SCOP 1.73: Protein: Exonuclease domain of family B DNA polymerases

Lineage for Protein: Exonuclease domain of family B DNA polymerases

Root: SCOP 1.73
Class c: Alpha and beta proteins (a/b) [51349] (141 folds)
Fold 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
Superfamily c.55.3: Ribonuclease H-like [53098] (12 families)
consists of one domain of this fold
Family c.55.3.5: DnaQ-like 3'-5' exonuclease [53118] (14 proteins)
contains Pfam PF00929
Protein Exonuclease domain of family B DNA polymerases [53125] (8 species)
elaborated with additional structures and the N-terminal subdomain

Species:

Archaeon Desulfurococcus tok [TaxId:108142] [53130] (2 PDB entries)
additional N-terminal subdomain contains rudimental OB-fold but complete ferredoxin-like fold
1. Domain for 1d5a:
  - Domain d1d5aa1: 1d5a A:1-347 [33723]
    Other proteins in same PDB: d1d5aa2
    complexed with mg, so4
2. Domain for 1qqc:
  - Domain d1qqca1: 1qqc A:1-347 [33724]
    Other proteins in same PDB: d1qqca2
    complexed with mg, so4
Archaeon Pyrococcus kodakaraensis [TaxId:311400] [53131] (2 PDB entries)
additional N-terminal subdomain contains rudimental OB-fold but complete ferredoxin-like fold
1. Domain for 1wn7:
  - Domain d1wn7a1: 1wn7 A:1-347 [121088]
    Other proteins in same PDB: d1wn7a2
    complexed with gol, ni; mutant
2. Domain for 1wns:
  - Domain d1wnsa1: 1wns A:1-347 [109437]
    Other proteins in same PDB: d1wnsa2
Archaeon Thermococcus gorgonarius [TaxId:71997] [53128] (1 PDB entry)
additional N-terminal subdomain contains rudimental OB-fold but complete ferredoxin-like fold
- Domain for 1tgo:
  - Domain d1tgoa1: 1tgo A:1-347 [33721]
    Other proteins in same PDB: d1tgoa2
Archaeon Thermococcus sp., 9on-7 [TaxId:35749] [53129] (1 PDB entry)
additional N-terminal subdomain contains rudimental OB-fold but complete ferredoxin-like fold
- Domain for 1qht:
  - Domain d1qhta1: 1qht A:1-347 [33722]
    Other proteins in same PDB: d1qhta2
    mutant
Bacteriophage RB69 [TaxId:12353] [53127] (10 PDB entries)
additional N-terminal subdomain contains rudimental OB-fold and rudimental ferredoxin-like fold
1. Domain for 1clq:
  - Domain d1clqa1: 1clq A:1-375 [33717]
    Other proteins in same PDB: d1clqa2
2. Domain for 1ig9:
  - Domain d1ig9a1: 1ig9 A:1-375 [62367]
    Other proteins in same PDB: d1ig9a2
    complexed with ca, doc, ttp; mutant
3. Domain for 1ih7:
  - Domain d1ih7a1: 1ih7 A:1-375 [62375]
    Other proteins in same PDB: d1ih7a2
    complexed with gmp, k
4. Domains for 1q9x:
  1. Domain d1q9xa1: 1q9x A:1-375 [96328]
    Other proteins in same PDB: d1q9xa2, d1q9xb2, d1q9xc2, d1q9xd2
  2. Domain d1q9xb1: 1q9x B:1-375 [96330]
    Other proteins in same PDB: d1q9xa2, d1q9xb2, d1q9xc2, d1q9xd2
  3. Domain d1q9xc1: 1q9x C:1-375 [96332]
    Other proteins in same PDB: d1q9xa2, d1q9xb2, d1q9xc2, d1q9xd2
  4. Domain d1q9xd1: 1q9x D:1-375 [96334]
    Other proteins in same PDB: d1q9xa2, d1q9xb2, d1q9xc2, d1q9xd2
    complexed with 3dr, ca, dgp, doc; mutant
5. Domain for 1q9y:
  - Domain d1q9ya1: 1q9y A:1-375 [96336]
    Other proteins in same PDB: d1q9ya2
    complexed with 8og, ca, dcp, doc; mutant
6. Domains for 1waf:
  1. Domain d1wafa1: 1waf A:1-375 [33719]
    Other proteins in same PDB: d1wafa2, d1wafb2
  2. Domain d1wafb1: 1waf B:1-375 [33720]
    Other proteins in same PDB: d1wafa2, d1wafb2
    complexed with gmp
7. Domain for 1waj:
  - Domain d1waja1: 1waj A:1-375 [33718]
    Other proteins in same PDB: d1waja2
    complexed with 5gp
8. Domain for 2atq:
  - Domain d2atqa1: 2atq A:1-375 [127303]
    Other proteins in same PDB: d2atqa2
    automatically matched to d1clqa1
    complexed with gdp, zn; mutant
9. Domains for 2dy4:
  1. Domain d2dy4a1: 2dy4 A:1-375 [131882]
    Other proteins in same PDB: d2dy4a2, d2dy4b2, d2dy4c2, d2dy4d2
    automatically matched to d1clqa1
    complexed with ctg; mutant
  2. Domain d2dy4b1: 2dy4 B:1-375 [131884]
    Other proteins in same PDB: d2dy4a2, d2dy4b2, d2dy4c2, d2dy4d2
    automatically matched to d1clqa1
    complexed with ctg; mutant
  3. Domain d2dy4c1: 2dy4 C:1-375 [131886]
    Other proteins in same PDB: d2dy4a2, d2dy4b2, d2dy4c2, d2dy4d2
    automatically matched to d1clqa1
    complexed with ctg; mutant
  4. Domain d2dy4d1: 2dy4 D:1-375 [131888]
    Other proteins in same PDB: d2dy4a2, d2dy4b2, d2dy4c2, d2dy4d2
    automatically matched to d1clqa1
    complexed with ctg; mutant
10. Domains for 2p5o:
  1. Domain d2p5oa1: 2p5o A:1-375 [139498]
    Other proteins in same PDB: d2p5oa2, d2p5ob2, d2p5oc2, d2p5od2
    automatically matched to d1clqa1
    complexed with 3dr; mutant
  2. Domain d2p5ob1: 2p5o B:1-375 [139500]
    Other proteins in same PDB: d2p5oa2, d2p5ob2, d2p5oc2, d2p5od2
    automatically matched to d1clqa1
    complexed with 3dr; mutant
  3. Domain d2p5oc1: 2p5o C:1-375 [139502]
    Other proteins in same PDB: d2p5oa2, d2p5ob2, d2p5oc2, d2p5od2
    automatically matched to d1clqa1
    complexed with 3dr; mutant
  4. Domain d2p5od1: 2p5o D:1-375 [139504]
    Other proteins in same PDB: d2p5oa2, d2p5ob2, d2p5oc2, d2p5od2
    automatically matched to d1clqa1
    complexed with 3dr; mutant
Bacteriophage T4 [TaxId:10665] [53126] (2 PDB entries)
additional N-terminal subdomain contains rudimental OB-fold
1. Domains for 1noy:
  1. Domain d1noya_: 1noy A: [33713]
  2. Domain d1noyb_: 1noy B: [33714]
    exonuclease domain only
    protein/DNA complex; complexed with mn, zn
2. Domains for 1noz:
  1. Domain d1noza_: 1noz A: [33715]
  2. Domain d1nozb_: 1noz B: [33716]
    exonuclease domain only
Escherichia coli [TaxId:562] [102482] (1 PDB entry)
DNA polymerase II, additional N-terminal subdomain has an OB-fold with a ferredoxin-like fold insertion
- Domain for 1q8i:
  - Domain d1q8ia1: 1q8i A:2-389 [96208]
    Other proteins in same PDB: d1q8ia2
    mutant
Sulfolobus solfataricus [TaxId:2287] [117647] (1 PDB entry)
- Domain for 1s5j:
  - Domain d1s5ja1: 1s5j A:40-449 [112040]
    Other proteins in same PDB: d1s5ja2
    complexed with mg, sul

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:

Protein Exonuclease domain of family B DNA polymerases from c.55.3.5: DnaQ-like 3'-5' exonuclease first appeared (with stable ids) in SCOP 1.55, called Protein Exonuclease domain of family B (archaeal and phage) DNA polymerases from c.55.3.5: DnaQ-like 3'-5' exonuclease
Protein Exonuclease domain of family B DNA polymerases from c.55.3.5: DnaQ-like 3'-5' exonuclease appears in SCOP 1.71
Protein Exonuclease domain of family B DNA polymerases from c.55.3.5: DnaQ-like 3'-5' exonuclease appears in SCOP 1.75
Protein Exonuclease domain of family B DNA polymerases from c.55.3.5: DnaQ-like 3'-5' exonuclease appears in the current release, SCOPe 2.08