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

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

doi:10.1073/pnas.2021120118

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

Journal Article · Mon Mar 01 00:00:00 EST 2021 · Proc. Natl. Acad. Sci. USA

DOI:https://doi.org/10.1073/pnas.2021120118· OSTI ID:1770395

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

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: DOE - Office Of Science; National Institutes of Health (NIH)

OSTI ID:: 1770395

Journal Information:: Proc. Natl. Acad. Sci. USA, Vol. 118, Issue (19)

Country of Publication:: United States

Language:: ENGLISH

References (54)

Repair of nitrous acid damage to DNA in Escherichia coli Da Roza, Ricardo; Friedberg, Errol C.; Duncan, Bruce K. Biochemistry, Vol. 16, Issue 22 https://doi.org/10.1021/bi00641a030	journal	November 1977
RNA Editing Enzyme APOBEC1 and Some of Its Homologs Can Act as DNA Mutators Harris, Reuben S.; Petersen-Mahrt, Svend K.; Neuberger, Michael S. Molecular Cell, Vol. 10, Issue 5, p. 1247-1253 https://doi.org/10.1016/S1097-2765(02)00742-6	journal	November 2002
Instability and decay of the primary structure of DNA Lindahl, Tomas Nature, Vol. 362, Issue 6422 https://doi.org/10.1038/362709a0	journal	April 1993
Mutagenic deamination of cytosine residues in DNA Duncan, Bruce K.; Miller, Jeffrey H. Nature, Vol. 287, Issue 5782 https://doi.org/10.1038/287560a0	journal	October 1980
Miscoding Properties of 2′-Deoxyinosine, a Nitric Oxide-Derived DNA Adduct, during Translesion Synthesis Catalyzed by Human DNA Polymerases Yasui, Manabu; Suenaga, Emi; Koyama, Naoki Journal of Molecular Biology, Vol. 377, Issue 4 https://doi.org/10.1016/j.jmb.2008.01.033	journal	April 2008
A sensitive genetic assay for the detection of cytosine deamination: determination of rate constants and the activation energy Frederico, Lisa A.; Kunkel, Thomas A.; Shaw, Barbara Ramsay Biochemistry, Vol. 29, Issue 10 https://doi.org/10.1021/bi00462a015	journal	March 1990
Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage Gaudelli, Nicole M.; Komor, Alexis C.; Rees, Holly A. Nature, Vol. 551, Issue 7681 https://doi.org/10.1038/nature24644	journal	October 2017
Heat-induced deamination of cytosine residues in deoxyribonucleic acid Lindahl, Tomas; Nyberg, Barbro Biochemistry, Vol. 13, Issue 16 https://doi.org/10.1021/bi00713a035	journal	July 1974
The rate of hydrolytic deamination of 5-methylcytosine in double-stranded DNA Shen, Jiang-Cheng; Rideout, William M.; Jones, Peter A. Nucleic Acids Research, Vol. 22, Issue 6 https://doi.org/10.1093/nar/22.6.972	journal	January 1994
Inosine in DNA and RNA Alseth, Ingrun; Dalhus, Bjørn; Bjørås, Magnar Current Opinion in Genetics & Development, Vol. 26 https://doi.org/10.1016/j.gde.2014.07.008	journal	June 2014
Hypoxanthine in deoxyribonucleic acid: generation by heat-induced hydrolysis of adenine residues and release in free form by a deoxyribonucleic acid glycosylase from calf thymus Karran, Peter; Lindahl, Tomas Biochemistry, Vol. 19, Issue 26 https://doi.org/10.1021/bi00567a010	journal	December 1980
Cytosine deamination and the precipitous decline of spontaneous mutation during Earth's history Lewis, Charles A.; Crayle, Jesse; Zhou, Shuntai Proceedings of the National Academy of Sciences, Vol. 113, Issue 29 https://doi.org/10.1073/pnas.1607580113	journal	July 2016
The spectrum of APOBEC3 activity: From anti-viral agents to anti-cancer opportunities Green, Abby M.; Weitzman, Matthew D. DNA Repair, Vol. 83 https://doi.org/10.1016/j.dnarep.2019.102700	journal	November 2019
APOBEC Enzymes as Targets for Virus and Cancer Therapy Olson, Margaret E.; Harris, Reuben S.; Harki, Daniel A. Cell Chemical Biology, Vol. 25, Issue 1 https://doi.org/10.1016/j.chembiol.2017.10.007	journal	January 2018
APOBEC Enzymes: Mutagenic Fuel for Cancer Evolution and Heterogeneity Swanton, C.; McGranahan, N.; Starrett, G. J. Cancer Discovery, Vol. 5, Issue 7 https://doi.org/10.1158/2159-8290.CD-15-0344	journal	June 2015
Uracil in DNA – occurrence, consequences and repair Krokan, Hans E.; Drabløs, Finn; Slupphaug, Geir Oncogene, Vol. 21, Issue 58 https://doi.org/10.1038/sj.onc.1205996	journal	December 2002
DNA glycosylases in the base excision repair of DNA Krokan, Hans E.; Standal, Rune; Slupphaug, Geir Biochemical Journal, Vol. 325, Issue 1 https://doi.org/10.1042/bj3250001	journal	July 1997
Dna Repair Mechanisms for the Recognition and Removal of Damaged dna Bases Mol, Clifford D.; Parikh, Sudip S.; Putnam, Christopher D. Annual Review of Biophysics and Biomolecular Structure, Vol. 28, Issue 1 https://doi.org/10.1146/annurev.biophys.28.1.101	journal	June 1999
DNA N-glycosidases: properties of uracil-DNA glycosidase from Escherichia coli. Lindahl, T.; Ljungquist, S.; Siegert, W. Journal of Biological Chemistry, Vol. 252, Issue 10 https://doi.org/10.1016/S0021-9258(17)40386-3	journal	May 1977
Dissecting the Broad Substrate Specificity of Human 3-Methyladenine-DNA Glycosylase O'Brien, Patrick J.; Ellenberger, Tom Journal of Biological Chemistry, Vol. 279, Issue 11 https://doi.org/10.1074/jbc.M312232200	journal	December 2003
Error-free versus mutagenic processing of genomic uracil—Relevance to cancer Krokan, Hans E.; Sætrom, Pål; Aas, Per Arne DNA Repair, Vol. 19 https://doi.org/10.1016/j.dnarep.2014.03.028	journal	July 2014
Deoxyxanthosine in DNA is repaired by Escherichia coli endonuclease V He, Bin; Qing, Hong; Kow, Yoke W. Mutation Research/DNA Repair, Vol. 459, Issue 2 https://doi.org/10.1016/S0921-8777(99)00063-4	journal	March 2000
Purification and characterization of a novel deoxyinosine-specific enzyme, deoxyinosine 3' endonuclease, from Escherichia coli. Yao, M.; Hatahet, Z.; Melamede, R. J. Journal of Biological Chemistry, Vol. 269, Issue 23 https://doi.org/10.1016/S0021-9258(17)34002-4	journal	June 1994
Alternative Excision Repair Pathways Yasui, A. Cold Spring Harbor Perspectives in Biology, Vol. 5, Issue 6 https://doi.org/10.1101/cshperspect.a012617	journal	May 2013
EndoQ and EndoV work individually for damaged DNA base repair in Pyrococcus furiosus Ishino, Sonoko; Makita, Naruto; Shiraishi, Miyako Biochimie, Vol. 118 https://doi.org/10.1016/j.biochi.2015.06.015	journal	November 2015
A functional endonuclease Q exists in the bacterial domain: identification and characterization of endonuclease Q from Bacillus pumilus Shiraishi, Miyako; Ishino, Sonoko; Cann, Isaac Bioscience, Biotechnology, and Biochemistry, Vol. 81, Issue 5 https://doi.org/10.1080/09168451.2016.1277946	journal	May 2017
A novel endonuclease that may be responsible for damaged DNA base repair in Pyrococcus furiosus Shiraishi, Miyako; Ishino, Sonoko; Yamagami, Takeshi Nucleic Acids Research, Vol. 43, Issue 5 https://doi.org/10.1093/nar/gkv121	journal	February 2015
Structural Basis of DNA Loop Recognition by Endonuclease V Rosnes, Ida; Rowe, Alexander D.; Vik, Erik S. Structure, Vol. 21, Issue 2 https://doi.org/10.1016/j.str.2012.12.007	journal	February 2013
PCNA is involved in the EndoQ-mediated DNA repair process in Thermococcales Shiraishi, Miyako; Ishino, Sonoko; Yoshida, Kotaro Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep25532	journal	May 2016
Crystal structure of the novel lesion-specific endonuclease PfuEndoQ from Pyrococcus furiosus Miyazono, Ken-ichi; Ishino, Sonoko; Makita, Naruto Nucleic Acids Research, Vol. 46, Issue 9 https://doi.org/10.1093/nar/gky261	journal	April 2018
Analysis and prediction of the different types of β-turn in proteins Wilmot, C. M.; Thornton, J. M. Journal of Molecular Biology, Vol. 203, Issue 1 https://doi.org/10.1016/0022-2836(88)90103-9	journal	September 1988
Uracil-DNA glycosylase-DNA substrate and product structures: Conformational strain promotes catalytic efficiency by coupled stereoelectronic effects Parikh, S. S.; Walcher, G.; Jones, G. D. Proceedings of the National Academy of Sciences, Vol. 97, Issue 10 https://doi.org/10.1073/pnas.97.10.5083	journal	May 2000
Structures of endonuclease V with DNA reveal initiation of deaminated adenine repair Dalhus, Bjørn; Arvai, Andrew S.; Rosnes, Ida Nature Structural & Molecular Biology, Vol. 16, Issue 2 https://doi.org/10.1038/nsmb.1538	journal	January 2009
Inhibiting APOBEC3 Activity with Single-Stranded DNA Containing 2′-Deoxyzebularine Analogues Kvach, Maksim V.; Barzak, Fareeda M.; Harjes, Stefan Biochemistry, Vol. 58, Issue 5 https://doi.org/10.1021/acs.biochem.8b00858	journal	November 2018
Molecular Basis of Substrate Recognition of Endonuclease Q from the Euryarchaeon Pyrococcus furiosus Shiraishi, Miyako; Iwai, Shigenori Journal of Bacteriology, Vol. 202, Issue 2 https://doi.org/10.1128/JB.00542-19	journal	November 2019
Recent advances in the structural mechanisms of DNA glycosylases Brooks, Sonja C.; Adhikary, Suraj; Rubinson, Emily H. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Vol. 1834, Issue 1 https://doi.org/10.1016/j.bbapap.2012.10.005	journal	January 2013
DNA Base Flipping: A General Mechanism for Writing, Reading, and Erasing DNA Modifications Hong, Samuel; Cheng, Xiaodong Advances in Experimental Medicine and Biology https://doi.org/10.1007/978-3-319-43624-1_14	book	January 2016
Extrahelical Damaged Base Recognition by DNA Glycosylase Enzymes Stivers, James T. Chemistry - A European Journal, Vol. 14, Issue 3 https://doi.org/10.1002/chem.200701501	journal	January 2008
Uracil-DNA glycosylases-Structural and functional perspectives on an essential family of DNA repair enzymes: Uracil-DNA Glycosylases Schormann, N.; Ricciardi, R.; Chattopadhyay, D. Protein Science, Vol. 23, Issue 12 https://doi.org/10.1002/pro.2554	journal	October 2014
A nucleotide-flipping mechanism from the structure of human uracil–DNA glycosylase bound to DNA Slupphaug, Geir; Mol, Clifford D.; Kavli, Bodil Nature, Vol. 384, Issue 6604 https://doi.org/10.1038/384087a0	journal	November 1996
Structure of the DNA Repair Enzyme Endonuclease IV and Its DNA Complex Hosfield, David J.; Guan, Yue; Haas, Brian J. Cell, Vol. 98, Issue 3 https://doi.org/10.1016/S0092-8674(00)81968-6	journal	August 1999
DNA-bound structures and mutants reveal abasic DNA binding by APE1 DNA repair and coordination Mol, Clifford D.; Izumi, Tadahide; Mitra, Sankar Nature, Vol. 403, Issue 6768 https://doi.org/10.1038/35000249	journal	January 2000
Central base pair flipping and discrimination by PspGI Szczepanowski, Roman H.; Carpenter, Michael A.; Czapinska, Honorata Nucleic Acids Research, Vol. 36, Issue 19 https://doi.org/10.1093/nar/gkn622	journal	October 2008
High-fidelity DNA replication in Mycobacterium tuberculosis relies on a trinuclear zinc center Baños-Mateos, Soledad; van Roon, Anne-Marie M.; Lang, Ulla F. Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/s41467-017-00886-w	journal	October 2017
Structural and Mechanistic Characterization of l -Histidinol Phosphate Phosphatase from the Polymerase and Histidinol Phosphatase Family of Proteins Ghodge, Swapnil V.; Fedorov, Alexander A.; Fedorov, Elena V. Biochemistry, Vol. 52, Issue 6 https://doi.org/10.1021/bi301496p	journal	January 2013
Crystal Structure of Monofunctional Histidinol Phosphate Phosphatase from Thermus thermophilus HB8 ^‡ Omi, Rie; Goto, Masaru; Miyahara, Ikuko Biochemistry, Vol. 46, Issue 44 https://doi.org/10.1021/bi701204r	journal	November 2007
Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase Wu, Jinjun; Samara, Nadine L.; Kuraoka, Isao Molecular Cell, Vol. 76, Issue 1 https://doi.org/10.1016/j.molcel.2019.06.046	journal	October 2019
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/S0907444909047337	journal	January 2010
Toward the structural genomics of complexes: Crystal structure of a PE/PPE protein complex from Mycobacterium tuberculosis Strong, M.; Sawaya, M. R.; Wang, S. Proceedings of the National Academy of Sciences, Vol. 103, Issue 21 https://doi.org/10.1073/pnas.0602606103	journal	May 2006
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/S0021889807021206	journal	July 2007
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
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
CURVES+ web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures Blanchet, C.; Pasi, M.; Zakrzewska, K. Nucleic Acids Research, Vol. 39, Issue suppl https://doi.org/10.1093/nar/gkr316	journal	May 2011
Crystal Structure of the DNA Deaminase APOBEC3B Catalytic Domain Shi, Ke; Carpenter, Michael A.; Kurahashi, Kayo Journal of Biological Chemistry, Vol. 290, Issue 47 https://doi.org/10.1074/jbc.M115.679951	journal	September 2015

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