Superfamily: "Winged helix" DNA-binding domain

contains a small beta-sheet (wing)
uperfamily

Lineage:

1. Root: scop
2. Class: All alpha proteins [46456]
3. Fold: DNA/RNA-binding 3-helical bundle [46688]
   core: 3-helices; bundle, closed or partly opened, right-handed twist; up-and down
4. Superfamily: "Winged helix" DNA-binding domain [46785]
   contains a small beta-sheet (wing)
   uperfamily

Families:

1. Biotin repressor-like [46786] (2)
2. LexA repressor, N-terminal DNA-binding domain [46789] (1)
3. Arginine repressor (ArgR), N-terminal DNA-binding domain [46792] (3)
4. Transcriptional repressor Rex, N-terminal domain [101007] (1)
5. CAP C-terminal domain-like [46796] (9)
6. Lrp/AsnC-like transcriptional regulator N-terminal domain [68967] (4)
   Swapped dimer with the "wing" C-terminal strands
7. ArsR-like transcriptional regulators [46801] (4)
   The N- and C-terminal helical extensions to the common fold form the dimer interface
8. Transcriptional regulator IclR, N-terminal domain [74676] (1)
9. MarR-like transcriptional regulators [63379] (20)
   The N- and C-terminal helical extensions to the common fold form the dimer interface
10. DNA-binding protein Mj223 [81690] (1)
    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
11. Penicillinase repressor [101016] (4)
    homologous to the MarR-like family in the DNA-binding region but has a different dimerisation subdomain
12. GntR-like transcriptional regulators [46804] (4)
13. N-terminal domain of Bacillus PurR [101021] (1)
14. Replication terminator protein (RTP) [46807] (1)
15. LysR-like transcriptional regulators [88979] (2)
    contains long helix in the C-terminal extension; forms dimer similar to the RTP dimer
16. N-terminal domain of molybdate-dependent transcriptional regulator ModE [46810] (1)
    contains beta-hairpin in the N-terminal extension and two helices in the C-terminal extension
17. Transcription factor MotA, activation domain [46813] (1)
    The N- and C-terminal helical extensions to the common fold form the dimer interface (distinct from that of ArsR-like family)
18. Transcription factor E/IIe-alpha, N-terminal domain [101024] (1)
    contains extra N-terminal helix
19. FUR-like [101027] (1)
    contains extra N-terminal helix and an alpha+beta dimerisation subdomain
20. Replication initiation protein [46816] (3)
    duplication: tandem repeat of two "winged helix" domains arranged with the pseudo twofold symmetry
21. Helicase DNA-binding domain [46819] (5)
    follows the extended AAA-ATPase domain
22. RecQ helicase DNA-binding domain-like [101030] (3)
    follows the tandem AAA-ATPase domain
23. SCF ubiquitin ligase complex WHB domain [74679] (4)
24. C-terminal fragment of elongation factor SelB [74683] (1)
25. Restriction endonuclease FokI, N-terminal (recognition) domain [46824] (1)
26. TnsA endonuclease, C-terminal domain [46782] (1)
27. Plant O-methyltransferase, N-terminal domain [63475] (5)
    unknown function
28. Linker histone H1/H5 [46827] (3)
29. Forkhead DNA-binding domain [46832] (6)
30. DNA-binding domain from rap30 [46841] (1)
31. C-terminal domain of the rap74 subunit of TFIIF [63480] (1)
32. C-terminal domain of RPA32 [46844] (1)
33. DEP domain [63483] (5)
    membrane-binding domain
34. Cell cycle transcription factor e2f-dp [46847] (2)
    heterodimer of two homologous chains
35. The central core domain of TFIIE beta [46850] (1)
36. Z-DNA binding domain [46853] (4)
    Pfam 02295
37. P4 origin-binding domain-like [46856] (2)
    C-terminus passes through the first loop
38. ets domain [46859] (9)
39. Heat-shock transcription factor [46873] (2)
40. Interferon regulatory factor [46877] (3)
    Pfam 00605
41. 39 kda initiator binding protein, IBP39, N-terminal domain [101045] (1)
42. Iron-dependent repressor protein [46882] (3)
43. Dissimilatory sulfite reductase DsvD [101048] (1)
44. La domain [101051] (3)
    Pfam 05383; RNA-binding domain
45. Methionine aminopeptidase, insert domain [46887] (2)
    circularly permuted version of the "winged helix" fold
46. PCI domain (PINT motif) [109671] (2)
    Pfam 01399
47. F93-like [109674] (3)
    contains long helix in the C-terminal extension; forms dimer similar to the RTP and LysR dimers
48. Archaeal DNA-binding protein [109677] (1)
    contains long helix in the C-terminal extension; forms dimer similar to the RTP and LysR dimers
49. TrmB-like [109680] (2)
    The N- and C-terminal helical extensions to the common fold form the dimer interface, distinct from other known families
50. Heat-inducible transcription repressor HrcA, N-terminal domain [109683] (1)
    similar domain organization to the transcriptional regulator IclR
51. DNA replication factor Cdt1 [109686] (1)
52. Eukaryotic translation initiation factor 3 subunit 12, eIF3k, C-terminal domain [109689] (1)
    C-terminal part of Pfam 06272
53. Vacuolar sorting protein domain [109692] (3)
    duplication: tandem repeat of two "winged-helix" domains
54. Transcriptional regulator Rrf2 [109699] (2)
    Pfam 02082
55. Rio2 serine protein kinase N-terminal domain [109702] (1)
56. Rad21/Rec8-like [116795] (1)
    Pfam 04824
57. Hypothetical protein PH1932 [116798] (1)
    contains new dimerisation all-alpha C-terminal subdomain
58. An Obfc1 domain [116801] (1)
    helix-loop insertion in the HTH motif
59. ScpB/YpuH-like [116804] (1)
    Pfam 04079
    duplication: tandem repeat of two 'winged helix' domains; forms a dimer via the C-terminal domain
60. PadR-like [116807] (3)
    Pfam 03551; related to the MarR-like family (Pfam 01047)
61. Hypothetical protein YhgG [116812] (1)
62. ROK associated domain [140279] (3)
    found N-terminal to ROK domain in some proteins
63. PF1790-like [140286] (1)
    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. MukF N-terminal domain-like [140289] (1)
    N-terminal part of Pfam 03882
65. CodY HTH domain [140292] (1)
    Pfam 08222
66. FtsK C-terminal domain-like [140295] (2)
    PfamB 000224
67. Nudix-associated domain [140299] (2)
    PfamB 002148; this domain is C-terminal to the Nudix domain in some bacterial proteins
68. HxlR-like [140304] (5)
    Pfam 01638; DUF24; the N- and C-terminal helical extensions to the common fold form the dimer interface similar to that of the ArsR-like family (scop_fa 46801)
69. Marine metagenome family WH1 [158296] (1)
70. ReutB4095-like [158299] (1)
    probable biological unit is a homohexamer
71. PH0730 N-terminal domain-like [158302] (1)
72. FaeA-like [158305] (1)
    Pfam 04703
73. STY4665 C-terminal domain-like [158308] (1)
    Pfam 07515; DUF1528; the "wing" hairpin, linker between helices 1 and 2 and the C-terminal tail together form an open beta-sheet barrel
74. PSPTO2686-like [158311] (1)
    Pfam 04337; DUF480; duplication: two "winged helix" domains are tightly packed "back-to-back" about pseudo twofold axis
75. RHA1_ro06458-like [158314] (1)
76. YjcQ-like [158317] (1)
    Pfam 09639
77. F112-like [158320] (1)
78. MerB N-terminal domain-like [158323] (1)
79. CED-4 C-terminal domain-like [158326] (1)
    similar domain architecture to AAA+ helicases
80. ELL N2 domain-like [158329] (1)
    PfamB 026212; includes recent PDB entry 2e5n
81. PF0610-like [158332] (1)
    PfamB 016993; insertion of a zinc-ribbon subdomain in the beta-hairpin "wing"
82. Rv2827c N-terminal domain-like [158335] (1)
    ~80 N-terminal residues of Pfam 09407' DUF2005
83. Rps19E-like [158338] (1)
    Pfam 01090; local sequence similarity to members of the GntR-like family
84. RPO3F domain-like [158341] (2)
    middle region of Pfam 05158

Generated from scop database 1.75 with scopm 1.101 on Wed Jun 3 10:42:06 2009 Copyright © 1994-2009 The scop authors / scop@mrc-lmb.cam.ac.uk