Atomic structure and nonhomologous end-joining function of the polymerase component of bacterial DNA ligase D Journal Article
| Authors: | Zhu, H.; Nandakumar, J.; Aniukwu, J.; Wang, L. K.; Glickman, M. S.; Lima, C. D.; Shuman, S. |
| Article Title: | Atomic structure and nonhomologous end-joining function of the polymerase component of bacterial DNA ligase D |
| Abstract: | 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-Å 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. © 2006 by The National Academy of Sciences of the USA. |
| Keywords: | unclassified drug; mutation; nonhuman; protein domain; dna recombination; dna repair; phosphatase; enzyme activity; bacteria (microorganisms); dna strand breakage; molecular sequence data; base sequence; crystal structure; models, molecular; crystallography, x-ray; protein structure, tertiary; binding sites; catalysis; adenosine triphosphate; conformation; protein folding; polydeoxyribonucleotide synthase; enzyme structure; mycobacterium; corynebacterineae; archaebacterium; archaea; enzyme mechanism; structural homology, protein; dna ligases; enzyme active site; double-strand breaks; ribonucleotide; pseudomonas aeruginosa; dna-directed dna polymerase; dna ligase d; manganese; pseudomonas; mycobacteria; deoxyadenosine triphosphate |
| Journal Title: | Proceedings of the National Academy of Sciences of the United States of America |
| Volume: | 103 |
| Issue: | 6 |
| ISSN: | 0027-8424 |
| Publisher: | National Academy of Sciences |
| Date Published: | 2006-02-07 |
| Start Page: | 1711 |
| End Page: | 1716 |
| Language: | English |
| DOI: | 10.1073/pnas.0509083103 |
| PUBMED: | 16446439 |
| PROVIDER: | scopus |
| PMCID: | PMC1413644 |
| DOI/URL: | |
| Notes: | --- - "Cited By (since 1996): 26" - "Export Date: 4 June 2012" - "CODEN: PNASA" - "Source: Scopus" |
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