Fold: DNA/RNA-binding 3-helical bundle

core: 3-helices; bundle, closed or partly opened, right-handed twist; up-and down

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

Superfamilies:

1. Homeodomain-like [46689] (17)
   consists only of helices
   1. Homeodomain [46690] (41)
      Pfam 00046
   2. Recombinase DNA-binding domain [46728] (5)
   3. Myb/SANT domain [46739] (13)
   4. SLIDE domain [100998] (1)
      myb-related probable DNA-binding motif
   5. GARP response regulators [81683] (1)
      plant myb-related DNA-binding motif
   6. DNA-binding domain of telomeric protein [46745] (2)
      part of Pfam 00249 (Myb/SANT domain)
   7. Paired domain [46748] (3)
      duplication: consists of two domains of this fold
   8. DNA-binding domain of rap1 [46753] (1)
      duplication: consist of two domains of this fold
   9. Centromere-binding [46756] (2)
      duplication: tandem repeat of two similar domains
   10. FIS-like [100918] (4)
   11. AraC type transcriptional activator [46759] (2)
       duplication: consists of two structural repeats bipartite HTH protein
   12. Tetracyclin repressor-like, N-terminal domain [46764] (28)
   13. Middle operon regulator, Mor [109659] (1)
       contains extra N-terminal dimerisation subdomain: alpha-hairpin (27-72) dimer is a four-helical bundle with right-handed twist
   14. Psq domain [140213] (1)
       Pfam 05225
   15. Alr1493-like [140216] (1)
       Pfam 04255; DUF433; contains extra C-terminal helix and N-terminal dimerisation interlock subdomain (scop_cf 47405)
   16. Nanomeric phage protein-like [140219] (1)
       contains additional N and C-terminal helices and the C-terminal beta-strand forming an intersubunit beta-barrel with a channel
   17. SWIRM domain [140222] (3)
       Pfam 04433; contains extra N-terminal helix
2. Methylated DNA-protein cysteine methyltransferase, C-terminal domain [46767] (1)
   1. Methylated DNA-protein cysteine methyltransferase, C-terminal domain [46768] (3)
3. ARID-like [46774] (1)
   contains extra helices at both N- and C-termini
   1. ARID domain [46775] (4)
4. "Winged helix" DNA-binding domain [46785] (68)
   contains a small beta-sheet (wing)
   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] (6)
   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] (16)
      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] (3)
       homologous to the MarR-like family in the DNA-binding region but has a different dimerisation subdomain
   12. GntR-like transcriptional regulators [46804] (2)
   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] (2)
       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] (2)
       follows the tandem AAA-ATPase domain
   23. SCF ubiquitin ligase complex WHB domain [74679] (3)
   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. Hypothetical protein F93 [109674] (1)
       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] (4)
       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)
5. C-terminal effector domain of the bipartite response regulators [46894] (3)
   binds to DNA and RNA polymerase; the N-terminal, receiver domain belongs to the CheY family
   1. PhoB-like [46895] (6)
      contains 4-stranded meander beta-sheet in the N-terminal extension
   2. GerE-like (LuxR/UhpA family of transcriptional regulators) [46900] (5)
      contains additional, fourth helix in the C-terminal extension
   3. Spo0A [46903] (2)
      elaborated with additional helices
6. TrpR-like [48295] (2)
   contains an extra shared helix after the HTH motif
   1. Trp repressor, TrpR [48296] (1)
      intertwined dimer of identical 6-helical subunits
   2. Chromosomal replication initiation factor DnaA C-terminal domain IV [81695] (2)
      monomeric; contains additional N-terminal helices
7. Ribosomal protein L11, C-terminal domain [46906] (1)
   1. Ribosomal protein L11, C-terminal domain [46907] (3)
8. Ribosomal protein S18 [46911] (1)
   1. Ribosomal protein S18 [46912] (1)
9. Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 [46915] (1)
   1. Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 [46916] (2)
10. N-terminal Zn binding domain of HIV integrase [46919] (1)
    1. N-terminal Zn binding domain of HIV integrase [46920] (2)
       Zn-binding site is near the C-terminus
11. RNA polymerase subunit RPB10 [46924] (1)
    1. RNA polymerase subunit RPB10 [46925] (2)
       Zn-binding site is near the N-terminus
12. Sigma3 and sigma4 domains of RNA polymerase sigma factors [88659] (3)
    1. Sigma3 domain [88660] (3)
    2. Sigma4 domain [88665] (7)
    3. YlxM/p13-like [109706] (2)
       Pfam 04297; UPF0122
       structural and detectable sequence similarity to Sigma4 domain; contains extra C-terminal all-alpha oligomerization subdomain; forms different, helix-swapped dimers
13. KorB DNA-binding domain-like [109709] (1)
    contains HTH motif in the common core; also contains extra N-terminal helix and C-terminal subdomain of 4 helices (left-handed superhelix)
    1. KorB DNA-binding domain-like [109710] (2)
       [N-terminal half of Pfam 06613]
14. Rps17e-like [116820] (1)
    1. Rps17e-like [116821] (1)
       Pfam 00833

Generated from scop database 1.73 with scopm 1.101 on Wed Nov 21 11:18:32 2007 Copyright © 1994-2007 The scop authors / scop@mrc-lmb.cam.ac.uk