SCOPe 2.01: Protein: Exonuclease domain of family B DNA polymerases

Lineage for Protein: Exonuclease domain of family B DNA polymerases

Root: SCOPe 2.01
Class c: Alpha and beta proteins (a/b) [51349] (147 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] (15 families)
consists of one domain of this fold
Family c.55.3.5: DnaQ-like 3'-5' exonuclease [53118] (16 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:

Bacteriophage RB69 [TaxId:12353] [53127] (15 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
    protein/DNA complex; complexed with ca, gdp
2. Domain for 1ig9:
  - Domain d1ig9a1: 1ig9 A:1-375 [62367]
    Other proteins in same PDB: d1ig9a2
    protein/DNA complex; complexed with ca, ttp
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
    protein/DNA complex; complexed with 3dr, ca, dgp, doc
  2. Domain 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. Domain 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. Domain 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:
  - Domain d1q9ya1: 1q9y A:1-375 [96336]
    Other proteins in same PDB: d1q9ya2
    protein/DNA complex; complexed with ca, dcp
6. Domains for 1waf:
  1. Domain d1wafa1: 1waf A:1-375 [33719]
    Other proteins in same PDB: d1wafa2, d1wafb2
    complexed with gmp
  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, d2atqb1
    automatically matched to d1clqa1
    protein/DNA complex; complexed with gdp, zn
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
    protein/DNA complex
  2. Domain d2dy4b1: 2dy4 B:1-375 [131884]
    Other proteins in same PDB: d2dy4a2, d2dy4b2, d2dy4c2, d2dy4d2
    automatically matched to d1clqa1
    protein/DNA complex
  3. Domain d2dy4c1: 2dy4 C:1-375 [131886]
    Other proteins in same PDB: d2dy4a2, d2dy4b2, d2dy4c2, d2dy4d2
    automatically matched to d1clqa1
    protein/DNA complex
  4. Domain d2dy4d1: 2dy4 D:1-375 [131888]
    Other proteins in same PDB: d2dy4a2, d2dy4b2, d2dy4c2, d2dy4d2
    automatically matched to d1clqa1
    protein/DNA complex
10. Domains for 2oyq:
  1. Domain d2oyqa1: 2oyq A:1-375 [149070]
    Other proteins in same PDB: d2oyqa2, d2oyqb2, d2oyqc2, d2oyqd2
    automatically matched to d1clqa1
    protein/DNA complex; complexed with mg, n5p
  2. Domain d2oyqb1: 2oyq B:1-375 [149072]
    Other proteins in same PDB: d2oyqa2, d2oyqb2, d2oyqc2, d2oyqd2
    automatically matched to d1clqa1
    protein/DNA complex; complexed with mg, n5p
  3. Domain d2oyqc1: 2oyq C:1-375 [149074]
    Other proteins in same PDB: d2oyqa2, d2oyqb2, d2oyqc2, d2oyqd2
    automatically matched to d1clqa1
    protein/DNA complex; complexed with mg, n5p
  4. Domain d2oyqd1: 2oyq D:2-375 [149076]
    Other proteins in same PDB: d2oyqa2, d2oyqb2, d2oyqc2, d2oyqd2
    automatically matched to d1clqa1
    protein/DNA complex; complexed with mg, n5p
11. Domain for 2ozm:
  - Domain d2ozma1: 2ozm A:1-375 [149115]
    Other proteins in same PDB: d2ozma2
    automatically matched to d1clqa1
    protein/DNA complex; complexed with mg, n5p
12. Domain for 2ozs:
  - Domain d2ozsa1: 2ozs A:1-375 [149127]
    Other proteins in same PDB: d2ozsa2
    automatically matched to d1clqa1
    protein/DNA complex; complexed with dtp, mg
13. Domains for 2p5g:
  1. Domain d2p5ga1: 2p5g A:1-375 [149240]
    Other proteins in same PDB: d2p5ga2, d2p5gb2, d2p5gc2, d2p5gd2
    automatically matched to d1clqa1
    protein/DNA complex
  2. Domain d2p5gb1: 2p5g B:1-375 [149242]
    Other proteins in same PDB: d2p5ga2, d2p5gb2, d2p5gc2, d2p5gd2
    automatically matched to d1clqa1
    protein/DNA complex
  3. Domain d2p5gc1: 2p5g C:1-375 [149244]
    Other proteins in same PDB: d2p5ga2, d2p5gb2, d2p5gc2, d2p5gd2
    automatically matched to d1clqa1
    protein/DNA complex
  4. Domain d2p5gd1: 2p5g D:2-375 [149246]
    Other proteins in same PDB: d2p5ga2, d2p5gb2, d2p5gc2, d2p5gd2
    automatically matched to d1clqa1
    protein/DNA complex
14. Domains for 2p5o:
  1. Domain d2p5oa1: 2p5o A:1-375 [139498]
    Other proteins in same PDB: d2p5oa2, d2p5ob2, d2p5oc2, d2p5od2
    automatically matched to d1clqa1
    protein/DNA complex
  2. Domain d2p5ob1: 2p5o B:1-375 [139500]
    Other proteins in same PDB: d2p5oa2, d2p5ob2, d2p5oc2, d2p5od2
    automatically matched to d1clqa1
    protein/DNA complex
  3. Domain d2p5oc1: 2p5o C:1-375 [139502]
    Other proteins in same PDB: d2p5oa2, d2p5ob2, d2p5oc2, d2p5od2
    automatically matched to d1clqa1
    protein/DNA complex
  4. Domain d2p5od1: 2p5o D:1-375 [139504]
    Other proteins in same PDB: d2p5oa2, d2p5ob2, d2p5oc2, d2p5od2
    automatically matched to d1clqa1
    protein/DNA complex
15. Domain for 3cq8:
  - Domain d3cq8a1: 3cq8 A:1-375 [156927]
    Other proteins in same PDB: d3cq8a2
    automatically matched to d1clqa1
    protein/DNA complex; complexed with ca, gol, na, ttp; 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]
    exonuclease domain only
    protein/DNA complex; complexed with mn, zn
  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]
    exonuclease domain only
  2. Domain d1nozb_: 1noz B: [33716]
    exonuclease domain only
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
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

Pyrococcus 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

Domain for 1wn7:
- Domain d1wn7a1: 1wn7 A:1-347 [121088]
  Other proteins in same PDB: d1wn7a2
  complexed with gol, ni; mutant
Domain for 1wns:
- Domain d1wnsa1: 1wns A:1-347 [109437]
  Other proteins in same PDB: d1wnsa2

Sulfolobus solfataricus [TaxId:2287] [117647] (1 PDB entry)
Uniprot P26811 40-864
- Domain for 1s5j:
  - Domain d1s5ja1: 1s5j A:40-449 [112040]
    Other proteins in same PDB: d1s5ja2
    complexed with mg, so4
Thermococcus gorgonarius [TaxId:71997] [53128] (3 PDB entries)
additional N-terminal subdomain contains rudimental OB-fold but complete ferredoxin-like fold
1. Domain for 1tgo:
  - Domain d1tgoa1: 1tgo A:1-347 [33721]
    Other proteins in same PDB: d1tgoa2
2. Domain for 2vwj:
  - Domain d2vwja1: 2vwj A:1-347 [153675]
    Other proteins in same PDB: d2vwja2
    automatically matched to d1qqca1
    complexed with k
3. Domain for 2vwk:
  - Domain d2vwka1: 2vwk A:1-347 [153677]
    Other proteins in same PDB: d2vwka2
    automatically matched to d1tgoa1
    complexed with na, so4
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

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 1.75
Protein Exonuclease domain of family B DNA polymerases from c.55.3.5: DnaQ-like 3'-5' exonuclease appears in SCOPe 2.02
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