Active site plasticity and possible modes of chemical inhibition of the human DNA deaminase APOBEC3B

Ke Shi, Özlem Demir, Michael A Carpenter, Surajit Banerjee, Daniel A Harki, Rommie E. Amaro, Reuben S. Harris, Hideki Aihara

Research output: Contribution to journalArticlepeer-review

Abstract

The single-stranded DNA cytosine deaminase APOBEC3B (A3B) functions in innate immunity against viruses, but it is also strongly implicated in eliciting mutations in cancer genomes. Because of the critical role of A3B in promoting virus and tumor evolution, small molecule inhibitors are desirable. However, there is no reported structure for any of the APOBEC3-family enzymes in complex with a small molecule bound in the active site, which hampers the development of small molecules targeting A3B. Here we report high-resolution structures of an active A3B catalytic domain chimera with loop 7 residues exchanged with those from the corresponding region of APOBEC3G (A3G). The structures reveal novel open conformations lacking the catalytically essential zinc ion, with the highly conserved active site residues extensively rearranged. These inactive conformations are stabilized by 2-pyrimidone or an iodide ion bound in the active site. Molecular dynamics simulations corroborate the remarkable plasticity of the engineered active site and identify key interactions that stabilize the native A3B active site. These data provide insights into A3B active site dynamics and suggest possible modes of its inhibition by small molecules, which would aid in rational design of selective A3B inhibitors for constraining virus and tumor evolution.

Original languageEnglish (US)
Article number doi: 10.1096/fba.2019-00068
Pages (from-to)49-58
Number of pages10
JournalFASEB BioAdvances
Volume2
Issue number1
DOIs
StatePublished - Dec 14 2019

Bibliographical note

Funding Information:
We thank Stephanie Breunig for synthesizing 2'-deoxyzebularine, Justin Oakland for performing the zinc content analysis, and Kayo Orellana for purifying the proteins used in this study. This work was supported by grants from the US National Institutes of Health (NCI P01-CA234228 to RSH, HA, REA, and DAH, NIGMS R01-GM118000 to RSH and HA, NIGMS R35-GM118047 to HA, NIGMS R01-GM110129 to DAH, DP2-OD007237 and NIGMS P41-GM103426 to REA) and the NSF (CHE060073N to REA). This work is based upon research conducted at the Northeastern Collaborative Access Team beamlines, which are funded by the US National Institutes of Health (NIGMS P30 GM124165). The Pilatus 6M detector on 24-ID-C beamline is funded by a NIH-ORIP HEI 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 No. DE-AC02-06CH11357, and those of the Minnesota Supercomputing Institute. RSH is the Margaret Harvey Schering Land Grant Chair for Cancer Research, a Distinguished McKnight University Professor, and an Investigator of the Howard Hughes Medical Institute.

Funding Information:
We thank Stephanie Breunig for synthesizing 2'‐deoxyzebularine, Justin Oakland for performing the zinc content analysis, and Kayo Orellana for purifying the proteins used in this study. This work was supported by grants from the US National Institutes of Health (NCI P01‐CA234228 to RSH, HA, REA, and DAH, NIGMS R01‐GM118000 to RSH and HA, NIGMS R35‐GM118047 to HA, NIGMS R01‐GM110129 to DAH, DP2‐OD007237 and NIGMS P41‐GM103426 to REA) and the NSF (CHE060073N to REA). This work is based upon research conducted at the Northeastern Collaborative Access Team beamlines, which are funded by the US National Institutes of Health (NIGMS P30 GM124165). The Pilatus 6M detector on 24‐ID‐C beamline is funded by a NIH‐ORIP HEI 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 No. DE‐AC02‐06CH11357, and those of the Minnesota Supercomputing Institute. RSH is the Margaret Harvey Schering Land Grant Chair for Cancer Research, a Distinguished McKnight University Professor, and an Investigator of the Howard Hughes Medical Institute.

Publisher Copyright:
© 2019 The Authors.

Keywords

  • active site plasticity
  • APOBEC3B
  • cytosine deaminase
  • DNA mutation
  • enzymes
  • molecular dynamics simulations
  • protein structure
  • small molecule
  • x-ray crystallography
  • zinc ion

PubMed: MeSH publication types

  • Journal Article

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