Solution structure and DNA-binding properties of the phosphoesterase domain of DNA ligase D Journal Article
| Authors: | Natarajan, A.; Dutta, K.; Temel, D. B.; Nair, P. A.; Shuman, S.; Ghose, R. |
| Article Title: | Solution structure and DNA-binding properties of the phosphoesterase domain of DNA ligase D |
| Abstract: | The phosphoesterase (PE) domain of the bacterial DNA repair enzyme LigD possesses distinctive manganese-dependent 3′-phosphomonoesterase and 3′-phosphodiesterase activities. PE exemplifies a new family of DNA end-healing enzymes found in all phylogenetic domains. Here, we determined the structure of the PE domain of Pseudomonas aeruginosa LigD (PaePE) using solution NMR methodology. PaePE has a disordered N-terminus and a well-folded core that differs in instructive ways from the crystal structure of a PaePEMn 2+ sulfate complex, especially at the active site that is found to be conformationally dynamic. Chemical shift perturbations in the presence of primer-template duplexes with 3′-deoxynucleotide, 3′-deoxynucleotide 3′-phosphate, or 3′ ribonucleotide termini reveal the surface used by PaePE to bind substrate DNA and suggest a more efficient engagement in the presence of a 3′-ribonucleotide. Spectral perturbations measured in the presence of weakly catalytic (Cd 2+) and inhibitory (Zn 2+) metals provide evidence for significant conformational changes at and near the active site, compared to the relatively modest changes elicited by Mn 2+. © 2011 The Author(s). |
| Keywords: | controlled study; unclassified drug; dna-binding proteins; nonhuman; protein domain; fluorescence; protein binding; protein interaction; bacteria (microorganisms); dna; amino terminal sequence; nuclear magnetic resonance spectroscopy; crystal structure; models, molecular; crystallography, x-ray; protein structure, tertiary; conformational transition; protein folding; zinc; dna binding; polydeoxyribonucleotide synthase; enzyme structure; metals; proton nuclear magnetic resonance; dna ligases; enzyme active site; enzyme conformation; nuclear magnetic resonance, biomolecular; pseudomonas aeruginosa; dna ligase d; manganese; deoxyribonucleotide; cadmium; nuclear overhauser effect; manganese sulfate |
| Journal Title: | Nucleic Acids Research |
| Volume: | 40 |
| Issue: | 5 |
| ISSN: | 0305-1048 |
| Publisher: | Oxford University Press |
| Date Published: | 2012-03-01 |
| Start Page: | 2076 |
| End Page: | 2088 |
| Language: | English |
| DOI: | 10.1093/nar/gkr950 |
| PROVIDER: | scopus |
| PMCID: | PMC3300020 |
| PUBMED: | 22084199 |
| DOI/URL: | |
| Notes: | --- - "Export Date: 2 April 2012" - "CODEN: NARHA" - "Source: Scopus" |
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