Structural basis for recognition of distinct deaminated DNA lesions by endonuclease Q

Ke Shi, Nicholas H. Moeller, Surajit Banerjee, Jennifer L. McCann, Michael A. Carpenter, Lulu Yin, Ramkumar Moorthy, Kayo Orellana, Daniel A. Harki, Reuben S. Harris, Hideki Aihara

Research output: Contribution to journalArticlepeer-review

Abstract

Spontaneous deamination of DNA cytosine and adenine into uracil and hypoxanthine, respectively, causes C to T and A to G transition mutations if left unrepaired. Endonuclease Q (EndoQ) initiates the repair of these premutagenic DNA lesions in prokaryotes by cleaving the phosphodiester backbone 5′ of either uracil or hypoxanthine bases or an apurinic/apyrimidinic (AP) lesion generated by the excision of these damaged bases. To understand how EndoQ achieves selectivity toward these structurally diverse substrates without cleaving undamaged DNA, we determined the crystal structures of Pyrococcus furiosus EndoQ bound to DNA substrates containing uracil, hypoxanthine, or an AP lesion. The structures show that substrate engagement by EndoQ depends both on a highly distorted conformation of the DNA backbone, in which the target nucleotide is extruded out of the helix, and direct hydrogen bonds with the deaminated bases. A concerted swing motion of the zinc-binding and C-terminal helical domains of EndoQ toward its catalytic domain allows the enzyme to clamp down on a sharply bent DNA substrate, shaping a deep active-site pocket that accommodates the extruded deaminated base. Within this pocket, uracil and hypoxanthine bases interact with distinct sets of amino acid residues, with positioning mediated by an essential magnesium ion. The EndoQ–DNA complex structures reveal a unique mode of damaged DNA recognition and provide mechanistic insights into the initial step of DNA damage repair by the alternative excision repair pathway. Furthermore, we demonstrate that the unique activity of EndoQ is useful for studying DNA deamination and repair in mammalian systems.

Original languageEnglish (US)
Article numbere2021120118
JournalProceedings of the National Academy of Sciences of the United States of America
Volume118
Issue number10
DOIs
StatePublished - Mar 9 2021

Bibliographical note

Funding Information:
This work was supported by NIH Grants R35-GM118047 (to H.A.) and P01-CA234228 (to D.A.H., R.S.H., and H.A.). This work is based on research conducted at the NE-CAT beamlines, which are funded by the NIH (P30 GM124165). The Pilatus 6M detector on 24-ID-C beamline is funded by a NIH-Office of Research Infrastructure Programs High-End Instrumentation grant (S10 RR029205). This research used resources of the Advanced Photon Source, a US Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract DE-AC02-06CH11357, and those of the Minnesota Supercomputing Institute. R.S.H. is the Margaret Harvey Schering Land Grant Chair for Cancer Research, a Distinguished University McKnight Professor, and an Investigator of the Howard Hughes Medical Institute.

Publisher Copyright:
© 2021 National Academy of Sciences. All rights reserved.

Keywords

  • DNA damage repair
  • DNA deamination
  • Deoxyinosine
  • Deoxyuridine
  • Endonuclease

PubMed: MeSH publication types

  • Journal Article

Fingerprint Dive into the research topics of 'Structural basis for recognition of distinct deaminated DNA lesions by endonuclease Q'. Together they form a unique fingerprint.

Cite this