SCOP 1.73: Family c.55.3.5: DnaQ-like 3'-5' exonuclease

Lineage for Family c.55.3.5: DnaQ-like 3'-5' exonuclease

1. Root: SCOP 1.73

2. Class c: Alpha and beta proteins (a/b) [51349] (141 folds)

3. 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

4. Superfamily c.55.3: Ribonuclease H-like [53098] (12 families)
   consists of one domain of this fold

5. Family c.55.3.5: DnaQ-like 3'-5' exonuclease [53118] (14 proteins)
   contains Pfam PF00929

Proteins:

1. Exonuclease domain of family B DNA polymerases [53125] (8 species)
   elaborated with additional structures and the N-terminal subdomain

   1. Species Archaeon Desulfurococcus tok [TaxId:108142] [53130] (2 PDB entries)
      additional N-terminal subdomain contains rudimental OB-fold but complete ferredoxin-like fold

   2. Species Archaeon Pyrococcus kodakaraensis [TaxId:311400] [53131] (2 PDB entries)
      additional N-terminal subdomain contains rudimental OB-fold but complete ferredoxin-like fold

   3. Species Archaeon Thermococcus gorgonarius [TaxId:71997] [53128] (1 PDB entry)
      additional N-terminal subdomain contains rudimental OB-fold but complete ferredoxin-like fold

   4. Species Archaeon Thermococcus sp., 9on-7 [TaxId:35749] [53129] (1 PDB entry)
      additional N-terminal subdomain contains rudimental OB-fold but complete ferredoxin-like fold

   5. Species Bacteriophage RB69 [TaxId:12353] [53127] (10 PDB entries)
      additional N-terminal subdomain contains rudimental OB-fold and rudimental ferredoxin-like fold

   6. Species Bacteriophage T4 [TaxId:10665] [53126] (2 PDB entries)
      additional N-terminal subdomain contains rudimental OB-fold

   7. Species 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

   8. Species Sulfolobus solfataricus [TaxId:2287] [117647] (1 PDB entry)

2. Exonuclease domain of phi29 DNA polymerase [117650] (1 species)

   • Species Bacteriophage phi-29 [TaxId:10756] [117651] (4 PDB entries)

3. Exonuclease domain of prokaryotic DNA polymerase [53119] (3 species)
   part of Klenow fragment, KF

   1. Species Bacillus stearothermophilus, newly identified strain as yet unnamed [TaxId:1422] [53122] (42 PDB entries)

   2. Species Escherichia coli [TaxId:562] [53120] (14 PDB entries)

   3. Species Thermus aquaticus [TaxId:271] [53121] (13 PDB entries)

4. Exonuclease domain of T7 DNA polymerase [53123] (1 species)

   • Species Bacteriophage T7 [TaxId:10760] [53124] (16 PDB entries)

5. Exonuclease ERI1 [117648] (1 species)

   • Species Human (Homo sapiens) [TaxId:9606] [117649] (1 PDB entry)

6. Exonuclease I [53132] (1 species)
   also includes an alpha+beta domain with SH3-like like motif and non-globular C-terminal all-alpha region

   • Species Escherichia coli [TaxId:562] [53133] (1 PDB entry)

7. Exosome complex exonuclease RRP6 [142493] (1 species)

   • Species Baker's yeast (Saccharomyces cerevisiae) [TaxId:4932] [142494] (4 PDB entries)

8. Hypothetical protein AT5G06450 [102483] (1 species)
   forms a ring-shaped hexamer; function unknown

   • Species Thale-cress (Arabidopsis thaliana) [TaxId:3702] [102484] (2 PDB entries)

9. Interferon-stimulated gene 20 kDa protein, ISG20 [117652] (1 species)

   • Species Human (Homo sapiens) [TaxId:9606] [117653] (1 PDB entry)

10. N-terminal exonuclease domain of the epsilon subunit of DNA polymerase III [82444] (1 species)

    • Species Escherichia coli [TaxId:562] [82445] (4 PDB entries)

11. Oligoribonuclease [89719] (2 species)

    1. Species Escherichia coli [TaxId:562] [142492] (1 PDB entry)

    2. Species Haemophilus influenzae [TaxId:727] [89720] (1 PDB entry)
       HI1715

12. Ribonuclease D, catalytic domain [142495] (1 species)

    • Species Escherichia coli [TaxId:562] [142496] (1 PDB entry)

13. Ribonuclease T [142497] (1 species)

    • Species Pseudomonas aeruginosa [TaxId:287] [142498] (1 PDB entry)

14. Three prime repair exonuclease 2, TREX2 [142499] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [142500] (1 PDB entry)

More info for Family c.55.3.5: DnaQ-like 3'-5' exonuclease

Timeline for Family c.55.3.5: DnaQ-like 3'-5' exonuclease:

• Family c.55.3.5: DnaQ-like 3'-5' exonuclease first appeared (with stable ids) in SCOP 1.55
  
• Family c.55.3.5: DnaQ-like 3'-5' exonuclease appears in SCOP 1.71
  
• Family c.55.3.5: DnaQ-like 3'-5' exonuclease appears in SCOP 1.75
  
• Family c.55.3.5: DnaQ-like 3'-5' exonuclease appears in the current release, SCOPe 2.08