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

  1. Root: SCOPe 2.08
  2. Class c: Alpha and beta proteins (a/b) [51349] (148 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] (18 families) (S)
    consists of one domain of this fold
  5. Family c.55.3.5: DnaQ-like 3'-5' exonuclease [53118] (17 proteins)
    contains Pfam PF00929

Proteins:

  1. Arenavirus nucleoprotein C-terminal domain [310781] (1 species)
    C-terminal half of Pfam PF00843
  2. 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] (93 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] (1 PDB entry)
      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
  3. Exonuclease domain of phi29 DNA polymerase [117650] (1 species)
  4. 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] (43 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] (29 PDB entries)
  5. Exonuclease domain of T7 DNA polymerase [53123] (1 species)
  6. Exonuclease ERI1 [117648] (1 species)
  7. 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)
  8. Exosome complex exonuclease RRP6 [142493] (1 species)
  9. Hypothetical protein AT5G06450 [102483] (1 species)
    forms a ring-shaped hexamer; function unknown
  10. Interferon-stimulated gene 20 kDa protein, ISG20 [117652] (1 species)
  11. N-terminal exonuclease domain of the epsilon subunit of DNA polymerase III [82444] (1 species)
  12. 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
  13. Ribonuclease D, catalytic domain [142495] (1 species)
  14. Ribonuclease T [142497] (1 species)
  15. Three prime repair exonuclease 1, TREX1 [159631] (1 species)
  16. Three prime repair exonuclease 2, TREX2 [142499] (2 species)
    1. Species Human (Homo sapiens) [TaxId:9606] [142500] (1 PDB entry)
      Uniprot Q9BQ50 44-271
    2. Species Mouse (Mus musculus) [TaxId:10090] [359904] (2 PDB entries)
  17. automated matches [190162] (6 species)
    not a true protein
    1. Species Colwellia psychrerythraea [TaxId:167879] [365713] (3 PDB entries)
    2. Species Coxiella burnetii [TaxId:777] [196134] (1 PDB entry)
    3. Species Escherichia coli K-12 [TaxId:83333] [225829] (2 PDB entries)
    4. Species Escherichia coli [TaxId:562] [187263] (14 PDB entries)
    5. Species Escherichia coli [TaxId:83333] [267960] (3 PDB entries)
    6. Species Thermococcus gorgonarius [TaxId:71997] [225933] (6 PDB entries)

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: