Crystal Structure of the First Eubacterial Mre11 Nuclease Reveals Novel Features that May Discriminate Substrates During DNA Repair

Debanu Das, Davide Moiani, Herbert L. Axelrod, Mitchell D. Miller, Daniel McMullan, Kevin K. Jin, Polat Abdubek, Tamara Astakhova, Prasad Burra, Dennis Carlton, Hsiu Ju Chiu, Thomas Clayton, Marc C. Deller, Lian Duan, Dustin Ernst, Julie Feuerhelm, Joanna C. Grant, Anna Grzechnik, Slawomir K. Grzechnik, Gye Won HanLukasz Jaroszewski, Heath E. Klock, Mark W. Knuth, Piotr Kozbial, S. Sri Krishna, Abhinav Kumar, David Marciano, Andrew T. Morse, Edward Nigoghossian, Linda Okach, Jessica Paulsen, Ron Reyes, Christopher L. Rife, Natasha Sefcovic, Henry J. Tien, Christine B. Trame, Henry van den Bedem, Dana Weekes, Qingping Xu, Keith O. Hodgson, John Wooley, Marc André Elsliger, Ashley M. Deacon, Adam Godzik, Scott A. Lesley, John A. Tainer, Ian A. Wilson

Research output: Contribution to journalArticlepeer-review

37 Scopus citations

Abstract

Mre11 nuclease plays a central role in the repair of cytotoxic and mutagenic DNA double-strand breaks. As X-ray structural information has been available only for the Pyrococcus furiosus enzyme (PfMre11), the conserved and variable features of this nuclease across the domains of life have not been experimentally defined. Our crystal structure and biochemical studies demonstrate that TM1635 from Thermotoga maritima, originally annotated as a putative nuclease, is an Mre11 endo/exonuclease (TmMre11) and the first such structure from eubacteria. TmMre11 and PfMre11 display similar overall structures, despite sequence identity in the twilight zone of only ∼20%. However, they differ substantially in their DNA-specificity domains and in their dimeric organization. Residues in the nuclease domain are highly conserved, but those in the DNA-specificity domain are not. The structural differences likely affect how Mre11 from different organisms recognize and interact with single-stranded DNA, double-stranded DNA and DNA hairpin structures during DNA repair. The TmMre11 nuclease active site has no bound metal ions, but is conserved in sequence and structure with the exception of a histidine that is important in PfMre11 nuclease activity. Nevertheless, biochemical characterization confirms that TmMre11 possesses both endonuclease and exonuclease activities on single-stranded and double-stranded DNA substrates, respectively.

Original languageEnglish (US)
Pages (from-to)647-663
Number of pages17
JournalJournal of Molecular Biology
Volume397
Issue number3
DOIs
StatePublished - Apr 2 2010
Externally publishedYes

Keywords

  • DNA repair
  • Mre11
  • crystal structure
  • nuclease
  • structural genomics

ASJC Scopus subject areas

  • Biophysics
  • Structural Biology
  • Molecular Biology

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