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

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.

Authors:
 [1];  [2];  [1];  [3];  [1];  [2];  [1];  [1]
  1. Univ. of Minnesota, Minneapolis, MN (United States)
  2. Univ. of California, San Diego, La Jolla, CA (United States)
  3. Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS), Northeastern Collaborative Access Team; Cornell Univ., Ithaca, NY (United States)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
National Institutes of Health (NIH); National Science Foundation (NSF); USDOE Office of Science (SC)
OSTI Identifier:
1606455
Grant/Contract Number:  
NCI P01-CA234228; NIGMS R01-GM118000; NIGMS R35-GM118047; NIGMS R01-GM110129; DP2-OD007237; NIGMS P41-GM103426; CHE060073N; NIGMS P30 GM124165; S10 RR029205; AC02-06CH11357
Resource Type:
Accepted Manuscript
Journal Name:
Geography and Sustainability
Additional Journal Information:
Journal Volume: 2; Journal Issue: 1; Journal ID: ISSN 2573-9832
Publisher:
Elsevier
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; active site plasticity; APOBEC3B; cytosine deaminase; DNA mutation; enzymes; molecular dynamics simulations; protein structure; small molecule; x‐ray crystallography; zinc ion

Citation Formats

Shi, Ke, Demir, Özlem, Carpenter, Michael A., Banerjee, Surajit, Harki, Daniel A., Amaro, Rommie E., Harris, Reuben S., and Aihara, Hideki. Active site plasticity and possible modes of chemical inhibition of the human DNA deaminase APOBEC3B. United States: N. p., 2019. Web. https://doi.org/10.1096/fba.2019-00068.
Shi, Ke, Demir, Özlem, Carpenter, Michael A., Banerjee, Surajit, Harki, Daniel A., Amaro, Rommie E., Harris, Reuben S., & Aihara, Hideki. Active site plasticity and possible modes of chemical inhibition of the human DNA deaminase APOBEC3B. United States. https://doi.org/10.1096/fba.2019-00068
Shi, Ke, Demir, Özlem, Carpenter, Michael A., Banerjee, Surajit, Harki, Daniel A., Amaro, Rommie E., Harris, Reuben S., and Aihara, Hideki. Mon . "Active site plasticity and possible modes of chemical inhibition of the human DNA deaminase APOBEC3B". United States. https://doi.org/10.1096/fba.2019-00068. https://www.osti.gov/servlets/purl/1606455.
@article{osti_1606455,
title = {Active site plasticity and possible modes of chemical inhibition of the human DNA deaminase APOBEC3B},
author = {Shi, Ke and Demir, Özlem and Carpenter, Michael A. and Banerjee, Surajit and Harki, Daniel A. and Amaro, Rommie E. and Harris, Reuben S. and Aihara, Hideki},
abstractNote = {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.},
doi = {10.1096/fba.2019-00068},
journal = {Geography and Sustainability},
number = 1,
volume = 2,
place = {United States},
year = {2019},
month = {12}
}

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