2fao

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Crystal Structure of Pseudomonas aeruginosa LigD polymerase domain

Structural highlights

2fao is a 2 chain structure with sequence from Pseudomonas aeruginosa. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.5Å
Ligands:SO4
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

LIGD_PSEAE With Ku probably forms a non-homologous end joining (NHEJ) repair enzyme, which repairs dsDNA breaks (DSB) with reduced fidelity. Acts as a DNA ligase on singly nicked dsDNA, fills dsDNA gaps (3- or 4- nucleotide gaps, prefers a 5'-phosphate at the gap distal end, prefers dNTPs over rNTPs) (PubMed:20018881), has DNA-directed DNA polymerase activity (templated primer extension) and DNA-directed RNA polymerase activity (PubMed:15897197), adds 1 or 2 non-templated rNTP (or less well dNTP) to ssDNA or blunt-end dsDNA (primer extension). Has 3' resection activity, removing 3'-rNMPs from DNA using its 3'-ribonuclease and 3'-phosphatase activities sequentially. Resection requires a 2'-OH in the penultimate nucleoside position (i.e. a ribo- not deoxyribonucleoside) (PubMed:15897197), although the 3'-phosphatase activity does not, and its specific activity is 16-fold higher on a DNA substrate (PubMed:16046407). On appropriate substrates will extend a DNA primer to the end of the template strand and then incorporate a non-templated nucleotide.[1] [2] [3] The preference of the polymerase domain for rNTPs over dNTPs may be advantageous in quiescent cells where the dNTP pool may be limiting.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

References

  1. ↑ Zhu H, Shuman S. Novel 3'-ribonuclease and 3'-phosphatase activities of the bacterial non-homologous end-joining protein, DNA ligase D. J Biol Chem. 2005 Jul 15;280(28):25973-81. PMID:15897197 doi:10.1074/jbc.M504002200
  2. ↑ Zhu H, Wang LK, Shuman S. Essential constituents of the 3'-phosphoesterase domain of bacterial DNA ligase D, a nonhomologous end-joining enzyme. J Biol Chem. 2005 Oct 7;280(40):33707-15. PMID:16046407 doi:10.1074/jbc.M506838200
  3. ↑ Zhu H, Shuman S. Gap filling activities of Pseudomonas DNA ligase D (LigD) polymerase and functional interactions of LigD with the DNA end-binding Ku protein. J Biol Chem. 2010 Feb 12;285(7):4815-25. PMID:20018881 doi:10.1074/jbc.M109.073874

Contents


PDB ID 2fao

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