46804] (4 proteins)

7. a.4.5.7: Replication terminator protein (RTP) [46807] (1 protein)

8. a.4.5.8: N-terminal domain of molybdate-dependent transcriptional regulator ModE [46810] (1 protein)
   contains beta-hairpin in the N-terminal extension and two helices in the C-terminal extension

9. a.4.5.9: Transcription factor MotA, activation domain [46813] (1 protein)
   The N- and C-terminal helical extensions to the common fold form the dimer interface (distinct from that of ArsR-like family)

10. a.4.5.10: Replication initiation protein [46816] (3 proteins)
    duplication: tandem repeat of two "winged helix" domains arranged with the pseudo twofold symmetry

11. a.4.5.11: Helicase DNA-binding domain [46819] (4 proteins)
    follows the extended AAA-ATPase domain

12. a.4.5.12: Restriction endonuclease FokI, N-terminal (recognition) domain [46824] (1 protein)

13. a.4.5.13: Linker histone H1/H5 [46827] (3 proteins)

14. a.4.5.14: Forkhead DNA-binding domain [46832] (7 proteins)

15. a.4.5.15: DNA-binding domain from rap30 [46841] (1 protein)

16. a.4.5.16: C-terminal domain of RPA32 [46844] (1 protein)

17. a.4.5.17: Cell cycle transcription factor e2f-dp [46847] (2 proteins)
    heterodimer of two homologous chains

18. a.4.5.18: The central core domain of TFIIE beta [46850] (1 protein)

19. a.4.5.19: Z-DNA binding domain [46853] (5 proteins)
    Pfam PF02295

20. a.4.5.20: P4 origin-binding domain-like [46856] (2 proteins)
    C-terminus passes through the first loop

21. a.4.5.21: ets domain [46859] (9 proteins)

22. a.4.5.22: Heat-shock transcription factor [46873] (1 protein)

23. a.4.5.23: Interferon regulatory factor [46877] (4 proteins)
    Pfam PF00605

24. a.4.5.24: Iron-dependent repressor protein [46882] (3 proteins)

25. a.4.5.25: Methionine aminopeptidase, insert domain [46887] (1 protein)
    circularly permuted version of the "winged helix" fold

26. a.4.5.27: TnsA endonuclease, C-terminal domain [46782] (1 protein)

27. a.4.5.28: MarR-like transcriptional regulators [63379] (20 proteins)
    The N- and C-terminal helical extensions to the common fold form the dimer interface

28. a.4.5.29: Plant O-methyltransferase, N-terminal domain [63475] (5 proteins)
    unknown function

29. a.4.5.30: C-terminal domain of the rap74 subunit of TFIIF [63480] (1 protein)

30. a.4.5.31: DEP domain [63483] (4 proteins)
    membrane-binding domain

31. a.4.5.32: Lrp/AsnC-like transcriptional regulator N-terminal domain [68967] (4 proteins)
    Swapped dimer with the "wing" C-terminal strands

32. a.4.5.33: Transcriptional regulator IclR, N-terminal domain [74676] (1 protein)

33. a.4.5.34: SCF ubiquitin ligase complex WHB domain [74679] (3 proteins)

34. a.4.5.35: C-terminal fragment of elongation factor SelB [74683] (1 protein)

35. a.4.5.36: DNA-binding protein Mj223 [81690] (1 protein)
    homologous to the MarR-like family in the DNA-binding region but dimerizes differently through the N- and C-terminal helical extensions to the common fold

36. a.4.5.37: LysR-like transcriptional regulators [88979] (2 proteins)
    contains long helix in the C-terminal extension; forms dimer similar to the RTP dimer

37. a.4.5.38: Transcriptional repressor Rex, N-terminal domain [101007] (1 protein)

38. a.4.5.39: Penicillinase repressor [101016] (4 proteins)
    homologous to the MarR-like family in the DNA-binding region but has a different dimerisation subdomain

39. a.4.5.40: N-terminal domain of Bacillus PurR [101021] (1 protein)

40. a.4.5.41: Transcription factor E/IIe-alpha, N-terminal domain [101024] (1 protein)
    contains extra N-terminal helix

41. a.4.5.42: FUR-like [101027] (1 protein)
    contains extra N-terminal helix and an alpha+beta dimerisation subdomain

42. a.4.5.43: RecQ helicase DNA-binding domain-like [101030] (3 proteins)
    follows the tandem AAA-ATPase domain

43. a.4.5.44: 39 kda initiator binding protein, IBP39, N-terminal domain [101045] (1 protein)

44. a.4.5.45: Dissimilatory sulfite reductase DsvD [101048] (2 proteins)

45. a.4.5.46: La domain [101051] (2 proteins)
    Pfam PF05383; RNA-binding domain

46. a.4.5.47: PCI domain (PINT motif) [109671] (2 proteins)
    Pfam PF01399

47. a.4.5.48: F93-like [109674] (4 proteins)
    contains long helix in the C-terminal extension; forms dimer similar to the RTP and LysR dimers

48. a.4.5.49: Archaeal DNA-binding protein [109677] (1 protein)
    contains long helix in the C-terminal extension; forms dimer similar to the RTP and LysR dimers

49. a.4.5.50: TrmB-like [109680] (2 proteins)
    The N- and C-terminal helical extensions to the common fold form the dimer interface, distinct from other known families

50. a.4.5.51: Heat-inducible transcription repressor HrcA, N-terminal domain [109683] (1 protein)
    similar domain organization to the transcriptional regulator IclR

51. a.4.5.52: DNA replication factor Cdt1 [109686] (1 protein)

52. a.4.5.53: Eukaryotic translation initiation factor 3 subunit 12, eIF3k, C-terminal domain [109689] (1 protein)
    C-terminal part of Pfam PF06272

53. a.4.5.54: Vacuolar sorting protein domain [109692] (3 proteins)
    duplication: tandem repeat of two "winged-helix" domains

54. a.4.5.55: Transcriptional regulator Rrf2 [109699] (2 proteins)
    Pfam PF02082

55. a.4.5.56: Rio2 serine protein kinase N-terminal domain [109702] (1 protein)

56. a.4.5.57: Rad21/Rec8-like [116795] (1 protein)
    Pfam PF04824

57. a.4.5.58: Hypothetical protein PH1932 [116798] (1 protein)
    contains new dimerisation all-alpha C-terminal subdomain

58. a.4.5.59: An Obfc1 domain [116801] (1 protein)
    helix-loop insertion in the HTH motif

59. a.4.5.60: ScpB/YpuH-like [116804] (1 protein)
    Pfam PF04079
    duplication: tandem repeat of two 'winged helix' domains; forms a dimer via the C-terminal domain

60. a.4.5.61: PadR-like [116807] (3 proteins)
    Pfam PF03551; related to the MarR-like family (Pfam PF01047)

61. a.4.5.62: Hypothetical protein YhgG [116812] (2 proteins)

62. a.4.5.63: ROK associated domain [140279] (3 proteins)
    found N-terminal to ROK domain in some proteins

63. a.4.5.64: PF1790-like [140286] (1 protein)
    sequence similarity to PH1932 in the N-terminal domain; the C-terminal domain provides new dimerisation interface made of a beta-hairpin and a coiled coil

64. a.4.5.65: MukF N-terminal domain-like [140289] (1 protein)
    N-terminal part of Pfam PF03882

65. a.4.5.66: CodY HTH domain [140292] (1 protein)
    Pfam PF08222

66. a.4.5.67: FtsK C-terminal domain-like [140295] (2 proteins)
    PfamB PB000224

67. a.4.5.68: Nudix-associated domain [140299] (2 proteins)
    PfamB PB002148; this domain is C-terminal to the Nudix domain in some bacterial proteins

68. a.4.5.69: HxlR-like [140304] (6 proteins)
    Pfam PF01638; DUF24; the N- and C-terminal helical extensions to the common fold form the dimer interface similar to that of the ArsR-like family (46801)

69. a.4.5.70: Marine metagenome family WH1 [158296] (1 protein)

70. a.4.5.71: ReutB4095-like [158299] (1 protein)
    probable biological unit is a homohexamer

71. a.4.5.72: PH0730 N-terminal domain-like [158302] (1 protein)

72. a.4.5.73: FaeA-like [158305] (1 protein)
    Pfam PF04703

73. a.4.5.74: STY4665 C-terminal domain-like [158308] (1 protein)
    Pfam PF07515; DUF1528; the "wing" hairpin, linker between helices 1 and 2 and the C-terminal tail together form an open beta-sheet barrel

74. a.4.5.75: PSPTO2686-like [158311] (1 protein)
    Pfam PF04337; DUF480; duplication: two "winged helix" domains are tightly packed "back-to-back" about pseudo twofold axis

75. a.4.5.76: RHA1_ro06458-like [158314] (1 protein)

76. a.4.5.77: YjcQ-like [158317] (1 protein)
    Pfam PF09639

77. a.4.5.78: F112-like [158320] (1 protein)

78. a.4.5.79: MerB N-terminal domain-like [158323] (1 protein)

79. a.4.5.80: CED-4 C-terminal domain-like [158326] (1 protein)
    similar domain architecture to AAA+ helicases

80. a.4.5.81: ELL N2 domain-like [158329] (1 protein)
    PfamB PB026212; includes recent PDB entry 2e5n

81. a.4.5.82: PF0610-like [158332] (1 protein)
    PfamB PB016993; insertion of a zinc-ribbon subdomain in the beta-hairpin "wing"

82. a.4.5.83: Rv2827c N-terminal domain-like [158335] (1 protein)
    ~80 N-terminal residues of Pfam PF09407' DUF2005

83. a.4.5.84: Rps19E-like [158338] (1 protein)
    Pfam PF01090; local sequence similarity to members of the GntR-like family

84. a.4.5.85: RPO3F domain-like [158341] (1 protein)
    middle region of Pfam PF05158

85. a.4.5.0: automated matches [191329] (1 protein)
    not a true family

More info for Superfamily a.4.5: "Winged helix" DNA-binding domain

Timeline for Superfamily a.4.5: "Winged helix" DNA-binding domain:

• Superfamily a.4.5: "Winged helix" DNA-binding domain first appeared (with stable ids) in SCOP 1.55
  
• Superfamily a.4.5: "Winged helix" DNA-binding domain appears in SCOPe 2.01
  
• Superfamily a.4.5: "Winged helix" DNA-binding domain appears in SCOPe 2.03
  
• Superfamily a.4.5: "Winged helix" DNA-binding domain appears in the current release, SCOPe 2.08, called Superfamily a.4.5: 'Winged helix' DNA-binding domain