SCOPe 2.03: Protein: Family B DNA polymerase

Lineage for Protein: Family B DNA polymerase

Root: SCOPe 2.03
Class e: Multi-domain proteins (alpha and beta) [56572] (66 folds)
Fold e.8: DNA/RNA polymerases [56671] (1 superfamily)
divided into morphological domains including "palm", "thumb" and "fingers"; the catalytic "palm" domain is conserved to all members
Superfamily e.8.1: DNA/RNA polymerases [56672] (7 families)
"palm" domain has a ferredoxin-like fold, related to that of an adenylyl cyclase domain
Family e.8.1.1: DNA polymerase I [56673] (5 proteins)
Protein Family B DNA polymerase [56680] (7 species)

Species:

Bacteriophage RB69 [TaxId:12353] [56681] (49 PDB entries)
1. Domain for 1clq:
  - Domain d1clqa2: 1clq A:376-903 [43006]
    Other proteins in same PDB: d1clqa1
    protein/DNA complex; complexed with ca, gdp
2. Domain for 1ig9:
  - Domain d1ig9a2: 1ig9 A:376-901 [62368]
    Other proteins in same PDB: d1ig9a1
    protein/DNA complex; complexed with ca, ttp
3. Domain for 1ih7:
  - Domain d1ih7a2: 1ih7 A:376-903 [62376]
    Other proteins in same PDB: d1ih7a1
    complexed with gmp, k
4. Domains for 1q9x:
  1. Domain d1q9xa2: 1q9x A:376-903 [96329]
    Other proteins in same PDB: d1q9xa1, d1q9xb1, d1q9xc1, d1q9xd1
    protein/DNA complex; complexed with 3dr, ca, dgp, doc
  2. Domain d1q9xb2: 1q9x B:376-903 [96331]
    Other proteins in same PDB: d1q9xa1, d1q9xb1, d1q9xc1, d1q9xd1
    protein/DNA complex; complexed with 3dr, ca, dgp, doc
  3. Domain d1q9xc2: 1q9x C:376-903 [96333]
    Other proteins in same PDB: d1q9xa1, d1q9xb1, d1q9xc1, d1q9xd1
    protein/DNA complex; complexed with 3dr, ca, dgp, doc
  4. Domain d1q9xd2: 1q9x D:376-903 [96335]
    Other proteins in same PDB: d1q9xa1, d1q9xb1, d1q9xc1, d1q9xd1
    protein/DNA complex; complexed with 3dr, ca, dgp, doc
5. Domain for 1q9y:
  - Domain d1q9ya2: 1q9y A:376-902 [96337]
    Other proteins in same PDB: d1q9ya1
    protein/DNA complex; complexed with ca, dcp
6. Domains for 1waf:
  1. Domain d1wafa2: 1waf A:376-903 [43008]
    Other proteins in same PDB: d1wafa1, d1wafb1
    complexed with gmp
  2. Domain d1wafb2: 1waf B:376-903 [43009]
    Other proteins in same PDB: d1wafa1, d1wafb1
    complexed with gmp
7. Domain for 1waj:
  - Domain d1waja2: 1waj A:376-903 [43007]
    Other proteins in same PDB: d1waja1
    complexed with 5gp
8. Domain for 2atq:
  - Domain d2atqa2: 2atq A:376-903 [127304]
    Other proteins in same PDB: d2atqa1, d2atqb1
    automatically matched to d1clqa2
    protein/DNA complex; complexed with gdp, zn
9. Domains for 2dtu:
  1. Domain d2dtua2: 2dtu A:376-903 [230660]
    Other proteins in same PDB: d2dtua1, d2dtub1, d2dtuc1, d2dtud1
    automated match to d1ih7a2
    protein/DNA complex
  2. Domain d2dtub2: 2dtu B:376-903 [230665]
    Other proteins in same PDB: d2dtua1, d2dtub1, d2dtuc1, d2dtud1
    automated match to d1ih7a2
    protein/DNA complex
  3. Domain d2dtuc2: 2dtu C:376-899 [230668]
    Other proteins in same PDB: d2dtua1, d2dtub1, d2dtuc1, d2dtud1
    automated match to d1ih7a2
    protein/DNA complex
  4. Domain d2dtud2: 2dtu D:376-898 [230666]
    Other proteins in same PDB: d2dtua1, d2dtub1, d2dtuc1, d2dtud1
    automated match to d1ih7a2
    protein/DNA complex
10. Domains for 2dy4:
  1. Domain d2dy4a2: 2dy4 A:376-902 [131883]
    Other proteins in same PDB: d2dy4a1, d2dy4b1, d2dy4c1, d2dy4d1
    automated match to d1q9xa2
    protein/DNA complex
  2. Domain d2dy4b2: 2dy4 B:376-902 [131885]
    Other proteins in same PDB: d2dy4a1, d2dy4b1, d2dy4c1, d2dy4d1
    automated match to d1q9xa2
    protein/DNA complex
  3. Domain d2dy4c2: 2dy4 C:376-900 [131887]
    Other proteins in same PDB: d2dy4a1, d2dy4b1, d2dy4c1, d2dy4d1
    automated match to d1ig9a2
    protein/DNA complex
  4. Domain d2dy4d2: 2dy4 D:376-897 [131889]
    Other proteins in same PDB: d2dy4a1, d2dy4b1, d2dy4c1, d2dy4d1
    automated match to d1ig9a2
    protein/DNA complex
11. Domains for 2oyq:
  1. Domain d2oyqa2: 2oyq A:376-903 [149071]
    Other proteins in same PDB: d2oyqa1, d2oyqb1, d2oyqc1, d2oyqd1
    automatically matched to d1clqa2
    protein/DNA complex; complexed with mg, n5p
  2. Domain d2oyqb2: 2oyq B:376-899 [149073]
    Other proteins in same PDB: d2oyqa1, d2oyqb1, d2oyqc1, d2oyqd1
    automatically matched to d1clqa2
    protein/DNA complex; complexed with mg, n5p
  3. Domain d2oyqc2: 2oyq C:376-900 [149075]
    Other proteins in same PDB: d2oyqa1, d2oyqb1, d2oyqc1, d2oyqd1
    automated match to d1ig9a2
    protein/DNA complex; complexed with mg, n5p
  4. Domain d2oyqd2: 2oyq D:376-898 [149077]
    Other proteins in same PDB: d2oyqa1, d2oyqb1, d2oyqc1, d2oyqd1
    automated match to d1ig9a2
    protein/DNA complex; complexed with mg, n5p
12. Domain for 2ozm:
  - Domain d2ozma2: 2ozm A:376-903 [149116]
    Other proteins in same PDB: d2ozma1
    automated match to d1q9xa2
    protein/DNA complex; complexed with mg, n5p
13. Domain for 2ozs:
  - Domain d2ozsa2: 2ozs A:376-903 [149128]
    Other proteins in same PDB: d2ozsa1
    automated match to d1q9xa2
    protein/DNA complex; complexed with dtp, mg
14. Domains for 2p5g:
  1. Domain d2p5ga2: 2p5g A:376-903 [149241]
    Other proteins in same PDB: d2p5ga1, d2p5gb1, d2p5gc1, d2p5gd1
    automated match to d1q9xa2
    protein/DNA complex
  2. Domain d2p5gb2: 2p5g B:376-899 [149243]
    Other proteins in same PDB: d2p5ga1, d2p5gb1, d2p5gc1, d2p5gd1
    automatically matched to d1clqa2
    protein/DNA complex
  3. Domain d2p5gc2: 2p5g C:376-898 [149245]
    Other proteins in same PDB: d2p5ga1, d2p5gb1, d2p5gc1, d2p5gd1
    automated match to d1ig9a2
    protein/DNA complex
  4. Domain d2p5gd2: 2p5g D:376-899 [149247]
    Other proteins in same PDB: d2p5ga1, d2p5gb1, d2p5gc1, d2p5gd1
    automated match to d1ig9a2
    protein/DNA complex
15. Domains for 2p5o:
  1. Domain d2p5oa2: 2p5o A:376-902 [139499]
    Other proteins in same PDB: d2p5oa1, d2p5ob1, d2p5oc1, d2p5od1
    automatically matched to d1clqa2
    protein/DNA complex
  2. Domain d2p5ob2: 2p5o B:376-901 [139501]
    Other proteins in same PDB: d2p5oa1, d2p5ob1, d2p5oc1, d2p5od1
    automatically matched to d1clqa2
    protein/DNA complex
  3. Domain d2p5oc2: 2p5o C:376-898 [139503]
    Other proteins in same PDB: d2p5oa1, d2p5ob1, d2p5oc1, d2p5od1
    automatically matched to d1clqa2
    protein/DNA complex
  4. Domain d2p5od2: 2p5o D:376-896 [139505]
    Other proteins in same PDB: d2p5oa1, d2p5ob1, d2p5oc1, d2p5od1
    automatically matched to d1clqa2
    protein/DNA complex
16. Domain for 3cfo:
  - Domain d3cfoa2: 3cfo A:376-906 [231887]
    Other proteins in same PDB: d3cfoa1
    automated match to d1ih7a2
    complexed with gmp, so4; mutant
17. Domain for 3cq8:
  - Domain d3cq8a2: 3cq8 A:376-902 [156928]
    Other proteins in same PDB: d3cq8a1
    automatically matched to d1clqa2
    protein/DNA complex; complexed with ca, gol, na, ttp; mutant
18. Domains for 3l8b:
  1. Domain d3l8ba2: 3l8b A:376-903 [232822]
    Other proteins in same PDB: d3l8ba1, d3l8bb1
    automated match to d1ih7a2
    protein/DNA complex; complexed with so4
  2. Domain d3l8bb2: 3l8b B:376-903 [232823]
    Other proteins in same PDB: d3l8ba1, d3l8bb1
    automated match to d1ih7a2
    protein/DNA complex; complexed with so4
19. Domain for 3lzi:
  - Domain d3lzia2: 3lzi A:376-903 [232891]
    Other proteins in same PDB: d3lzia1
    automated match to d1ih7a2
    protein/DNA complex; complexed with ca, dtp
20. Domain for 3lzj:
  - Domain d3lzja2: 3lzj A:376-903 [232890]
    Other proteins in same PDB: d3lzja1
    automated match to d1ih7a2
    protein/DNA complex; complexed with ca, ctp
21. Domain for 3nci:
  - Domain d3ncia2: 3nci A:376-903 [213878]
    Other proteins in same PDB: d3ncia1
    automated match to d1q9xa2
    protein/DNA complex; complexed with ca, dcp
22. Domain for 3ne6:
  - Domain d3ne6a2: 3ne6 A:376-903 [233011]
    Other proteins in same PDB: d3ne6a1
    automated match to d1ih7a2
    protein/DNA complex; complexed with ca, dcp
23. Domain for 3qes:
  - Domain d3qesa2: 3qes A:376-902 [233321]
    Other proteins in same PDB: d3qesa1
    automated match to d1ih7a2
    protein/DNA complex; complexed with ca, dgt
24. Domain for 3qet:
  - Domain d3qeta2: 3qet A:376-903 [233323]
    Other proteins in same PDB: d3qeta1
    automated match to d1ih7a2
    protein/DNA complex; complexed with ca, ttp
25. Domain for 3scx:
  - Domain d3scxa2: 3scx A:376-903 [233529]
    Other proteins in same PDB: d3scxa1
    automated match to d1ih7a2
    protein/DNA complex; complexed with ca, dup; mutant
26. Domain for 3spy:
  - Domain d3spya2: 3spy A:376-901 [233590]
    Other proteins in same PDB: d3spya1
    automated match to d1ih7a2
    protein/DNA complex; complexed with mg, upc
27. Domain for 3spz:
  - Domain d3spza2: 3spz A:376-903 [233592]
    Other proteins in same PDB: d3spza1
    automated match to d1ih7a2
    protein/DNA complex; complexed with ca, upc
28. Domain for 3sq1:
  - Domain d3sq1a2: 3sq1 A:376-901 [233594]
    Other proteins in same PDB: d3sq1a1
    automated match to d1ih7a2
    protein/DNA complex; complexed with ca, dup
29. Domain for 3sq2:
  - Domain d3sq2a2: 3sq2 A:376-902 [233596]
    Other proteins in same PDB: d3sq2a1
    automated match to d1ih7a2
    protein/DNA complex; complexed with ca, ttp
30. Domain for 3sun:
  - Domain d3suna2: 3sun A:376-895 [233639]
    Other proteins in same PDB: d3suna1
    automated match to d1ih7a2
    protein/DNA complex; complexed with ca, ttp
31. Domain for 3suo:
  - Domain d3suoa2: 3suo A:376-900 [233641]
    Other proteins in same PDB: d3suoa1
    automated match to d1ih7a2
    protein/DNA complex; complexed with ca, ttp
32. Domain for 3uiq:
  - Domain d3uiqa2: 3uiq A:376-901 [217393]
    Other proteins in same PDB: d3uiqa1
    automated match to d1ih7a2
    protein/DNA complex; complexed with ca, dup
33. Domain for 4dtj:
  - Domain d4dtja2: 4dtj A:376-901 [220020]
    Other proteins in same PDB: d4dtja1
    automated match to d1ig9a2
    protein/DNA complex; complexed with ca, ttp
34. Domain for 4dtm:
  - Domain d4dtma2: 4dtm A:376-901 [220022]
    Other proteins in same PDB: d4dtma1
    automated match to d1ig9a2
    protein/DNA complex; complexed with ca, dcp
35. Domain for 4du1:
  - Domain d4du1a2: 4du1 A:376-901 [220028]
    Other proteins in same PDB: d4du1a1
    automated match to d1ig9a2
    protein/DNA complex; complexed with ca, dtp
36. Domain for 4du3:
  - Domain d4du3a2: 4du3 A:376-901 [220030]
    Other proteins in same PDB: d4du3a1
    automated match to d1ig9a2
    protein/DNA complex; complexed with ca, dtp
37. Domain for 4du4:
  - Domain d4du4a2: 4du4 A:376-902 [220032]
    Other proteins in same PDB: d4du4a1
    automated match to d1q9xa2
    protein/DNA complex; complexed with ca, dtp
38. Domain for 4i9l:
  - Domain d4i9la2: 4i9l A:376-903 [229485]
    Other proteins in same PDB: d4i9la1
    automated match to d1ih7a2
    complexed with cl, gmp, so4; mutant
39. Domain for 4j2a:
  - Domain d4j2aa2: 4j2a A:376-901 [237017]
    Other proteins in same PDB: d4j2aa1
    automated match to d1ih7a2
    protein/DNA complex; complexed with ca, ttp
40. Domain for 4j2b:
  - Domain d4j2ba2: 4j2b A:376-901 [237015]
    Other proteins in same PDB: d4j2ba1
    automated match to d1ih7a2
    protein/DNA complex; complexed with atp, ca
41. Domain for 4j2e:
  - Domain d4j2ea2: 4j2e A:376-901 [237019]
    Other proteins in same PDB: d4j2ea1
    automated match to d1ih7a2
    protein/DNA complex; complexed with atp, ca
42. Domains for 4khn:
  1. Domain d4khna2: 4khn A:376-901 [235166]
    Other proteins in same PDB: d4khna1, d4khnb1
    automated match to d4khnb2
    protein/DNA complex; complexed with ca, gol, na, so4, xg4; mutant
  2. Domain d4khnb2: 4khn B:376-901 [228219]
    Other proteins in same PDB: d4khna1, d4khnb1
    automated match to d1ih7a2
    protein/DNA complex; complexed with ca, gol, na, so4, xg4; mutant
43. Domain for 4khq:
  - Domain d4khqa2: 4khq A:376-902 [228217]
    Other proteins in same PDB: d4khqa1
    automated match to d1ih7a2
    protein/DNA complex; complexed with ca, dup, na; mutant
44. Domain for 4khs:
  - Domain d4khsa2: 4khs A:376-902 [235170]
    Other proteins in same PDB: d4khsa1
    automated match to d4khqa2
    protein/DNA complex; complexed with ca, cl, na, ttp; mutant
45. Domain for 4khu:
  - Domain d4khua2: 4khu A:376-902 [235172]
    Other proteins in same PDB: d4khua1
    automated match to d4khqa2
    protein/DNA complex; complexed with ca, na, ttp; mutant
46. Domain for 4khw:
  - Domain d4khwa2: 4khw A:376-902 [235174]
    Other proteins in same PDB: d4khwa1
    automated match to d4khqa2
    protein/DNA complex; complexed with ca, na, ttp; mutant
47. Domain for 4khy:
  - Domain d4khya2: 4khy A:376-902 [235168]
    Other proteins in same PDB: d4khya1
    automated match to d4khqa2
    protein/DNA complex; complexed with ca, na, ttp; mutant
48. Domain for 4ki4:
  - Domain d4ki4a2: 4ki4 A:376-901 [235176]
    Other proteins in same PDB: d4ki4a1
    automated match to d4khqa2
    protein/DNA complex; complexed with ca, gol, na, ttp; mutant
49. Domain for 4ki6:
  - Domain d4ki6a2: 4ki6 A:376-902 [235178]
    Other proteins in same PDB: d4ki6a1
    automated match to d4khqa2
    protein/DNA complex; complexed with ca, na, po4, ttp; mutant
Desulfurococcus tok [TaxId:108142] [56684] (2 PDB entries)
1. Domain for 1d5a:
  - Domain d1d5aa2: 1d5a A:348-756 [43012]
    Other proteins in same PDB: d1d5aa1
    complexed with mg, so4
2. Domain for 1qqc:
  - Domain d1qqca2: 1qqc A:348-756 [43013]
    Other proteins in same PDB: d1qqca1
    complexed with mg, so4
Escherichia coli [TaxId:562] [103399] (1 PDB entry)
- Domain for 1q8i:
  - Domain d1q8ia2: 1q8i A:390-783 [96209]
    Other proteins in same PDB: d1q8ia1
Pyrococcus kodakaraensis [TaxId:311400] [56685] (2 PDB entries)
Uniprot P56689 1-758 # 93% sequence identity; Thermococcus kodakarensis KOD1 TaxID: 69014
1. Domain for 1wn7:
  - Domain d1wn7a2: 1wn7 A:348-756 [121089]
    Other proteins in same PDB: d1wn7a1
    complexed with gol, ni; mutant
2. Domain for 1wns:
  - Domain d1wnsa2: 1wns A:348-758 [109438]
    Other proteins in same PDB: d1wnsa1
Sulfolobus solfataricus [TaxId:2287] [118192] (1 PDB entry)
Uniprot P26811 40-864
- Domain for 1s5j:
  - Domain d1s5ja2: 1s5j A:450-864 [112041]
    Other proteins in same PDB: d1s5ja1
    complexed with mg, so4
Thermococcus gorgonarius [TaxId:71997] [56682] (3 PDB entries)
1. Domain for 1tgo:
  - Domain d1tgoa2: 1tgo A:348-773 [43010]
    Other proteins in same PDB: d1tgoa1
2. Domain for 2vwj:
  - Domain d2vwja2: 2vwj A:348-756 [153676]
    Other proteins in same PDB: d2vwja1
    automatically matched to d1qqca2
    complexed with k
3. Domain for 2vwk:
  - Domain d2vwka2: 2vwk A:348-773 [153678]
    Other proteins in same PDB: d2vwka1
    automatically matched to d1tgoa2
    complexed with na, so4
Thermococcus sp., 9on-7 [TaxId:35749] [56683] (1 PDB entry)
- Domain for 1qht:
  - Domain d1qhta2: 1qht A:348-750 [43011]
    Other proteins in same PDB: d1qhta1

More info for Protein Family B DNA polymerase from e.8.1.1: DNA polymerase I

Timeline for Protein Family B DNA polymerase from e.8.1.1: DNA polymerase I:

Protein Family B DNA polymerase from e.8.1.1: DNA polymerase I first appeared (with stable ids) in SCOP 1.55, called Protein T4-like DNA polymerase from e.8.1.1: DNA polymerase I
Protein Family B DNA polymerase from e.8.1.1: DNA polymerase I appears in SCOPe 2.02
Protein Family B DNA polymerase from e.8.1.1: DNA polymerase I appears in SCOPe 2.04
Protein Family B DNA polymerase from e.8.1.1: DNA polymerase I appears in the current release, SCOPe 2.08