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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]
+ Show Author Affiliations
  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 Laboratory (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:
FASEB BioAdvances
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. doi:10.1096/fba.2019-00068.
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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
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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.
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@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 = {FASEB BioAdvances},
number = 1,
volume = 2,
place = {United States},
year = {Mon Dec 02 00:00:00 EST 2019},
month = {Mon Dec 02 00:00:00 EST 2019}
}
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https://doi.org/10.1096/fba.2019-00068
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Works referenced in this record:

Human Papillomavirus E6 Triggers Upregulation of the Antiviral and Cancer Genomic DNA Deaminase APOBEC3B
journal, October 2014

  • Vieira, Valdimara C.; Leonard, Brandon; White, Elizabeth A.
  • mBio, Vol. 5, Issue 6
  • DOI: 10.1128/mBio.02234-14

Conformational Switch Regulates the DNA Cytosine Deaminase Activity of Human APOBEC3B
journal, December 2017

Sticky fingers: zinc-fingers as protein-recognition motifs
journal, February 2007

Determinants of Oligonucleotide Selectivity of APOBEC3B
journal, August 2018

  • Wagner, Jeffrey R.; Demir, Özlem; Carpenter, Michael A.
  • Journal of Chemical Information and Modeling, Vol. 59, Issue 5
  • DOI: 10.1021/acs.jcim.8b00427

Inhibition of the lymphoid tyrosine phosphatase: The effect of zinc(II) ions and chelating ligand fragments on enzymatic activity
journal, August 2014

  • Thorson, Megan K.; Puerta, David T.; Cohen, Seth M.
  • Bioorganic & Medicinal Chemistry Letters, Vol. 24, Issue 16
  • DOI: 10.1016/j.bmcl.2014.06.016

Structural classification of zinc fingers: SURVEY AND SUMMARY
journal, January 2003

Crystal Structure of the APOBEC3G Catalytic Domain Reveals Potential Oligomerization Interfaces
journal, January 2010

  • Shandilya, Shivender M. D.; Nalam, Madhavi N. L.; Nalivaika, Ellen A.
  • Structure, Vol. 18, Issue 1
  • DOI: 10.1016/j.str.2009.10.016

Crystal structure of APOBEC3A bound to single-stranded DNA reveals structural basis for cytidine deamination and specificity
journal, April 2017

  • Kouno, Takahide; Silvas, Tania V.; Hilbert, Brendan J.
  • Nature Communications, Vol. 8, Issue 1
  • DOI: 10.1038/ncomms15024

APOBEC3B is an enzymatic source of mutation in breast cancer
journal, February 2013

  • Burns, Michael B.; Lackey, Lela; Carpenter, Michael A.
  • Nature, Vol. 494, Issue 7437
  • DOI: 10.1038/nature11881

Mechanisms underlying mutational signatures in human cancers
journal, July 2014

  • Helleday, Thomas; Eshtad, Saeed; Nik-Zainal, Serena
  • Nature Reviews Genetics, Vol. 15, Issue 9
  • DOI: 10.1038/nrg3729

1.92 Angstrom Zinc-Free APOBEC3F Catalytic Domain Crystal Structure
journal, June 2016

The Amber biomolecular simulation programs
journal, January 2005

  • Case, David A.; Cheatham, Thomas E.; Darden, Tom
  • Journal of Computational Chemistry, Vol. 26, Issue 16
  • DOI: 10.1002/jcc.20290

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB
journal, July 2015

  • Maier, James A.; Martinez, Carmenza; Kasavajhala, Koushik
  • Journal of Chemical Theory and Computation, Vol. 11, Issue 8
  • DOI: 10.1021/acs.jctc.5b00255

Association of a germline copy number polymorphism of APOBEC3A and APOBEC3B with burden of putative APOBEC-dependent mutations in breast cancer
journal, April 2014

  • Nik-Zainal, Serena; Wedge, David C.; Alexandrov, Ludmil B.
  • Nature Genetics, Vol. 46, Issue 5
  • DOI: 10.1038/ng.2955

Perspective: APOBEC mutagenesis in drug resistance and immune escape in HIV and cancer evolution
journal, March 2018

  • Venkatesan, S.; Rosenthal, R.; Kanu, N.
  • Annals of Oncology, Vol. 29, Issue 3
  • DOI: 10.1093/annonc/mdy003

Modeling the Embrace of a Mutator: APOBEC Selection of Nucleic Acid Ligands
journal, August 2018

Features and development of Coot
journal, March 2010

  • Emsley, P.; Lohkamp, B.; Scott, W. G.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4
  • DOI: 10.1107/S0907444910007493

Enhancing immunity to HIV through APOBEC
journal, October 2008

Epstein–Barr virus BORF2 inhibits cellular APOBEC3B to preserve viral genome integrity
journal, November 2018

  • Cheng, Adam Z.; Yockteng-Melgar, Jaime; Jarvis, Matthew C.
  • Nature Microbiology, Vol. 4, Issue 1
  • DOI: 10.1038/s41564-018-0284-6

The DNA cytosine deaminase APOBEC3H haplotype I likely contributes to breast and lung cancer mutagenesis
journal, September 2016

  • Starrett, Gabriel J.; Luengas, Elizabeth M.; McCann, Jennifer L.
  • Nature Communications, Vol. 7, Issue 1
  • DOI: 10.1038/ncomms12918

PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
  • DOI: 10.1107/S0907444909052925

The structure of Escherichia coli cytosine deaminase 1 1Edited by I. A. Wilson
journal, January 2002

  • Ireton, Gregory C.; McDermott, Gerry; Black, Margaret E.
  • Journal of Molecular Biology, Vol. 315, Issue 4
  • DOI: 10.1006/jmbi.2001.5277

The DNA cytosine deaminase APOBEC3B promotes tamoxifen resistance in ER-positive breast cancer
journal, October 2016

  • Law, Emily K.; Sieuwerts, Anieta M.; LaPara, Kelly
  • Science Advances, Vol. 2, Issue 10
  • DOI: 10.1126/sciadv.1601737

Crystal structure of the catalytic domain of HIV-1 restriction factor APOBEC3G in complex with ssDNA
journal, June 2018

Crystal Structure of the DNA Deaminase APOBEC3B Catalytic Domain
journal, September 2015

  • Shi, Ke; Carpenter, Michael A.; Kurahashi, Kayo
  • Journal of Biological Chemistry, Vol. 290, Issue 47
  • DOI: 10.1074/jbc.M115.679951

Elevated APOBEC3B Correlates with Poor Outcomes for Estrogen-Receptor-Positive Breast Cancers
journal, August 2014

  • Sieuwerts, Anieta M.; Willis, Scooter; Burns, Michael B.
  • Hormones and Cancer, Vol. 5, Issue 6
  • DOI: 10.1007/s12672-014-0196-8

APOBEC Enzymes as Targets for Virus and Cancer Therapy
journal, January 2018

The Local Dinucleotide Preference of APOBEC3G Can Be Altered from 5′-CC to 5′-TC by a Single Amino Acid Substitution
journal, November 2013

  • Rathore, Anurag; Carpenter, Michael A.; Demir, Özlem
  • Journal of Molecular Biology, Vol. 425, Issue 22
  • DOI: 10.1016/j.jmb.2013.07.040

Protein motifs 5. Zinc fingers.
journal, May 1995

An APOBEC3A hypermutation signature is distinguishable from the signature of background mutagenesis by APOBEC3B in human cancers
journal, August 2015

  • Chan, Kin; Roberts, Steven A.; Klimczak, Leszek J.
  • Nature Genetics, Vol. 47, Issue 9
  • DOI: 10.1038/ng.3378

Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B
journal, December 2016

  • Shi, Ke; Carpenter, Michael A.; Banerjee, Surajit
  • Nature Structural & Molecular Biology, Vol. 24, Issue 2
  • DOI: 10.1038/nsmb.3344

Crystal Structure of Yeast Cytosine Deaminase: INSIGHTS INTO ENZYME MECHANISM AND EVOLUTION
journal, March 2003

  • Ko, Tzu-Ping; Lin, Jing-Jer; Hu, Chih-Yung
  • Journal of Biological Chemistry, Vol. 278, Issue 21
  • DOI: 10.1074/jbc.M300874200

Hypermutation in human cancer genomes: footprints and mechanisms
journal, November 2014

  • Roberts, Steven A.; Gordenin, Dmitry A.
  • Nature Reviews Cancer, Vol. 14, Issue 12
  • DOI: 10.1038/nrc3816

APOBEC3 proteins mediate the clearance of foreign DNA from human cells
journal, January 2010

  • Stenglein, Mark D.; Burns, Michael B.; Li, Ming
  • Nature Structural & Molecular Biology, Vol. 17, Issue 2
  • DOI: 10.1038/nsmb.1744

XDS
journal, January 2010

  • Kabsch, Wolfgang
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2
  • DOI: 10.1107/S0907444909047337

Inhibition of Cytidine Deaminase by Derivatives of 1-(β-D-Ribofuranosyl)-Dihydropyrimidin-2-One (Zebularine)
journal, December 1992

  • Barchi, Joseph J.; Haces, Alberto; Marquez, Victor E.
  • Nucleosides and Nucleotides, Vol. 11, Issue 10
  • DOI: 10.1080/07328319208017823

Phaser crystallographic software
journal, July 2007

  • McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
  • Journal of Applied Crystallography, Vol. 40, Issue 4
  • DOI: 10.1107/S0021889807021206

Mechanisms of human lymphoid chromosomal translocations
journal, May 2016

The Amber biomolecular simulation programs
journal, January 2005

  • Case, David A.; Cheatham, Thomas E.; Darden, Tom
  • Journal of Computational Chemistry, Vol. 26, Issue 16
  • DOI: 10.1002/jcc.20290

Elevated APOBEC3B Correlates with Poor Outcomes for Estrogen-Receptor-Positive Breast Cancers
journal, August 2014

  • Sieuwerts, Anieta M.; Willis, Scooter; Burns, Michael B.
  • Hormones and Cancer, Vol. 5, Issue 6
  • DOI: 10.1007/s12672-014-0196-8

Inhibition of the lymphoid tyrosine phosphatase: The effect of zinc(II) ions and chelating ligand fragments on enzymatic activity
journal, August 2014

  • Thorson, Megan K.; Puerta, David T.; Cohen, Seth M.
  • Bioorganic & Medicinal Chemistry Letters, Vol. 24, Issue 16
  • DOI: 10.1016/j.bmcl.2014.06.016

APOBEC Enzymes as Targets for Virus and Cancer Therapy
journal, January 2018

The Local Dinucleotide Preference of APOBEC3G Can Be Altered from 5′-CC to 5′-TC by a Single Amino Acid Substitution
journal, November 2013

  • Rathore, Anurag; Carpenter, Michael A.; Demir, Özlem
  • Journal of Molecular Biology, Vol. 425, Issue 22
  • DOI: 10.1016/j.jmb.2013.07.040

1.92 Angstrom Zinc-Free APOBEC3F Catalytic Domain Crystal Structure
journal, June 2016

Crystal Structure of the APOBEC3G Catalytic Domain Reveals Potential Oligomerization Interfaces
journal, January 2010

  • Shandilya, Shivender M. D.; Nalam, Madhavi N. L.; Nalivaika, Ellen A.
  • Structure, Vol. 18, Issue 1
  • DOI: 10.1016/j.str.2009.10.016

Sticky fingers: zinc-fingers as protein-recognition motifs
journal, February 2007

DNA Deamination Mediates Innate Immunity to Retroviral Infection
journal, June 2003

Zinc finger proteins: new insights into structural and functional diversity
journal, February 2001

Determinants of Oligonucleotide Selectivity of APOBEC3B
journal, August 2018

  • Wagner, Jeffrey R.; Demir, Özlem; Carpenter, Michael A.
  • Journal of Chemical Information and Modeling, Vol. 59, Issue 5
  • DOI: 10.1021/acs.jcim.8b00427

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB
journal, July 2015

  • Maier, James A.; Martinez, Carmenza; Kasavajhala, Koushik
  • Journal of Chemical Theory and Computation, Vol. 11, Issue 8
  • DOI: 10.1021/acs.jctc.5b00255

Small-molecule inhibition of HIV-1 Vif
journal, September 2008

  • Nathans, Robin; Cao, Hong; Sharova, Natalia
  • Nature Biotechnology, Vol. 26, Issue 10
  • DOI: 10.1038/nbt.1496

The DNA cytosine deaminase APOBEC3H haplotype I likely contributes to breast and lung cancer mutagenesis
journal, September 2016

  • Starrett, Gabriel J.; Luengas, Elizabeth M.; McCann, Jennifer L.
  • Nature Communications, Vol. 7, Issue 1
  • DOI: 10.1038/ncomms12918

Crystal structure of APOBEC3A bound to single-stranded DNA reveals structural basis for cytidine deamination and specificity
journal, April 2017

  • Kouno, Takahide; Silvas, Tania V.; Hilbert, Brendan J.
  • Nature Communications, Vol. 8, Issue 1
  • DOI: 10.1038/ncomms15024

Association of a germline copy number polymorphism of APOBEC3A and APOBEC3B with burden of putative APOBEC-dependent mutations in breast cancer
journal, April 2014

  • Nik-Zainal, Serena; Wedge, David C.; Alexandrov, Ludmil B.
  • Nature Genetics, Vol. 46, Issue 5
  • DOI: 10.1038/ng.2955

An APOBEC3A hypermutation signature is distinguishable from the signature of background mutagenesis by APOBEC3B in human cancers
journal, August 2015

  • Chan, Kin; Roberts, Steven A.; Klimczak, Leszek J.
  • Nature Genetics, Vol. 47, Issue 9
  • DOI: 10.1038/ng.3378

Human cells clear foreign DNA
journal, February 2010

  • Flintoft, Louisa
  • Nature Reviews Genetics, Vol. 11, Issue 3
  • DOI: 10.1038/nrg2757

Mechanisms underlying mutational signatures in human cancers
journal, July 2014

  • Helleday, Thomas; Eshtad, Saeed; Nik-Zainal, Serena
  • Nature Reviews Genetics, Vol. 15, Issue 9
  • DOI: 10.1038/nrg3729

Crystal structure of the catalytic domain of HIV-1 restriction factor APOBEC3G in complex with ssDNA
journal, June 2018

APOBEC restriction goes nuclear
journal, December 2018

Conformational Switch Regulates the DNA Cytosine Deaminase Activity of Human APOBEC3B
journal, December 2017

Innate Immune Signaling Induces High Levels of TC-specific Deaminase Activity in Primary Monocyte-derived Cells through Expression of APOBEC3A Isoforms
journal, July 2010

  • Thielen, Beth K.; McNevin, John P.; McElrath, M. Juliana
  • Journal of Biological Chemistry, Vol. 285, Issue 36
  • DOI: 10.1074/jbc.m110.102822

Perspective: APOBEC mutagenesis in drug resistance and immune escape in HIV and cancer evolution
journal, March 2018

  • Venkatesan, S.; Rosenthal, R.; Kanu, N.
  • Annals of Oncology, Vol. 29, Issue 3
  • DOI: 10.1093/annonc/mdy003

Structural classification of zinc fingers: SURVEY AND SUMMARY
journal, January 2003

The DNA cytosine deaminase APOBEC3B promotes tamoxifen resistance in ER-positive breast cancer
journal, October 2016

  • Law, Emily K.; Sieuwerts, Anieta M.; LaPara, Kelly
  • Science Advances, Vol. 2, Issue 10
  • DOI: 10.1126/sciadv.1601737

Functional Upregulation of the DNA Cytosine Deaminase APOBEC3B by Polyomaviruses
journal, May 2016

  • Verhalen, Brandy; Starrett, Gabriel J.; Harris, Reuben S.
  • Journal of Virology, Vol. 90, Issue 14
  • DOI: 10.1128/jvi.00771-16

APOBEC3B Upregulation and Genomic Mutation Patterns in Serous Ovarian Carcinoma
journal, October 2013

APOBEC Enzymes: Mutagenic Fuel for Cancer Evolution and Heterogeneity
journal, June 2015

PHENIX: a comprehensive Python-based system for macromolecular structure solution.
text, January 2010

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Apollo - University of Cambridge Repository
  • DOI: 10.17863/cam.45787
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