SCOPe 2.03: Family c.55.3.5: DnaQ-like 3'-5' exonuclease

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

1. Root: SCOPe 2.03

2. Class c: Alpha and beta proteins (a/b) [51349] (147 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] (15 families)
   consists of one domain of this fold

5. Family c.55.3.5: DnaQ-like 3'-5' exonuclease [53118] (16 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 Bacteriophage RB69 [TaxId:12353] [53127] (49 PDB entries)
      additional N-terminal subdomain contains rudimental OB-fold and rudimental ferredoxin-like fold

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

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

   4. 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

   5. Species 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

   6. Species Sulfolobus solfataricus [TaxId:2287] [117647] (1 PDB entry)
      Uniprot P26811 40-864

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

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

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

   • Species Bacteriophage phi-29 [TaxId:10756] [117651] (8 PDB entries)
     Uniprot P03680

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] (44 PDB entries)
      Uniprot Q45458 298-876 # 88% sequence identity ! Uniprot Q5KWC1 299-878 # 99% sequence identity; Geobacillus kaustophilus TaxID:1462

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

   3. Species Thermus aquaticus [TaxId:271] [53121] (24 PDB entries)

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

   • Species Bacteriophage T7 [TaxId:10760] [53124] (17 PDB entries)
     Uniprot P00581

5. Exonuclease ERI1 [117648] (1 species)

   • Species Human (Homo sapiens) [TaxId:9606] [117649] (1 PDB entry)
     Uniprot Q8IV48 122-321

6. Exonuclease I [53132] (2 species)
   also includes an alpha+beta domain with SH3-like like motif and non-globular C-terminal all-alpha region

   1. Species Escherichia coli K-12 [TaxId:83333] [159630] (3 PDB entries)

   2. 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)
     Uniprot Q12149 129-420

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)
     Uniprot Q96AZ6 6-178

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

    • Species Escherichia coli [TaxId:562] [82445] (2 PDB entries)

11. Oligoribonuclease [89719] (2 species)

    1. Species Escherichia coli [TaxId:562] [142492] (2 PDB entries)
       Uniprot P0A784 1-180

    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)
      Uniprot P09155 1-193

13. Ribonuclease T [142497] (1 species)

    • Species Pseudomonas aeruginosa [TaxId:287] [142498] (1 PDB entry)
      Uniprot Q9HY82 19-220

14. Three prime repair exonuclease 1, TREX1 [159631] (1 species)

    • Species Mouse (Mus musculus) [TaxId:10090] [159632] (6 PDB entries)
      Uniprot Q91XB0 5-234! Uniprot Q91XB0 9-234

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

    • Species Human (Homo sapiens) [TaxId:9606] [142500] (1 PDB entry)
      Uniprot Q9BQ50 44-271

16. automated matches [190162] (4 species)
    not a true protein

    1. Species Coxiella burnetii [TaxId:777] [196134] (1 PDB entry)

    2. Species Escherichia coli [TaxId:562] [187263] (6 PDB entries)

    3. Species Escherichia coli [TaxId:83333] [225829] (1 PDB entry)

    4. Species Thermococcus gorgonarius [TaxId:71997] [225933] (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 SCOPe 2.02
  
• Family c.55.3.5: DnaQ-like 3'-5' exonuclease appears in SCOPe 2.04
  
• Family c.55.3.5: DnaQ-like 3'-5' exonuclease appears in the current release, SCOPe 2.08