Analysis of the DNA joining repertoire of Chlorella virus DNA ligase and a new crystal structure of the ligase-adenylate intermediate Journal Article

Authors: Odell, M.; Malinina, L.; Sriskanda, V.; Teplova, M.; Shuman, S.
Article Title: Analysis of the DNA joining repertoire of Chlorella virus DNA ligase and a new crystal structure of the ligase-adenylate intermediate
Abstract: Chlorella virus DNA ligase is the smallest eukaryotic ATP-dependent DNA ligase known; it suffices for yeast cell growth in lieu of the essential yeast DNA ligase Cdc9. The Chlorella virus ligase-adenylate intermediate has an intrinsic nick sensing function and its DNA footprint extends 8-9 nt on the 3′-hydroxyl (3′-OH) side of the nick and 11-12 nt on the 5′-phosphate (5′-PO4) side. Here we establish the minimal length requirements for ligatable 3′-OH and 5′-PO4 strands at the nick (6 nt) and describe a new crystal structure of the ligase-adenylate in a state construed to reflect the configuration of the active site prior to nick recognition. Comparison with a previous structure of the ligase-adenylate bound to sulfate (a mimetic of the nick 5′-PO4) suggests how the positions and contacts of the active site components and the bound adenylate are remodeled by DNA binding. We find that the minimal Chlorella virus ligase is capable of catalyzing non-homologous end-joining reactions in vivo in yeast, a process normally executed by the structurally more complex cellular Lig4 enzyme. Our results suggest a model of ligase evolution in which: (i) a small 'pluripotent' ligase is the progenitor of the much larger ligases found presently in eukaryotic cells and (ii) gene duplications, variations within the core ligase structure and the fusion of new domains to the core structure (affording new protein-protein interactions) led to the compartmentalization of eukaryotic ligase function, i.e. by enhancing some components of the functional repertoire of the ancestral ligase while disabling others.
Keywords: controlled study; nonhuman; protein domain; cell compartmentalization; dna repair; cell growth; protein protein interaction; in vivo study; enzyme activity; dna; molecular evolution; dna viruses; eukaryota; gene duplication; base sequence; plasmids; crystal structure; crystallography, x-ray; protein structure, tertiary; binding sites; catalysis; protein folding; eukaryotic cell; dna binding; polydeoxyribonucleotide synthase; enzyme structure; phosphate; phosphates; dna determination; protein structure, secondary; yeast cell; chlorella virus; dna ligases; viral proteins; adenosine phosphate; virus dna; dna strand; adenosine monophosphate; sulfate; enzyme precursor; dna footprinting; virus enzyme; hydroxide; priority journal; article; cell enzyme
Journal Title: Nucleic Acids Research
Volume: 31
Issue: 17
ISSN: 0305-1048
Publisher: Oxford University Press  
Date Published: 2003-09-01
Start Page: 5090
End Page: 5100
Language: English
DOI: 10.1093/nar/gkg665
PUBMED: 12930960
PROVIDER: scopus
PMCID: PMC212790
Notes: Export Date: 12 September 2014 -- Source: Scopus
Citation Impact
MSK Authors
  1. Mark Odell
    5 Odell
  2. Stewart H Shuman
    502 Shuman
  3. Marianna Teplova
    17 Teplova