Solution NMR studies of chlorella virus DNA ligase-adenylate Journal Article
| Authors: | Piserchio, A.; Nair, P. A.; Shuman, S.; Ghose, R. |
| Article Title: | Solution NMR studies of chlorella virus DNA ligase-adenylate |
| Abstract: | DNA ligases are essential guardians of genome integrity by virtue of their ability to recognize and seal 3′-OH/5′-phosphate nicks in duplex DNA. The substrate binding and three chemical steps of the ligation pathway are coupled to global and local changes in ligase structure, involving both massive protein domain movements and subtle remodeling of atomic contacts in the active site. Here we applied solution NMR spectroscopy to study the conformational dynamics of the Chlorella virus DNA ligase (ChVLig), a minimized eukaryal ATP-dependent ligase consisting of nucleotidyltransferase, OB, and latch domains. Our analysis of backbone 15N spin relaxation and 15N,1H residual dipolar couplings of the covalent ChVLig-AMP intermediate revealed conformational sampling on fast (picosecond to nanosecond) and slow timescales (microsecond to millisecond), indicative of interdomain and intradomain flexibility. We identified local and global changes in ChVLig-AMP structure and dynamics induced by phosphate. In particular, the chemical shift perturbations elicited by phosphate were clustered in the peptide motifs that comprise the active site. We hypothesize that phosphate anion mimics some of the conformational transitions that occur when ligase-adenylate interacts with the nick 5′-phosphate. © 2009 Elsevier Ltd. All rights reserved. |
| Keywords: | controlled study; nonhuman; protein conformation; dna repair; dna; kinetics; recombinant fusion proteins; enzyme analysis; eukaryota; substrate specificity; nuclear magnetic resonance spectroscopy; models, molecular; thermodynamics; protein structure, tertiary; conformational transition; adenosine triphosphate; polydeoxyribonucleotide synthase; catalytic domain; phosphates; proton nuclear magnetic resonance; chlorella virus; paramecium; dna ligases; viral proteins; adenosine phosphate; nucleotidyltransferase; nucleic acid structure; dna conformation; nuclear magnetic resonance, biomolecular; virus dna; atp-dependent dna ligase; protein dynamics; residual dipolar couplings; spin-relaxation; global change; nitrogen nuclear magnetic resonance; adenosine monophosphate |
| Journal Title: | Journal of Molecular Biology |
| Volume: | 395 |
| Issue: | 2 |
| ISSN: | 0022-2836 |
| Publisher: | Academic Press Inc., Elsevier Science |
| Date Published: | 2010-01-15 |
| Start Page: | 291 |
| End Page: | 308 |
| Language: | English |
| DOI: | 10.1016/j.jmb.2009.11.007 |
| PUBMED: | 19913033 |
| PROVIDER: | scopus |
| PMCID: | PMC2813346 |
| DOI/URL: | |
| Notes: | --- - "Cited By (since 1996): 1" - "Export Date: 20 April 2011" - "CODEN: JMOBA" - "Source: Scopus" |
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