Lineage for Protein: Exonuclease domain of family B DNA polymerases

  1. Root: SCOPe 2.07
  2. 2413226Class c: Alpha and beta proteins (a/b) [51349] (148 folds)
  3. 2460924Fold c.55: Ribonuclease H-like motif [53066] (7 superfamilies)
    3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32145; strand 2 is antiparallel to the rest
  4. 2462855Superfamily c.55.3: Ribonuclease H-like [53098] (16 families) (S)
    consists of one domain of this fold
  5. 2463460Family c.55.3.5: DnaQ-like 3'-5' exonuclease [53118] (17 protein domains)
    contains Pfam PF00929
  6. 2463472Protein Exonuclease domain of family B DNA polymerases [53125] (8 species)
    elaborated with additional structures and the N-terminal subdomain

Species:

  1. 2463473Bacteriophage RB69 [TaxId:12353] [53127] (93 PDB entries)
    additional N-terminal subdomain contains rudimental OB-fold and rudimental ferredoxin-like fold
    1. Domain for 1clq:
    2. Domain for 1ig9:
    3. Domain for 1ih7:
    4. Domains for 1q9x:
      1. 2463551Domain d1q9xa1: 1q9x A:1-375 [96328]
        Other proteins in same PDB: d1q9xa2, d1q9xb2, d1q9xc2, d1q9xd2
        protein/DNA complex; complexed with 3dr, ca, dgp, doc
      2. 2463552Domain d1q9xb1: 1q9x B:1-375 [96330]
        Other proteins in same PDB: d1q9xa2, d1q9xb2, d1q9xc2, d1q9xd2
        protein/DNA complex; complexed with 3dr, ca, dgp, doc
      3. 2463553Domain d1q9xc1: 1q9x C:1-375 [96332]
        Other proteins in same PDB: d1q9xa2, d1q9xb2, d1q9xc2, d1q9xd2
        protein/DNA complex; complexed with 3dr, ca, dgp, doc
      4. 2463554Domain d1q9xd1: 1q9x D:1-375 [96334]
        Other proteins in same PDB: d1q9xa2, d1q9xb2, d1q9xc2, d1q9xd2
        protein/DNA complex; complexed with 3dr, ca, dgp, doc
    5. Domain for 1q9y:
    6. Domain for 1rv2:
    7. Domains for 1waf:
      1. 2463569Domain d1wafa1: 1waf A:1-375 [33719]
        Other proteins in same PDB: d1wafa2, d1wafb2
        complexed with gmp
      2. 2463570Domain d1wafb1: 1waf B:1-375 [33720]
        Other proteins in same PDB: d1wafa2, d1wafb2
        complexed with gmp
    8. Domain for 1waj:
    9. Domain for 2atq:
    10. Domains for 2dtu:
      1. 2463556Domain d2dtua1: 2dtu A:1-375 [230656]
        Other proteins in same PDB: d2dtua2, d2dtub2, d2dtuc2, d2dtud2
        automated match to d1ih7a1
        protein/DNA complex
      2. 2463557Domain d2dtub1: 2dtu B:1-375 [230654]
        Other proteins in same PDB: d2dtua2, d2dtub2, d2dtuc2, d2dtud2
        automated match to d1ih7a1
        protein/DNA complex
      3. 2463558Domain d2dtuc1: 2dtu C:1-375 [230655]
        Other proteins in same PDB: d2dtua2, d2dtub2, d2dtuc2, d2dtud2
        automated match to d1ih7a1
        protein/DNA complex
      4. 2463559Domain d2dtud1: 2dtu D:1-375 [230657]
        Other proteins in same PDB: d2dtua2, d2dtub2, d2dtuc2, d2dtud2
        automated match to d1ih7a1
        protein/DNA complex
    11. Domains for 2dy4:
      1. 2463575Domain d2dy4a1: 2dy4 A:1-375 [131882]
        Other proteins in same PDB: d2dy4a2, d2dy4b2, d2dy4c2, d2dy4d2
        automated match to d1q9xa1
        protein/DNA complex
      2. 2463576Domain d2dy4b1: 2dy4 B:1-375 [131884]
        Other proteins in same PDB: d2dy4a2, d2dy4b2, d2dy4c2, d2dy4d2
        automated match to d1q9xa1
        protein/DNA complex
      3. 2463577Domain d2dy4c1: 2dy4 C:1-375 [131886]
        Other proteins in same PDB: d2dy4a2, d2dy4b2, d2dy4c2, d2dy4d2
        automated match to d1ig9a1
        protein/DNA complex
      4. 2463578Domain d2dy4d1: 2dy4 D:1-375 [131888]
        Other proteins in same PDB: d2dy4a2, d2dy4b2, d2dy4c2, d2dy4d2
        automated match to d1ig9a1
        protein/DNA complex
    12. Domains for 2oyq:
      1. 2463593Domain d2oyqa1: 2oyq A:1-375 [149070]
        Other proteins in same PDB: d2oyqa2, d2oyqb2, d2oyqc2, d2oyqd2
        automated match to d2ozma1
        protein/DNA complex; complexed with mg, n5p
      2. 2463594Domain d2oyqb1: 2oyq B:1-375 [149072]
        Other proteins in same PDB: d2oyqa2, d2oyqb2, d2oyqc2, d2oyqd2
        automated match to d1ig9a1
        protein/DNA complex; complexed with mg, n5p
      3. 2463595Domain d2oyqc1: 2oyq C:1-375 [149074]
        Other proteins in same PDB: d2oyqa2, d2oyqb2, d2oyqc2, d2oyqd2
        automated match to d1ig9a1
        protein/DNA complex; complexed with mg, n5p
      4. 2463596Domain d2oyqd1: 2oyq D:2-375 [149076]
        Other proteins in same PDB: d2oyqa2, d2oyqb2, d2oyqc2, d2oyqd2
        automated match to d1ig9a1
        protein/DNA complex; complexed with mg, n5p
    13. Domain for 2ozm:
    14. Domain for 2ozs:
    15. Domains for 2p5g:
      1. 2463584Domain d2p5ga1: 2p5g A:1-375 [149240]
        Other proteins in same PDB: d2p5ga2, d2p5gb2, d2p5gc2, d2p5gd2
        automated match to d1q9xa1
        protein/DNA complex
      2. 2463585Domain d2p5gb1: 2p5g B:1-375 [149242]
        Other proteins in same PDB: d2p5ga2, d2p5gb2, d2p5gc2, d2p5gd2
        automated match to d1ig9a1
        protein/DNA complex
      3. 2463586Domain d2p5gc1: 2p5g C:1-375 [149244]
        Other proteins in same PDB: d2p5ga2, d2p5gb2, d2p5gc2, d2p5gd2
        automated match to d1ig9a1
        protein/DNA complex
      4. 2463587Domain d2p5gd1: 2p5g D:2-375 [149246]
        Other proteins in same PDB: d2p5ga2, d2p5gb2, d2p5gc2, d2p5gd2
        automated match to d1ig9a1
        protein/DNA complex
    16. Domains for 2p5o:
      1. 2463580Domain d2p5oa1: 2p5o A:1-375 [139498]
        Other proteins in same PDB: d2p5oa2, d2p5ob2, d2p5oc2, d2p5od2
        automatically matched to d1clqa1
        protein/DNA complex
      2. 2463581Domain d2p5ob1: 2p5o B:1-375 [139500]
        Other proteins in same PDB: d2p5oa2, d2p5ob2, d2p5oc2, d2p5od2
        automatically matched to d1clqa1
        protein/DNA complex
      3. 2463582Domain d2p5oc1: 2p5o C:1-375 [139502]
        Other proteins in same PDB: d2p5oa2, d2p5ob2, d2p5oc2, d2p5od2
        automatically matched to d1clqa1
        protein/DNA complex
      4. 2463583Domain d2p5od1: 2p5o D:1-375 [139504]
        Other proteins in same PDB: d2p5oa2, d2p5ob2, d2p5oc2, d2p5od2
        automatically matched to d1clqa1
        protein/DNA complex
    17. Domain for 3cfo:
    18. Domain for 3cq8:
    19. Domains for 3l8b:
      1. 2463518Domain d3l8ba1: 3l8b A:1-375 [232820]
        Other proteins in same PDB: d3l8ba2, d3l8bb2
        automated match to d1ih7a1
        protein/DNA complex; complexed with so4
      2. 2463519Domain d3l8bb1: 3l8b B:1-375 [232821]
        Other proteins in same PDB: d3l8ba2, d3l8bb2
        automated match to d1ih7a1
        protein/DNA complex; complexed with so4
    20. Domain for 3lds:
    21. Domain for 3lzi:
    22. Domain for 3lzj:
    23. Domain for 3nae:
    24. Domain for 3nci:
    25. Domain for 3ndk:
    26. Domain for 3ne6:
    27. Domain for 3ngi:
    28. Domain for 3nhg:
    29. Domain for 3qes:
    30. Domain for 3qet:
    31. Domains for 3rma:
      1. 2463589Domain d3rmaa1: 3rma A:1-375 [249140]
        Other proteins in same PDB: d3rmaa2, d3rmab2, d3rmac2, d3rmad2
        automated match to d3l8bb1
        protein/DNA complex
      2. 2463590Domain d3rmab1: 3rma B:1-375 [249142]
        Other proteins in same PDB: d3rmaa2, d3rmab2, d3rmac2, d3rmad2
        automated match to d3l8bb1
        protein/DNA complex
      3. 2463591Domain d3rmac1: 3rma C:1-375 [249144]
        Other proteins in same PDB: d3rmaa2, d3rmab2, d3rmac2, d3rmad2
        automated match to d3l8bb1
        protein/DNA complex
      4. 2463592Domain d3rmad1: 3rma D:1-375 [249146]
        Other proteins in same PDB: d3rmaa2, d3rmab2, d3rmac2, d3rmad2
        automated match to d3l8bb1
        protein/DNA complex
    32. Domains for 3rmb:
      1. 2463571Domain d3rmba1: 3rmb A:1-375 [249148]
        Other proteins in same PDB: d3rmba2, d3rmbb2, d3rmbc2, d3rmbd2
        automated match to d3l8bb1
        protein/DNA complex; complexed with so4
      2. 2463572Domain d3rmbb1: 3rmb B:1-375 [249150]
        Other proteins in same PDB: d3rmba2, d3rmbb2, d3rmbc2, d3rmbd2
        automated match to d3l8bb1
        protein/DNA complex; complexed with so4
      3. 2463573Domain d3rmbc1: 3rmb C:1-375 [249152]
        Other proteins in same PDB: d3rmba2, d3rmbb2, d3rmbc2, d3rmbd2
        automated match to d3l8bb1
        protein/DNA complex; complexed with so4
      4. 2463574Domain d3rmbd1: 3rmb D:1-375 [249154]
        Other proteins in same PDB: d3rmba2, d3rmbb2, d3rmbc2, d3rmbd2
        automated match to d3l8bb1
        protein/DNA complex; complexed with so4
    33. Domains for 3rmc:
      1. 2463601Domain d3rmca1: 3rmc A:1-375 [249156]
        Other proteins in same PDB: d3rmca2, d3rmcb2, d3rmcc2, d3rmcd2
        automated match to d3uiqa1
        protein/DNA complex
      2. 2463602Domain d3rmcb1: 3rmc B:1-375 [249158]
        Other proteins in same PDB: d3rmca2, d3rmcb2, d3rmcc2, d3rmcd2
        automated match to d3uiqa1
        protein/DNA complex
      3. 2463603Domain d3rmcc1: 3rmc C:1-375 [249160]
        Other proteins in same PDB: d3rmca2, d3rmcb2, d3rmcc2, d3rmcd2
        automated match to d3uiqa1
        protein/DNA complex
      4. 2463604Domain d3rmcd1: 3rmc D:1-375 [249162]
        Other proteins in same PDB: d3rmca2, d3rmcb2, d3rmcc2, d3rmcd2
        automated match to d3uiqa1
        protein/DNA complex
    34. Domains for 3rmd:
      1. 2463597Domain d3rmda1: 3rmd A:1-375 [249164]
        Other proteins in same PDB: d3rmda2, d3rmdb2, d3rmdc2, d3rmdd2
        automated match to d3l8bb1
        protein/DNA complex; complexed with dtp
      2. 2463598Domain d3rmdb1: 3rmd B:1-375 [249166]
        Other proteins in same PDB: d3rmda2, d3rmdb2, d3rmdc2, d3rmdd2
        automated match to d3l8bb1
        protein/DNA complex; complexed with dtp
      3. 2463599Domain d3rmdc1: 3rmd C:1-375 [249168]
        Other proteins in same PDB: d3rmda2, d3rmdb2, d3rmdc2, d3rmdd2
        automated match to d3l8bb1
        protein/DNA complex; complexed with dtp
      4. 2463600Domain d3rmdd1: 3rmd D:1-375 [249170]
        Other proteins in same PDB: d3rmda2, d3rmdb2, d3rmdc2, d3rmdd2
        automated match to d3l8bb1
        protein/DNA complex; complexed with dtp
    35. Domain for 3s9h:
    36. Domain for 3scx:
    37. Domain for 3si6:
    38. Domain for 3sjj:
    39. Domain for 3snn:
    40. Domain for 3spy:
    41. Domain for 3spz:
    42. Domain for 3sq0:
    43. Domain for 3sq1:
    44. Domain for 3sq2:
    45. Domain for 3sq4:
    46. Domain for 3sun:
    47. Domain for 3suo:
    48. Domain for 3sup:
    49. Domain for 3suq:
    50. Domains for 3tae:
      1. 2463545Domain d3taea1: 3tae A:1-375 [249841]
        Other proteins in same PDB: d3taea2, d3taeb2, d3taec2, d3taed2
        automated match to d3l8bb1
        protein/DNA complex; complexed with so4
      2. 2463546Domain d3taeb1: 3tae B:1-375 [249843]
        Other proteins in same PDB: d3taea2, d3taeb2, d3taec2, d3taed2
        automated match to d3l8bb1
        protein/DNA complex; complexed with so4
      3. 2463547Domain d3taec1: 3tae C:1-375 [249845]
        Other proteins in same PDB: d3taea2, d3taeb2, d3taec2, d3taed2
        automated match to d3l8bb1
        protein/DNA complex; complexed with so4
      4. 2463548Domain d3taed1: 3tae D:1-375 [249847]
        Other proteins in same PDB: d3taea2, d3taeb2, d3taec2, d3taed2
        automated match to d3l8bb1
        protein/DNA complex; complexed with so4
    51. Domains for 3tag:
      1. 2463562Domain d3taga1: 3tag A:1-375 [249849]
        Other proteins in same PDB: d3taga2, d3taga3, d3tagb2, d3tagc2, d3tagd2
        automated match to d3l8bb1
        protein/DNA complex; complexed with so4
      2. 2463563Domain d3tagb1: 3tag B:1-375 [249851]
        Other proteins in same PDB: d3taga2, d3taga3, d3tagb2, d3tagc2, d3tagd2
        automated match to d3l8bb1
        protein/DNA complex; complexed with so4
      3. 2463564Domain d3tagc1: 3tag C:1-375 [249853]
        Other proteins in same PDB: d3taga2, d3taga3, d3tagb2, d3tagc2, d3tagd2
        automated match to d3l8bb1
        protein/DNA complex; complexed with so4
      4. 2463565Domain d3tagd1: 3tag D:1-375 [249855]
        Other proteins in same PDB: d3taga2, d3taga3, d3tagb2, d3tagc2, d3tagd2
        automated match to d3l8bb1
        protein/DNA complex; complexed with so4
    52. Domain for 3uiq:
    53. Domain for 4dtj:
    54. Domain for 4dtm:
    55. Domain for 4dtn:
    56. Domain for 4dto:
    57. Domain for 4dtp:
    58. Domain for 4dtr:
    59. Domain for 4dts:
    60. Domain for 4dtu:
    61. Domain for 4dtx:
    62. Domain for 4du1:
    63. Domain for 4du3:
    64. Domain for 4du4:
    65. Domain for 4e3s:
    66. Domain for 4fj5:
    67. Domain for 4fj7:
    68. Domain for 4fj8:
    69. Domain for 4fj9:
    70. Domain for 4fjg:
    71. Domain for 4fjh:
    72. Domain for 4fji:
    73. Domain for 4fjj:
    74. Domain for 4fjk:
    75. Domain for 4fjl:
    76. Domain for 4fjm:
    77. Domain for 4fjn:
    78. Domain for 4fjx:
    79. Domain for 4fk0:
    80. Domain for 4fk2:
    81. Domain for 4fk4:
    82. Domain for 4i9l:
    83. Domain for 4j2a:
    84. Domain for 4j2b:
    85. Domain for 4j2e:
    86. Domains for 4khn:
      1. 2463543Domain d4khna1: 4khn A:1-375 [235165]
        Other proteins in same PDB: d4khna2, d4khnb2
        automated match to d4khnb1
        protein/DNA complex; complexed with ca, gol, na, so4, xg4; mutant
      2. 2463544Domain d4khnb1: 4khn B:1-375 [228218]
        Other proteins in same PDB: d4khna2, d4khnb2
        automated match to d1ih7a1
        protein/DNA complex; complexed with ca, gol, na, so4, xg4; mutant
    87. Domain for 4khq:
    88. Domain for 4khs:
    89. Domain for 4khu:
    90. Domain for 4khw:
    91. Domain for 4khy:
    92. Domain for 4ki4:
    93. Domain for 4ki6:
  2. 2463606Bacteriophage T4 [TaxId:10665] [53126] (2 PDB entries)
    additional N-terminal subdomain contains rudimental OB-fold
    1. Domains for 1noy:
      1. 2463607Domain d1noya_: 1noy A: [33713]
        exonuclease domain only
        protein/DNA complex; complexed with mn, zn
      2. 2463608Domain d1noyb_: 1noy B: [33714]
        exonuclease domain only
        protein/DNA complex; complexed with mn, zn
    2. Domains for 1noz:
      1. 2463609Domain d1noza_: 1noz A: [33715]
        exonuclease domain only
      2. 2463610Domain d1nozb_: 1noz B: [33716]
        exonuclease domain only
  3. 2463611Desulfurococcus tok [TaxId:108142] [53130] (2 PDB entries)
    additional N-terminal subdomain contains rudimental OB-fold but complete ferredoxin-like fold
    1. Domain for 1d5a:
    2. Domain for 1qqc:
  4. 2463614Escherichia coli [TaxId:562] [102482] (1 PDB entry)
    DNA polymerase II, additional N-terminal subdomain has an OB-fold with a ferredoxin-like fold insertion
  5. 2463616Pyrococcus kodakaraensis [TaxId:311400] [53131] (2 PDB entries)
    Uniprot P56689 1-758 # 93% sequence identity; Thermococcus kodakarensis KOD1 TaxID: 69014
    additional N-terminal subdomain contains rudimental OB-fold but complete ferredoxin-like fold
    1. Domain for 1wn7:
    2. Domain for 1wns:
  6. 2463619Sulfolobus solfataricus [TaxId:2287] [117647] (1 PDB entry)
    Uniprot P26811 40-864
  7. 2463621Thermococcus gorgonarius [TaxId:71997] [53128] (1 PDB entry)
    additional N-terminal subdomain contains rudimental OB-fold but complete ferredoxin-like fold
  8. 2463623Thermococcus sp., 9on-7 [TaxId:35749] [53129] (1 PDB entry)
    additional N-terminal subdomain contains rudimental OB-fold but complete ferredoxin-like fold

More info for Protein Exonuclease domain of family B DNA polymerases from c.55.3.5: DnaQ-like 3'-5' exonuclease

Timeline for Protein Exonuclease domain of family B DNA polymerases from c.55.3.5: DnaQ-like 3'-5' exonuclease: