2FAQ image
Deposition Date 2005-12-07
Release Date 2006-05-23
Last Version Date 2023-08-30
Entry Detail
PDB ID:
2FAQ
Title:
Crystal Structure of Pseudomonas aeruginosa LigD polymerase domain with ATP and Manganese
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.90 Å
R-Value Free:
0.22
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 21 21 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:probable ATP-dependent DNA ligase
Gene (Uniprot):ligD
Chain IDs:A, B
Chain Length:309
Number of Molecules:2
Biological Source:Pseudomonas aeruginosa
Primary Citation
Atomic structure and nonhomologous end-joining function of the polymerase component of bacterial DNA ligase D
Proc.Natl.Acad.Sci.USA 103 1711 1716 (2006)
PMID: 16446439 DOI: 10.1073/pnas.0509083103

Abstact

DNA ligase D (LigD) is a large polyfunctional protein that participates in a recently discovered pathway of nonhomologous end-joining in bacteria. LigD consists of an ATP-dependent ligase domain fused to a polymerase domain (Pol) and a phosphoesterase module. The Pol activity is remarkable for its dependence on manganese, its ability to perform templated and nontemplated primer extension reactions, and its preference for adding ribonucleotides to blunt DNA ends. Here we report the 1.5-A crystal structure of the Pol domain of Pseudomonas LigD and its complexes with manganese and ATP/dATP substrates, which reveal a minimized polymerase with a two-metal mechanism and a fold similar to that of archaeal DNA primase. Mutational analysis highlights the functionally relevant atomic contacts in the active site. Although distinct nucleoside conformations and contacts for ATP versus dATP are observed in the cocrystals, the functional analysis suggests that the ATP-binding mode is the productive conformation for dNMP and rNMP incorporation. We find that a mutation of Mycobacterium LigD that uniquely ablates the polymerase activity results in increased fidelity of blunt-end double-strand break repair in vivo by virtue of eliminating nucleotide insertions at the recombination junctions. Thus, LigD Pol is a direct catalyst of mutagenic nonhomologous end-joining in vivo. Our studies underscore a previously uncharacterized role for the primase-like polymerase family in DNA repair.

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