Structural Classification of Proteins
home mail help root up expand collapse

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] (19)
    consists only of helices
    link to SUPERFAMILY database - Superfamily
    1. Homeodomain [46690] (42) picpic
      Pfam 00046
    2. Recombinase DNA-binding domain [46728] (5) picpic
    3. Myb/SANT domain [46739] (15) picpic
    4. SLIDE domain [100998] (1) picpic
      myb-related probable DNA-binding motif
    5. GARP response regulators [81683] (1) picpic
      plant myb-related DNA-binding motif
    6. DNA-binding domain of telomeric protein [46745] (2) picpic
      part of Pfam 00249 (Myb/SANT domain)
    7. Paired domain [46748] (3) picpic
      duplication: consists of two domains of this fold
    8. DNA-binding domain of rap1 [46753] (1) picpic
      duplication: consist of two domains of this fold
    9. Centromere-binding [46756] (2) picpic
      duplication: tandem repeat of two similar domains
    10. FIS-like [100918] (4) picpic
    11. AraC type transcriptional activator [46759] (2) picpic
      duplication: consists of two structural repeats bipartite HTH protein
    12. Tetracyclin repressor-like, N-terminal domain [46764] (34) picpic
    13. Middle operon regulator, Mor [109659] (1) picpic
      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) picpic
      Pfam 05225
    15. Alr1493-like [140216] (1) picpic
      Pfam 04255; DUF433; contains extra C-terminal helix and N-terminal dimerisation interlock subdomain (scop_cf 47405)
    16. Nanomeric phage protein-like [140219] (1) picpic
      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) picpic
      Pfam 04433; contains extra N-terminal helix
    18. Cgl2762-like [158260] (1) picpic
      Pfam 01527; Transposase 8
    19. RpiR-like [158263] (1) picpic
      Pfam 01418; contains two extra helices, one at each termini; overall arrangment of five helices is similar to the helical core of the lambda integrase-like catalytic domain (scop_fa 56350)
  2. Methylated DNA-protein cysteine methyltransferase, C-terminal domain [46767] (1)
    link to SUPERFAMILY database - Superfamily
    1. Methylated DNA-protein cysteine methyltransferase, C-terminal domain [46768] (3) picpic
  3. ARID-like [46774] (1)
    contains extra helices at both N- and C-termini
    link to SUPERFAMILY database - Superfamily
    1. ARID domain [46775] (4) picpic
  4. "Winged helix" DNA-binding domain [46785] (84)
    contains a small beta-sheet (wing)
    link to SUPERFAMILY database - Superfamily
    1. Biotin repressor-like [46786] (2) picpic
    2. LexA repressor, N-terminal DNA-binding domain [46789] (1) picpic
    3. Arginine repressor (ArgR), N-terminal DNA-binding domain [46792] (3) picpic
    4. Transcriptional repressor Rex, N-terminal domain [101007] (1) picpic
    5. CAP C-terminal domain-like [46796] (9) picpic
    6. Lrp/AsnC-like transcriptional regulator N-terminal domain [68967] (4) picpic
      Swapped dimer with the "wing" C-terminal strands
    7. ArsR-like transcriptional regulators [46801] (4) picpic
      The N- and C-terminal helical extensions to the common fold form the dimer interface
    8. Transcriptional regulator IclR, N-terminal domain [74676] (1) picpic
    9. MarR-like transcriptional regulators [63379] (20) picpic
      The N- and C-terminal helical extensions to the common fold form the dimer interface
    10. DNA-binding protein Mj223 [81690] (1) picpic
      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) picpic
      homologous to the MarR-like family in the DNA-binding region but has a different dimerisation subdomain
    12. GntR-like transcriptional regulators [46804] (4) picpic
    13. N-terminal domain of Bacillus PurR [101021] (1) picpic
    14. Replication terminator protein (RTP) [46807] (1) picpic
    15. LysR-like transcriptional regulators [88979] (2) picpic
      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) picpic
      contains beta-hairpin in the N-terminal extension and two helices in the C-terminal extension
    17. Transcription factor MotA, activation domain [46813] (1) picpic
      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) picpic
      contains extra N-terminal helix
    19. FUR-like [101027] (1) picpic
      contains extra N-terminal helix and an alpha+beta dimerisation subdomain
    20. Replication initiation protein [46816] (3) picpic
      duplication: tandem repeat of two "winged helix" domains arranged with the pseudo twofold symmetry
    21. Helicase DNA-binding domain [46819] (5) picpic
      follows the extended AAA-ATPase domain
    22. RecQ helicase DNA-binding domain-like [101030] (3) picpic
      follows the tandem AAA-ATPase domain
    23. SCF ubiquitin ligase complex WHB domain [74679] (4) picpic
    24. C-terminal fragment of elongation factor SelB [74683] (1) picpic
    25. Restriction endonuclease FokI, N-terminal (recognition) domain [46824] (1) picpic
    26. TnsA endonuclease, C-terminal domain [46782] (1) picpic
    27. Plant O-methyltransferase, N-terminal domain [63475] (5) picpic
      unknown function
    28. Linker histone H1/H5 [46827] (3) picpic
    29. Forkhead DNA-binding domain [46832] (6) picpic
    30. DNA-binding domain from rap30 [46841] (1) picpic
    31. C-terminal domain of the rap74 subunit of TFIIF [63480] (1) picpic
    32. C-terminal domain of RPA32 [46844] (1) picpic
    33. DEP domain [63483] (5) picpic
      membrane-binding domain
    34. Cell cycle transcription factor e2f-dp [46847] (2) picpic
      heterodimer of two homologous chains
    35. The central core domain of TFIIE beta [46850] (1) picpic
    36. Z-DNA binding domain [46853] (4) picpic
      Pfam 02295
    37. P4 origin-binding domain-like [46856] (2) picpic
      C-terminus passes through the first loop
    38. ets domain [46859] (9) picpic
    39. Heat-shock transcription factor [46873] (2) picpic
    40. Interferon regulatory factor [46877] (3) picpic
      Pfam 00605
    41. 39 kda initiator binding protein, IBP39, N-terminal domain [101045] (1) picpic
    42. Iron-dependent repressor protein [46882] (3) picpic
    43. Dissimilatory sulfite reductase DsvD [101048] (1) picpic
    44. La domain [101051] (3) picpic
      Pfam 05383; RNA-binding domain
    45. Methionine aminopeptidase, insert domain [46887] (2) picpic
      circularly permuted version of the "winged helix" fold
    46. PCI domain (PINT motif) [109671] (2) picpic
      Pfam 01399
    47. F93-like [109674] (3) picpic
      contains long helix in the C-terminal extension; forms dimer similar to the RTP and LysR dimers
    48. Archaeal DNA-binding protein [109677] (1) picpic
      contains long helix in the C-terminal extension; forms dimer similar to the RTP and LysR dimers
    49. TrmB-like [109680] (2) picpic
      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) picpic
      similar domain organization to the transcriptional regulator IclR
    51. DNA replication factor Cdt1 [109686] (1) picpic
    52. Eukaryotic translation initiation factor 3 subunit 12, eIF3k, C-terminal domain [109689] (1) picpic
      C-terminal part of Pfam 06272
    53. Vacuolar sorting protein domain [109692] (3) picpic
      duplication: tandem repeat of two "winged-helix" domains
    54. Transcriptional regulator Rrf2 [109699] (2) picpic
      Pfam 02082
    55. Rio2 serine protein kinase N-terminal domain [109702] (1) picpic
    56. Rad21/Rec8-like [116795] (1) picpic
      Pfam 04824
    57. Hypothetical protein PH1932 [116798] (1) picpic
      contains new dimerisation all-alpha C-terminal subdomain
    58. An Obfc1 domain [116801] (1) picpic
      helix-loop insertion in the HTH motif
    59. ScpB/YpuH-like [116804] (1) picpic
      Pfam 04079
      duplication: tandem repeat of two 'winged helix' domains; forms a dimer via the C-terminal domain
    60. PadR-like [116807] (3) picpic
      Pfam 03551; related to the MarR-like family (Pfam 01047)
    61. Hypothetical protein YhgG [116812] (1) picpic
    62. ROK associated domain [140279] (3) picpic
      found N-terminal to ROK domain in some proteins
    63. PF1790-like [140286] (1) picpic
      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) picpic
      N-terminal part of Pfam 03882
    65. CodY HTH domain [140292] (1) picpic
      Pfam 08222
    66. FtsK C-terminal domain-like [140295] (2) picpic
      PfamB 000224
    67. Nudix-associated domain [140299] (2) picpic
      PfamB 002148; this domain is C-terminal to the Nudix domain in some bacterial proteins
    68. HxlR-like [140304] (5) picpic
      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) picpic
    70. ReutB4095-like [158299] (1) picpic
      probable biological unit is a homohexamer
    71. PH0730 N-terminal domain-like [158302] (1) picpic
    72. FaeA-like [158305] (1) picpic
      Pfam 04703
    73. STY4665 C-terminal domain-like [158308] (1) picpic
      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) picpic
      Pfam 04337; DUF480; duplication: two "winged helix" domains are tightly packed "back-to-back" about pseudo twofold axis
    75. RHA1_ro06458-like [158314] (1) picpic
    76. YjcQ-like [158317] (1) picpic
      Pfam 09639
    77. F112-like [158320] (1) picpic
    78. MerB N-terminal domain-like [158323] (1) picpic
    79. CED-4 C-terminal domain-like [158326] (1) picpic
      similar domain architecture to AAA+ helicases
    80. ELL N2 domain-like [158329] (1) picpic
      PfamB 026212; includes recent PDB entry 2e5n
    81. PF0610-like [158332] (1) picpic
      PfamB 016993; insertion of a zinc-ribbon subdomain in the beta-hairpin "wing"
    82. Rv2827c N-terminal domain-like [158335] (1) picpic
      ~80 N-terminal residues of Pfam 09407' DUF2005
    83. Rps19E-like [158338] (1) picpic
      Pfam 01090; local sequence similarity to members of the GntR-like family
    84. RPO3F domain-like [158341] (2) picpic
      middle region of Pfam 05158
  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
    link to SUPERFAMILY database - Superfamily
    1. PhoB-like [46895] (6) picpic
      contains 4-stranded meander beta-sheet in the N-terminal extension
    2. GerE-like (LuxR/UhpA family of transcriptional regulators) [46900] (5) picpic
      contains additional, fourth helix in the C-terminal extension
    3. Spo0A [46903] (2) picpic
      elaborated with additional helices
  6. TrpR-like [48295] (3)
    contains an extra shared helix after the HTH motif
    link to SUPERFAMILY database - Superfamily
    1. Trp repressor, TrpR [48296] (1) picpic
      intertwined dimer of identical 6-helical subunits
    2. Chromosomal replication initiation factor DnaA C-terminal domain IV [81695] (2) picpic
      monomeric; contains additional N-terminal helices
    3. SPO1678-like [158345] (1) picpic
      Pfam 06627; DUF1153
  7. Ribosomal protein L11, C-terminal domain [46906] (1)
    link to SUPERFAMILY database - Superfamily
    1. Ribosomal protein L11, C-terminal domain [46907] (6) picpic
  8. Ribosomal protein S18 [46911] (1)
    link to SUPERFAMILY database - Superfamily
    1. Ribosomal protein S18 [46912] (2) picpic
  9. Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 [46915] (1)
    link to SUPERFAMILY database - Superfamily
    1. Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 [46916] (2) picpic
  10. N-terminal Zn binding domain of HIV integrase [46919] (1)
    link to SUPERFAMILY database - Superfamily
    1. N-terminal Zn binding domain of HIV integrase [46920] (2) picpic
      Zn-binding site is near the C-terminus
  11. RNA polymerase subunit RPB10 [46924] (1)
    link to SUPERFAMILY database - Superfamily
    1. RNA polymerase subunit RPB10 [46925] (2) picpic
      Zn-binding site is near the N-terminus
  12. Sigma3 and sigma4 domains of RNA polymerase sigma factors [88659] (3)
    link to SUPERFAMILY database - Superfamily
    1. Sigma3 domain [88660] (3) picpic
    2. Sigma4 domain [88665] (7) picpic
    3. YlxM/p13-like [109706] (2) picpic
      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)
    link to SUPERFAMILY database - Superfamily
    1. KorB DNA-binding domain-like [109710] (2) picpic
      [N-terminal half of Pfam 06613]
  14. Rps17e-like [116820] (1)
    link to SUPERFAMILY database - Superfamily
    1. Rps17e-like [116821] (1) picpic
      Pfam 00833

Enter search key:

MRC
site 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