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Related Experiment Videos

Structural basis for nick recognition by a minimal pluripotent DNA ligase.

Pravin A Nair1, Jayakrishnan Nandakumar, Paul Smith

  • 1Molecular Biology and Structural Biology Programs, Sloan-Kettering Institute, New York, New York 10021, USA.

Nature Structural & Molecular Biology
|July 10, 2007
PubMed
Summary
This summary is machine-generated.

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Chlorella virus DNA ligase, the smallest known eukaryotic ligase, uses a unique beta-hairpin

Area of Science:

  • Structural Biology
  • Molecular Biology
  • Biochemistry

Background:

  • Cellular DNA ligases possess accessory domains for nick sensing and DNA binding.
  • Chlorella virus DNA ligase is the smallest known eukaryotic ligase, lacking these accessory domains.
  • The intrinsic nick-sensing capability of this viral ligase remains mechanistically uncharacterized.

Purpose of the Study:

  • To elucidate the structural basis of nick sensing and DNA repair activity in Chlorella virus DNA ligase.
  • To understand the mechanism of DNA adenylylation and catalysis by this unique viral enzyme.

Main Methods:

  • X-ray crystallography of Chlorella virus DNA ligase complexed with AMP and nicked DNA at 2.3-A resolution.
  • In crystallo assays to observe DNA nick sealing upon divalent cation addition.

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Main Results:

  • A novel DNA envelopment mode was revealed, featuring a beta-hairpin 'latch' from the OB domain interacting with the DNA major groove near the nick.
  • Specific interactions between the enzyme's active site, AMP, and the 3'-OH/5'-PO4 termini explain nick sensing and adenylylation.
  • Divalent cation addition induced DNA nick sealing in the crystal, confirming the observed complex as a functional intermediate.

Conclusions:

  • Chlorella virus DNA ligase employs a unique structural mechanism for nick sensing and DNA repair, distinct from cellular ligases.
  • The AMP-bound intermediate is crucial for both sensing DNA nicks and catalyzing the ligation reaction.
  • This study provides insights into viral DNA repair strategies and the fundamental mechanisms of DNA ligation.