SCOP 1.75: Protein: Family B DNA polymerase

Lineage for Protein: Family B DNA polymerase

Root: SCOP 1.75
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] (6 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] (4 proteins)
Protein Family B DNA polymerase [56680] (7 species)

Species:

Archaeon 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
Archaeon 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
Archaeon 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; mutant
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; mutant
Archaeon 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
    mutant
Bacteriophage RB69 [TaxId:12353] [56681] (15 PDB entries)
1. Domain for 1clq:
  - Domain d1clqa2: 1clq A:376-903 [43006]
    Other proteins in same PDB: d1clqa1
2. Domain for 1ig9:
  - Domain d1ig9a2: 1ig9 A:376-901 [62368]
    Other proteins in same PDB: d1ig9a1
    complexed with ca, doc, ttp; mutant
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
  2. Domain d1q9xb2: 1q9x B:376-903 [96331]
    Other proteins in same PDB: d1q9xa1, d1q9xb1, d1q9xc1, d1q9xd1
  3. Domain d1q9xc2: 1q9x C:376-903 [96333]
    Other proteins in same PDB: d1q9xa1, d1q9xb1, d1q9xc1, d1q9xd1
  4. Domain d1q9xd2: 1q9x D:376-903 [96335]
    Other proteins in same PDB: d1q9xa1, d1q9xb1, d1q9xc1, d1q9xd1
    complexed with 3dr, ca, dgp, doc; mutant
5. Domain for 1q9y:
  - Domain d1q9ya2: 1q9y A:376-902 [96337]
    Other proteins in same PDB: d1q9ya1
    complexed with 8og, ca, dcp, doc; mutant
6. Domains for 1waf:
  1. Domain d1wafa2: 1waf A:376-903 [43008]
    Other proteins in same PDB: d1wafa1, d1wafb1
  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
    complexed with gdp, zn; mutant
9. Domains for 2dy4:
  1. Domain d2dy4a2: 2dy4 A:376-902 [131883]
    Other proteins in same PDB: d2dy4a1, d2dy4b1, d2dy4c1, d2dy4d1
    automatically matched to d1clqa2
    complexed with ctg; mutant
  2. Domain d2dy4b2: 2dy4 B:376-902 [131885]
    Other proteins in same PDB: d2dy4a1, d2dy4b1, d2dy4c1, d2dy4d1
    automatically matched to d1clqa2
    complexed with ctg; mutant
  3. Domain d2dy4c2: 2dy4 C:376-900 [131887]
    Other proteins in same PDB: d2dy4a1, d2dy4b1, d2dy4c1, d2dy4d1
    automatically matched to d1clqa2
    complexed with ctg; mutant
  4. Domain d2dy4d2: 2dy4 D:376-897 [131889]
    Other proteins in same PDB: d2dy4a1, d2dy4b1, d2dy4c1, d2dy4d1
    automatically matched to d1clqa2
    complexed with ctg; mutant
10. Domains for 2oyq:
  1. Domain d2oyqa2: 2oyq A:376-903 [149071]
    Other proteins in same PDB: d2oyqa1, d2oyqb1, d2oyqc1, d2oyqd1
    automatically matched to d1clqa2
    complexed with 3dr, mg, n5i, n5p; mutant
  2. Domain d2oyqb2: 2oyq B:376-899 [149073]
    Other proteins in same PDB: d2oyqa1, d2oyqb1, d2oyqc1, d2oyqd1
    automatically matched to d1clqa2
    complexed with 3dr, mg, n5i, n5p; mutant
  3. Domain d2oyqc2: 2oyq C:376-900 [149075]
    Other proteins in same PDB: d2oyqa1, d2oyqb1, d2oyqc1, d2oyqd1
    automatically matched to d1clqa2
    complexed with 3dr, mg, n5i, n5p; mutant
  4. Domain d2oyqd2: 2oyq D:376-898 [149077]
    Other proteins in same PDB: d2oyqa1, d2oyqb1, d2oyqc1, d2oyqd1
    automatically matched to d1clqa2
    complexed with 3dr, mg, n5i, n5p; mutant
11. Domain for 2ozm:
  - Domain d2ozma2: 2ozm A:376-903 [149116]
    Other proteins in same PDB: d2ozma1
    automatically matched to d1clqa2
    complexed with 3dr, ddg, mg, n5p; mutant
12. Domain for 2ozs:
  - Domain d2ozsa2: 2ozs A:376-903 [149128]
    Other proteins in same PDB: d2ozsa1
    automatically matched to d1clqa2
    complexed with ddg, dtp, mg; mutant
13. Domains for 2p5g:
  1. Domain d2p5ga2: 2p5g A:376-903 [149241]
    Other proteins in same PDB: d2p5ga1, d2p5gb1, d2p5gc1, d2p5gd1
    automatically matched to d1clqa2
    complexed with 3dr; mutant
  2. Domain d2p5gb2: 2p5g B:376-899 [149243]
    Other proteins in same PDB: d2p5ga1, d2p5gb1, d2p5gc1, d2p5gd1
    automatically matched to d1clqa2
    complexed with 3dr; mutant
  3. Domain d2p5gc2: 2p5g C:376-898 [149245]
    Other proteins in same PDB: d2p5ga1, d2p5gb1, d2p5gc1, d2p5gd1
    automatically matched to d1clqa2
    complexed with 3dr; mutant
  4. Domain d2p5gd2: 2p5g D:376-899 [149247]
    Other proteins in same PDB: d2p5ga1, d2p5gb1, d2p5gc1, d2p5gd1
    automatically matched to d1clqa2
    complexed with 3dr; mutant
14. Domains for 2p5o:
  1. Domain d2p5oa2: 2p5o A:376-902 [139499]
    Other proteins in same PDB: d2p5oa1, d2p5ob1, d2p5oc1, d2p5od1
    automatically matched to d1clqa2
    complexed with 3dr; mutant
  2. Domain d2p5ob2: 2p5o B:376-901 [139501]
    Other proteins in same PDB: d2p5oa1, d2p5ob1, d2p5oc1, d2p5od1
    automatically matched to d1clqa2
    complexed with 3dr; mutant
  3. Domain d2p5oc2: 2p5o C:376-898 [139503]
    Other proteins in same PDB: d2p5oa1, d2p5ob1, d2p5oc1, d2p5od1
    automatically matched to d1clqa2
    complexed with 3dr; mutant
  4. Domain d2p5od2: 2p5o D:376-896 [139505]
    Other proteins in same PDB: d2p5oa1, d2p5ob1, d2p5oc1, d2p5od1
    automatically matched to d1clqa2
    complexed with 3dr; mutant
15. Domain for 3cq8:
  - Domain d3cq8a2: 3cq8 A:376-902 [156928]
    Other proteins in same PDB: d3cq8a1
    automatically matched to d1clqa2
    complexed with ca, gol, na, ttp; mutant
Escherichia coli [TaxId:562] [103399] (1 PDB entry)
- Domain for 1q8i:
  - Domain d1q8ia2: 1q8i A:390-783 [96209]
    Other proteins in same PDB: d1q8ia1
    mutant
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, sul

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 SCOP 1.73
Protein Family B DNA polymerase from e.8.1.1: DNA polymerase I appears in SCOPe 2.01
Protein Family B DNA polymerase from e.8.1.1: DNA polymerase I appears in the current release, SCOPe 2.08