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Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease.

Nakae S, Hijikata A, Tsuji T, Yonezawa K, Kouyama KI, Mayanagi K, Ishino S, Ishino Y, Shirai T
Structure 24 1960-1971 (2016)
Related entries: 5gkf, 5gkg, 5gkh, 5gki, 5gkj

Cited: 30 times
EuropePMC logo PMID: 27773688

Abstract

Archaeal NucS nuclease was thought to degrade the single-stranded region of branched DNA, which contains flapped and splayed DNA. However, recent findings indicated that EndoMS, the orthologous enzyme of NucS, specifically cleaves double-stranded DNA (dsDNA) containing mismatched bases. In this study, we determined the structure of the EndoMS-DNA complex. The complex structure of the EndoMS dimer with dsDNA unexpectedly revealed that the mismatched bases were flipped out into binding sites, and the overall architecture most resembled that of restriction enzymes. The structure of the apo form was similar to the reported structure of Pyrococcus abyssi NucS, indicating that movement of the C-terminal domain from the resting state was required for activity. In addition, a model of the EndoMS-PCNA-DNA complex was preliminarily verified with electron microscopy. The structures strongly support the idea that EndoMS acts in a mismatch repair pathway.

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  1. The Card1 nuclease provides defence during type III CRISPR immunity. Rostøl JT, Xie W, Kuryavyi V, Maguin P, Kao K, Froom R, Patel DJ, Marraffini LA. Nature 590 624-629 (2021)
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  3. Activation of the mismatch-specific endonuclease EndoMS/NucS by the replication clamp is required for high fidelity DNA replication. Ishino S, Skouloubris S, Kudo H, l'Hermitte-Stead C, Es-Sadik A, Lambry JC, Ishino Y, Myllykallio H. Nucleic Acids Res 46 6206-6217 (2018)
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  5. Exploring the Binding Mechanism and Dynamics of EndoMS/NucS to Mismatched dsDNA. Zhang Y, Huang S. Int J Mol Sci 20 E5142 (2019)
  6. research-article Bacterial Shedu immune nucleases share a common enzymatic core regulated by diverse sensor domains. Gu Y, Li H, Deep A, Enustun E, Zhang D, Corbett KD. bioRxiv 2023.08.10.552793 (2023)
  7. Engineering of the DNA replication and repair machinery to develop binary mutators for rapid genome evolution of Corynebacterium glutamicum. Cai N, Chen J, Gao N, Ni X, Lei Y, Pu W, Wang L, Che B, Fan L, Zhou W, Feng J, Wang Y, Zheng P, Sun J. Nucleic Acids Res 51 8623-8642 (2023)


Reviews citing this publication (9)

  1. DNA repair in the archaea-an emerging picture. White MF, Allers T. FEMS Microbiol Rev 42 514-526 (2018)
  2. Structure and mechanism of the Red recombination system of bacteriophage λ. Caldwell BJ, Bell CE. Prog Biophys Mol Biol 147 33-46 (2019)
  3. Archaeal DNA Repair Mechanisms. Marshall CJ, Santangelo TJ. Biomolecules 10 E1472 (2020)
  4. Bacterial DNA excision repair pathways. Wozniak KJ, Simmons LA. Nat Rev Microbiol 20 465-477 (2022)
  5. Haloferax volcanii-a model archaeon for studying DNA replication and repair. Pérez-Arnaiz P, Dattani A, Smith V, Allers T. Open Biol 10 200293 (2020)
  6. New Insights Into DNA Repair Revealed by NucS Endonucleases From Hyperthermophilic Archaea. Zhang L, Jiang D, Wu M, Yang Z, Oger PM. Front Microbiol 11 1263 (2020)
  7. An overview of 25 years of research on Thermococcus kodakarensis, a genetically versatile model organism for archaeal research. Rashid N, Aslam M. Folia Microbiol (Praha) 65 67-78 (2020)
  8. Repair of Hypoxanthine in DNA Revealed by DNA Glycosylases and Endonucleases From Hyperthermophilic Archaea. Lin T, Zhang L, Wu M, Jiang D, Li Z, Yang Z. Front Microbiol 12 736915 (2021)
  9. Control of Genome Stability by EndoMS/NucS-Mediated Non-Canonical Mismatch Repair. Cebrián-Sastre E, Martín-Blecua I, Gullón S, Blázquez J, Castañeda-García A. Cells 10 1314 (2021)

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