Structural snapshots of base excision by the cancer-associated variant MutY N146S reveal a retaining mechanism

Demir, Merve; Russelburg, L. Peyton; Lin, Wen-Jen; Trasviña-Arenas, Carlos H.; Huang, Beili; Yuen, Philip K.; Horvath, Martin P.; David, Sheila S.

doi:10.1093/nar/gkac1246

Title: Structural snapshots of base excision by the cancer-associated variant MutY N146S reveal a retaining mechanism

Journal Article · 11 January 2023 · Nucleic Acids Research

DOI: https://doi.org/10.1093/nar/gkac1246 · OSTI ID:1908839

Demir, Merve; Russelburg, L. Peyton;

; Trasviña-Arenas, Carlos H.; Huang, Beili; Yuen, Philip K.; Horvath, Martin P.;

Abstract DNA glycosylase MutY plays a critical role in suppression of mutations resulted from oxidative damage, as highlighted by cancer-association of the human enzyme. MutY requires a highly conserved catalytic Asp residue for excision of adenines misinserted opposite 8-oxo-7,8-dihydroguanine (OG). A nearby Asn residue hydrogen bonds to the catalytic Asp in structures of MutY and its mutation to Ser is an inherited variant in human MUTYH associated with colorectal cancer. We captured structural snapshots of N146S Geobacillus stearothermophilus MutY bound to DNA containing a substrate, a transition state analog and enzyme-catalyzed abasic site products to provide insight into the base excision mechanism of MutY and the role of Asn. Surprisingly, despite the ability of N146S to excise adenine and purine (P) in vitro, albeit at slow rates, N146S-OG:P complex showed a calcium coordinated to the purine base altering its conformation to inhibit hydrolysis. We obtained crystal structures of N146S Gs MutY bound to its abasic site product by removing the calcium from crystals of N146S-OG:P complex to initiate catalysis in crystallo or by crystallization in the absence of calcium. The product structures of N146S feature enzyme-generated β-anomer abasic sites that support a retaining mechanism for MutY-catalyzed base excision.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Advanced Light Source (ALS)

Sponsoring Organization:: National Institutes of Health (NIH); National Science Foundation (NSF); USDOE Office of Science (SC), Basic Energy Sciences (BES); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1908839

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: 3 Vol. 51; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United Kingdom

Language:: English

References (50)

UCSF Chimera?A visualization system for exploratory research and analysis Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C. Journal of Computational Chemistry, Vol. 25, Issue 13 https://doi.org/10.1002/jcc.20084	journal	January 2004
UCSF ChimeraX : Structure visualization for researchers, educators, and developers Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C. Protein Science, Vol. 30, Issue 1 https://doi.org/10.1002/pro.3943	journal	October 2020
Seeds to crystals Bergfors, Terese Journal of Structural Biology, Vol. 142, Issue 1 https://doi.org/10.1016/S1047-8477(03)00039-X	journal	April 2003
Dissection of nucleophilic and acid–base catalysis in glycosidases Zechel, David L.; Withers, Stephen G. Current Opinion in Chemical Biology, Vol. 5, Issue 6 https://doi.org/10.1016/S1367-5931(01)00260-5	journal	December 2001
Profiling base excision repair glycosylases with synthesized transition state analogs Chu, Aurea M.; Fettinger, James C.; David, Sheila S. Bioorganic & Medicinal Chemistry Letters, Vol. 21, Issue 17 https://doi.org/10.1016/j.bmcl.2011.05.085	journal	September 2011
Catalytic Contributions of Key Residues in the Adenine Glycosylase MutY Revealed by pH-dependent Kinetics and Cellular Repair Assays Brinkmeyer, Megan K.; Pope, Mary Ann; David, Sheila S. Chemistry & Biology, Vol. 19, Issue 2 https://doi.org/10.1016/j.chembiol.2011.11.011	journal	February 2012
When you’re strange: Unusual features of the MUTYH glycosylase and implications in cancer Raetz, Alan G.; David, Sheila S. DNA Repair, Vol. 80 https://doi.org/10.1016/j.dnarep.2019.05.005	journal	August 2019
A Structural Hinge in Eukaryotic MutY Homologues Mediates Catalytic Activity and Rad9–Rad1–Hus1 Checkpoint Complex Interactions Luncsford, Paz J.; Chang, Dau-Yin; Shi, Guoli Journal of Molecular Biology, Vol. 403, Issue 3 https://doi.org/10.1016/j.jmb.2010.08.045	journal	October 2010
Structural Insights into the Mechanism of Base Excision by MBD4 Pidugu, Lakshmi S.; Bright, Hilary; Lin, Wen-Jen Journal of Molecular Biology, Vol. 433, Issue 15 https://doi.org/10.1016/j.jmb.2021.167097	journal	July 2021
Unexpected Complexity in the Products Arising from NaOH-, Heat-, Amine-, and Glycosylase-Induced Strand Cleavage at an Abasic Site in DNA Haldar, Tuhin; Jha, Jay S.; Yang, Zhiyu Chemical Research in Toxicology, Vol. 35, Issue 2 https://doi.org/10.1021/acs.chemrestox.1c00409	journal	February 2022
Correlation between Charge Transport and Base Excision Repair in the MutY–DNA Glycosylase Teo, Ruijie D.; Du, Xiaochen; Vera, Héctor Luis Torres The Journal of Physical Chemistry B, Vol. 125, Issue 1 https://doi.org/10.1021/acs.jpcb.0c08598	journal	December 2020
Structure–Activity Relationships Reveal Key Features of 8-Oxoguanine: A Mismatch Detection by the MutY Glycosylase Manlove, Amelia H.; McKibbin, Paige L.; Doyle, Emily L. ACS Chemical Biology, Vol. 12, Issue 9 https://doi.org/10.1021/acschembio.7b00389	journal	August 2017
Structural Basis for Finding OG Lesions and Avoiding Undamaged G by the DNA Glycosylase MutY Russelburg, L. Peyton; O’Shea Murray, Valerie L.; Demir, Merve ACS Chemical Biology, Vol. 15, Issue 1 https://doi.org/10.1021/acschembio.9b00639	journal	October 2019
Dissecting the Electrostatic Interactions and pH-Dependent Activity of a Family 11 Glycosidase ^† ^, ^‡ Joshi, Manish D.; Sidhu, Gary; Nielsen, Jens E. Biochemistry, Vol. 40, Issue 34 https://doi.org/10.1021/bi0105429	journal	August 2001
A Residue in MutY Important for Catalysis Identified by Photocross-Linking and Mass Spectrometry Chepanoske, Cindy Lou; Lukianova, Olga A.; Lombard, Murielle Biochemistry, Vol. 43, Issue 3 https://doi.org/10.1021/bi035537e	journal	December 2003
Insight into the Roles of Tyrosine 82 and Glycine 253 in the Escherichia coli Adenine Glycosylase MutY Livingston, Alison L.; Kundu, Sucharita; Henderson Pozzi, Michelle Biochemistry, Vol. 44, Issue 43 https://doi.org/10.1021/bi050976u	journal	October 2005
Single-Turnover and Pre-Steady-State Kinetics of the Reaction of the Adenine Glycosylase MutY with Mismatch-Containing DNA Substrates Porello, Silvia L.; Leyes, Aquiles E.; David, Sheila S. Biochemistry, Vol. 37, Issue 42 https://doi.org/10.1021/bi981594+	journal	September 1998
Toward a Detailed Understanding of Base Excision Repair Enzymes: Transition State and Mechanistic Analyses of N -Glycoside Hydrolysis and N- Glycoside Transfer Berti, Paul J.; McCann, Joe A. B. Chemical Reviews, Vol. 106, Issue 2 https://doi.org/10.1021/cr040461t	journal	February 2006
Specific Recognition of Substrate Analogs by the DNA Mismatch Repair Enzyme MutY Porello, Silvia L.; Williams, Scott D.; Kuhn, Heiko Journal of the American Chemical Society, Vol. 118, Issue 44 https://doi.org/10.1021/ja9602206	journal	January 1996
Unique Hydrogen Bonding of Adenine with the Oxidatively Damaged Base 8-Oxoguanine Enables Specific Recognition and Repair by DNA Glycosylase MutY Majumdar, Chandrima; McKibbin, Paige L.; Krajewski, Allison E. Journal of the American Chemical Society, Vol. 142, Issue 48 https://doi.org/10.1021/jacs.0c06767	journal	November 2020
The Oxidation State of [4Fe4S] Clusters Modulates the DNA-Binding Affinity of DNA Repair Proteins Tse, Edmund C. M.; Zwang, Theodore J.; Barton, Jacqueline K. Journal of the American Chemical Society, Vol. 139, Issue 36 https://doi.org/10.1021/jacs.7b07230	journal	August 2017
Modulating the Nucleophile of a Glycoside Hydrolase through Site-Specific Incorporation of Fluoroglutamic Acids Kötzler, Miriam P.; Robinson, Kyle; Chen, Hong-Ming Journal of the American Chemical Society, Vol. 140, Issue 26 https://doi.org/10.1021/jacs.8b04235	journal	June 2018
Catalysis by hen egg-white lysozyme proceeds via a covalent intermediate Vocadlo, David J.; Davies, Gideon J.; Laine, Roger Nature, Vol. 412, Issue 6849 https://doi.org/10.1038/35090602	journal	August 2001
MutY catalytic core, mutant and bound adenine structures define specificity for DNA repair enzyme superfamily Guan, Yue; Manuel, Raymond C.; Arvai, Andrew S. Nature Structural Biology, Vol. 5, Issue 12 https://doi.org/10.1038/4168	journal	December 1998
Structural basis for removal of adenine mispaired with 8-oxoguanine by MutY adenine DNA glycosylase Fromme, J. Christopher; Banerjee, Anirban; Huang, Susan J. Nature, Vol. 427, Issue 6975 https://doi.org/10.1038/nature02306	journal	February 2004
Inherited variants of MYH associated with somatic G:C→T:A mutations in colorectal tumors Al-Tassan, Nada; Chmiel, Nikolas H.; Maynard, Julie Nature Genetics, Vol. 30, Issue 2 https://doi.org/10.1038/ng828	journal	January 2002
Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase Brieba, Luis G.; Eichman, Brandt F.; Kokoska, Robert J. The EMBO Journal, Vol. 23, Issue 17 https://doi.org/10.1038/sj.emboj.7600354	journal	August 2004
Glycosidase inhibition: assessing mimicry of the transition state Gloster, Tracey M.; Davies, Gideon J. Org. Biomol. Chem., Vol. 8, Issue 2 https://doi.org/10.1039/B915870G	journal	January 2010
Atomic substitution reveals the structural basis for substrate adenine recognition and removal by adenine DNA glycosylase Lee, S.; Verdine, G. L. Proceedings of the National Academy of Sciences, Vol. 106, Issue 44 https://doi.org/10.1073/pnas.0902908106	journal	October 2009
Escherichia coli MutY protein has both N-glycosylase and apurinic/apyrimidinic endonuclease activities on A.C and A.G mispairs. Tsai-Wu, J. J.; Liu, H. F.; Lu, A. L. Proceedings of the National Academy of Sciences, Vol. 89, Issue 18 https://doi.org/10.1073/pnas.89.18.8779	journal	September 1992
Structural Basis for Avoidance of Promutagenic DNA Repair by MutY Adenine DNA Glycosylase Wang, Lan; Lee, Seung-Joo; Verdine, Gregory L. Journal of Biological Chemistry, Vol. 290, Issue 28 https://doi.org/10.1074/jbc.M115.657866	journal	May 2015
Adenine Release Is Fast in MutY-catalyzed Hydrolysis of G:A and 8-Oxo-G:A DNA Mismatches McCann, Joe A. B.; Berti, Paul J. Journal of Biological Chemistry, Vol. 278, Issue 32 https://doi.org/10.1074/jbc.M212474200	journal	August 2003
Cancer-associated variants and a common polymorphism of MUTYH exhibit reduced repair of oxidative DNA damage using a GFP-based assay in mammalian cells Raetz, Alan G.; Xie, Yali; Kundu, Sucharita Carcinogenesis, Vol. 33, Issue 11 https://doi.org/10.1093/carcin/bgs270	journal	August 2012
Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil-DNA glycosylase with DNA Parikh, S. S. The EMBO Journal, Vol. 17, Issue 17 https://doi.org/10.1093/emboj/17.17.5214	journal	September 1998
Ligation-independent cloning of PCR products (LIC-PCR) Aslanidis, Charalampos; de Jong, Pieter J. Nucleic Acids Research, Vol. 18, Issue 20 https://doi.org/10.1093/nar/18.20.6069	journal	January 1990
Evidence that MutY is a monofunctional glycosylase capable of forming a covalent Schiff base intermediate with substrate DNA Williams, S. D.; David, S. S. Nucleic Acids Research, Vol. 26, Issue 22 https://doi.org/10.1093/nar/26.22.5123	journal	November 1998
Substrate recognition by Escherichia coli MutY using substrate analogs Chepanoske, C. L.; Porello, S. L.; Fujiwara, T. Nucleic Acids Research, Vol. 27, Issue 15 https://doi.org/10.1093/nar/27.15.3197	journal	August 1999
Efficient recognition of substrates and substrate analogs by the adenine glycosylase MutY requires the C-terminal domain Chmiel, N. H. Nucleic Acids Research, Vol. 29, Issue 2 https://doi.org/10.1093/nar/29.2.553	journal	January 2001
Revealing A-T and G-C Hoogsteen base pairs in stressed protein-bound duplex DNA Shi, Honglue; Kimsey, Isaac J.; Gu, Stephanie Nucleic Acids Research, Vol. 49, Issue 21 https://doi.org/10.1093/nar/gkab936	journal	November 2021
Structure and stereochemistry of the base excision repair glycosylase MutY reveal a mechanism similar to retaining glycosidases Woods, Ryan D.; O'Shea, Valerie L.; Chu, Aurea Nucleic Acids Research, Vol. 44, Issue 2 https://doi.org/10.1093/nar/gkv1469	journal	December 2015
Thymine DNA glycosylase exhibits negligible affinity for nucleobases that it removes from DNA Malik, Shuja S.; Coey, Christopher T.; Varney, Kristen M. Nucleic Acids Research, Vol. 43, Issue 19 https://doi.org/10.1093/nar/gkv890	journal	September 2015
Hyperproduction of Recombinant Ferredoxins in Escherichia coli by Coexpression of the ORF1-ORF2-iscS-iscU-iscA-hscB-hscA-fdx-ORF3 Gene Cluster Nakamura, M.; Saeki, K.; Takahashi, Y. Journal of Biochemistry, Vol. 126, Issue 1 https://doi.org/10.1093/oxfordjournals.jbchem.a022409	journal	July 1999
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/S0907444909047337	journal	January 2010
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution Headd, Jeffrey J.; Echols, Nathaniel; Afonine, Pavel V. Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 4 https://doi.org/10.1107/S0907444911047834	journal	March 2012
The GO system protects organisms from the mutagenic effect of the spontaneous lesion 8-hydroxyguanine (7,8-dihydro-8-oxoguanine). Michaels, M. L.; Miller, J. H. Journal of Bacteriology, Vol. 174, Issue 20 https://doi.org/10.1128/jb.174.20.6321-6325.1992	journal	January 1992
Inherited predisposition to colorectal adenomas caused by multiple rare alleles of MUTYH but not OGG1, NUDT1, NTH1 or NEIL 1, 2 or 3 Dallosso, A. R.; Dolwani, S.; Jones, N. Gut, Vol. 57, Issue 9 https://doi.org/10.1136/gut.2007.145748	journal	May 2008
Enzymatic Transition States, Transition-State Analogs, Dynamics, Thermodynamics, and Lifetimes Schramm, Vern L. Annual Review of Biochemistry, Vol. 80, Issue 1 https://doi.org/10.1146/annurev-biochem-061809-100742	journal	July 2011
FastCloning: a highly simplified, purification-free, sequence- and ligation-independent PCR cloning method Li, Chaokun; Wen, Aiyun; Shen, Benchang BMC Biotechnology, Vol. 11, Issue 1 https://doi.org/10.1186/1472-6750-11-92	journal	January 2011