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

  1. Root: SCOPe 2.07
  2. 2299346Class a: All alpha proteins [46456] (289 folds)
  3. 2304501Fold 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. 2305606Superfamily a.4.5: "Winged helix" DNA-binding domain [46785] (86 families) (S)
    contains a small beta-sheet (wing)

Families:

  1. 2305607a.4.5.1: Biotin repressor-like [46786] (2 protein domains)
    automatically mapped to Pfam PF08279
  2. 2305619a.4.5.2: LexA repressor, N-terminal DNA-binding domain [46789] (1 protein)
    automatically mapped to Pfam PF01726
  3. 2305626a.4.5.3: Arginine repressor (ArgR), N-terminal DNA-binding domain [46792] (2 protein domains)
    automatically mapped to Pfam PF01316
  4. 2305652a.4.5.4: CAP C-terminal domain-like [46796] (9 protein domains)
  5. 2305760a.4.5.5: ArsR-like transcriptional regulators [46801] (5 protein domains)
    The N- and C-terminal helical extensions to the common fold form the dimer interface
  6. 2305806a.4.5.6: GntR-like transcriptional regulators [46804] (4 protein domains)
  7. 2305828a.4.5.7: Replication terminator protein (RTP) [46807] (1 protein)
    automatically mapped to Pfam PF02334
  8. 2305848a.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. 2305859a.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)
    automatically mapped to Pfam PF09114
  10. 2305865a.4.5.10: Replication initiation protein [46816] (3 protein domains)
    duplication: tandem repeat of two "winged helix" domains arranged with the pseudo twofold symmetry
  11. 2305882a.4.5.11: Helicase DNA-binding domain [46819] (4 protein domains)
    follows the extended AAA-ATPase domain
  12. 2305911a.4.5.12: Restriction endonuclease FokI, N-terminal (recognition) domain [46824] (1 protein)
  13. 2305923a.4.5.13: Linker histone H1/H5 [46827] (3 protein domains)
    automatically mapped to Pfam PF00538
  14. 2305937a.4.5.14: Forkhead DNA-binding domain [46832] (7 protein domains)
  15. 2305977a.4.5.15: DNA-binding domain from rap30 [46841] (1 protein)
    automatically mapped to Pfam PF02270
  16. 2305982a.4.5.16: C-terminal domain of RPA32 [46844] (2 protein domains)
  17. 2305990a.4.5.17: Cell cycle transcription factor e2f-dp [46847] (2 protein domains)
    heterodimer of two homologous chains
  18. 2305997a.4.5.18: The central core domain of TFIIE beta [46850] (1 protein)
    automatically mapped to Pfam PF02186
  19. 2306002a.4.5.19: Z-DNA binding domain [46853] (5 protein domains)
    Pfam PF02295
  20. 2306049a.4.5.20: P4 origin-binding domain-like [46856] (2 protein domains)
    C-terminus passes through the first loop
  21. 2306061a.4.5.21: ets domain [46859] (9 protein domains)
  22. 2306133a.4.5.22: Heat-shock transcription factor [46873] (2 protein domains)
    automatically mapped to Pfam PF00447
  23. 2306161a.4.5.23: Interferon regulatory factor [46877] (4 protein domains)
    Pfam PF00605
  24. 2306193a.4.5.24: Iron-dependent repressor protein [46882] (4 protein domains)
    automatically mapped to Pfam PF01325
  25. 2306295a.4.5.25: Methionine aminopeptidase, insert domain [46887] (1 protein)
    circularly permuted version of the "winged helix" fold
  26. 2306326a.4.5.27: TnsA endonuclease, C-terminal domain [46782] (1 protein)
    automatically mapped to Pfam PF08721
  27. 2306333a.4.5.28: MarR-like transcriptional regulators [63379] (20 protein domains)
    The N- and C-terminal helical extensions to the common fold form the dimer interface
  28. 2306463a.4.5.29: Plant O-methyltransferase, N-terminal domain [63475] (5 protein domains)
    unknown function
  29. 2306503a.4.5.30: C-terminal domain of the rap74 subunit of TFIIF [63480] (1 protein)
    automatically mapped to Pfam PF05793
  30. 2306510a.4.5.31: DEP domain [63483] (5 protein domains)
    membrane-binding domain
  31. 2306538a.4.5.32: Lrp/AsnC-like transcriptional regulator N-terminal domain [68967] (4 protein domains)
    Swapped dimer with the "wing" C-terminal strands
    automatically mapped to Pfam PF13412
  32. 2306577a.4.5.33: Transcriptional regulator IclR, N-terminal domain [74676] (1 protein)
  33. 2306583a.4.5.34: SCF ubiquitin ligase complex WHB domain [74679] (3 protein domains)
  34. 2306602a.4.5.35: C-terminal fragment of elongation factor SelB [74683] (2 protein domains)
  35. 2306631a.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. 2306636a.4.5.37: LysR-like transcriptional regulators [88979] (2 protein domains)
    contains long helix in the C-terminal extension; forms dimer similar to the RTP dimer
  37. 2306651a.4.5.38: Transcriptional repressor Rex, N-terminal domain [101007] (1 protein)
  38. 2306670a.4.5.39: Penicillinase repressor [101016] (4 protein domains)
    homologous to the MarR-like family in the DNA-binding region but has a different dimerisation subdomain
    automatically mapped to Pfam PF03965
  39. 2306699a.4.5.40: N-terminal domain of Bacillus PurR [101021] (1 protein)
    automatically mapped to Pfam PF09182
  40. 2306714a.4.5.41: Transcription factor E/IIe-alpha, N-terminal domain [101024] (1 protein)
    contains extra N-terminal helix
    automatically mapped to Pfam PF02002
  41. 2306718a.4.5.42: FUR-like [101027] (1 protein)
    contains extra N-terminal helix and an alpha+beta dimerisation subdomain
    automatically mapped to Pfam PF01475
  42. 2306722a.4.5.43: RecQ helicase DNA-binding domain-like [101030] (3 protein domains)
    follows the tandem AAA-ATPase domain
  43. 2306733a.4.5.44: 39 kda initiator binding protein, IBP39, N-terminal domain [101045] (1 protein)
    automatically mapped to Pfam PF10416
  44. 2306743a.4.5.45: Dissimilatory sulfite reductase DsvD [101048] (2 protein domains)
    automatically mapped to Pfam PF08679
  45. 2306752a.4.5.46: La domain [101051] (2 protein domains)
    Pfam PF05383; RNA-binding domain
  46. 2306772a.4.5.47: C-terminal part of PCI (proteasome COP9/signalosome eIF3) domains (PINT motif) [109671] (11 protein domains)
    Pfam PF01399
    some members have long C-terminal tail with helix
  47. 2306812a.4.5.48: F93-like [109674] (4 protein domains)
    contains long helix in the C-terminal extension; forms dimer similar to the RTP and LysR dimers
  48. 2306827a.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. 2306833a.4.5.50: TrmB-like [109680] (2 protein domains)
    The N- and C-terminal helical extensions to the common fold form the dimer interface, distinct from other known families
  50. 2306842a.4.5.51: Heat-inducible transcription repressor HrcA, N-terminal domain [109683] (1 protein)
    similar domain organization to the transcriptional regulator IclR
  51. 2306848a.4.5.52: DNA replication factor Cdt1 [109686] (2 protein domains)
    automatically mapped to Pfam PF08839
  52. 2306857a.4.5.54: Vacuolar sorting protein domain [109692] (3 protein domains)
    duplication: tandem repeat of two "winged-helix" domains
  53. 2306888a.4.5.55: Transcriptional regulator Rrf2 [109699] (2 protein domains)
    Pfam PF02082
  54. 2306895a.4.5.56: Rio2 serine protein kinase N-terminal domain [109702] (1 protein)
    automatically mapped to Pfam PF09202
  55. 2306903a.4.5.57: Rad21/Rec8-like [116795] (1 protein)
    Pfam PF04824
  56. 2306910a.4.5.58: Hypothetical protein PH1932 [116798] (1 protein)
    contains new dimerisation all-alpha C-terminal subdomain
  57. 2306915a.4.5.59: An Obfc1 domain [116801] (1 protein)
    helix-loop insertion in the HTH motif
    automatically mapped to Pfam PF09170
  58. 2306919a.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
  59. 2306926a.4.5.61: PadR-like [116807] (3 protein domains)
    Pfam PF03551; related to the MarR-like family (Pfam PF01047)
  60. 2306937a.4.5.62: Hypothetical protein YhgG [116812] (2 protein domains)
    automatically mapped to Pfam PF09012
  61. 2306946a.4.5.63: ROK associated domain [140279] (3 protein domains)
    found N-terminal to ROK domain in some proteins
  62. 2306961a.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
  63. 2306968a.4.5.65: MukF N-terminal domain-like [140289] (1 protein)
    N-terminal part of Pfam PF03882
  64. 2306973a.4.5.66: CodY HTH domain [140292] (1 protein)
    Pfam PF08222
  65. 2306979a.4.5.67: FtsK C-terminal domain-like [140295] (2 protein domains)
    PfamB PB000224
    automatically mapped to Pfam PF09397
  66. 2307001a.4.5.68: Nudix-associated domain [140299] (2 protein domains)
    PfamB PB002148; this domain is C-terminal to the Nudix domain in some bacterial proteins
  67. 2307015a.4.5.69: HxlR-like [140304] (6 protein domains)
    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)
  68. 2307037a.4.5.70: Marine metagenome family WH1 [158296] (1 protein)
  69. 2307041a.4.5.71: ReutB4095-like [158299] (1 protein)
    probable biological unit is a homohexamer
  70. 2307046a.4.5.72: PH0730 N-terminal domain-like [158302] (1 protein)
  71. 2307050a.4.5.73: FaeA-like [158305] (1 protein)
    Pfam PF04703
  72. 2307054a.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
  73. 2307058a.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
  74. 2307065a.4.5.76: RHA1_ro06458-like [158314] (1 protein)
    automatically mapped to Pfam PF11625
  75. 2307069a.4.5.77: YjcQ-like [158317] (1 protein)
    Pfam PF09639
  76. 2307073a.4.5.78: F112-like [158320] (1 protein)
  77. 2307078a.4.5.79: MerB N-terminal domain-like [158323] (1 protein)
  78. 2307114a.4.5.80: CED-4 C-terminal domain-like [158326] (1 protein)
    similar domain architecture to AAA+ helicases
  79. 2307119a.4.5.81: ELL N2 domain-like [158329] (2 protein domains)
    PfamB PB026212; includes recent PDB entry 2e5n
    automatically mapped to Pfam PF10390
  80. 2307126a.4.5.82: PF0610-like [158332] (1 protein)
    PfamB PB016993; insertion of a zinc-ribbon subdomain in the beta-hairpin "wing"
  81. 2307130a.4.5.83: Rv2827c N-terminal domain-like [158335] (1 protein)
    ~80 N-terminal residues of Pfam PF09407' DUF2005
  82. 2307135a.4.5.84: Rps19E-like [158338] (1 protein)
    Pfam PF01090; local sequence similarity to members of the GntR-like family
  83. 2307139a.4.5.85: RPO3F domain-like [158341] (1 protein)
    middle region of Pfam PF05158
  84. 2307145a.4.5.86: RNA polymerase I subunit A49, winged helix domain [345952] (1 protein)
    C-terminal part of Pfam PF06870
    duplication: tandem repeat of two "winged-helix" domains
  85. 2307158a.4.5.87: Helicase RNA-binding domain [345953] (1 protein)
    follows the extended AAA-ATPase domain
  86. 2307165a.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: