Mechanism of Ribonucleotide Incorporation by Human DNA Polymerase η

Su, Yan; Egli, Martin; Guengerich, F. Peter

doi:10.1074/jbc.M115.706226

Mechanism of Ribonucleotide Incorporation by Human DNA Polymerase η

Journal Article · Wed Jan 06 00:00:00 EST 2016 · Journal of Biological Chemistry

DOI:https://doi.org/10.1074/jbc.M115.706226· OSTI ID:1243103

Su, Yan ^[1]; Egli, Martin ^[1]; Guengerich, F. Peter ^[1]

Vanderbilt Univ., Nashville, TN (United States)

Ribonucleotides and 2'-deoxyribonucleotides are the basic units for RNA and DNA, respectively, and the only difference is the extra 2'-OH group on the ribonucleotide sugar. Cellular rNTP concentrations are much higher than those of dNTP. When copying DNA, DNA polymerases not only select the base of the incoming dNTP to form a Watson-Crick pair with the template base but also distinguish the sugar moiety. Some DNA polymerases use a steric gate residue to prevent rNTP incorporation by creating a clash with the 2'-OH group. Y-family human DNA polymerase η (hpol η) is of interest because of its spacious active site (especially in the major groove) and tolerance of DNA lesions. Here, we show that hpol η maintains base selectivity when incorporating rNTPs opposite undamaged DNA and the DNA lesions 7,8-dihydro-8-oxo-2'-deoxyguanosine and cyclobutane pyrimidine dimer but with rates that are 103-fold lower than for inserting the corresponding dNTPs. X-ray crystal structures show that the hpol η scaffolds the incoming rNTP to pair with the template base (dG) or 7,8-dihydro-8-oxo-2'-deoxyguanosine with a significant propeller twist. As a result, the 2'-OH group avoids a clash with the steric gate, Phe-18, but the distance between primer end and Pα of the incoming rNTP increases by 1 Å, elevating the energy barrier and slowing polymerization compared with dNTP. In addition, Tyr-92 was identified as a second line of defense to maintain the position of Phe-18. Lastly, this is the first crystal structure of a DNA polymerase with an incoming rNTP opposite a DNA lesion.

View Accepted Manuscript (DOE)

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: National Inst. of Health; USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1243103

Journal Information:: Journal of Biological Chemistry, Journal Name: Journal of Biological Chemistry Journal Issue: 8 Vol. 291; ISSN 0021-9258

Publisher:: American Society for Biochemistry and Molecular BiologyCopyright Statement

Country of Publication:: United States

Language:: ENGLISH

References (57)

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
NMRPipe: A multidimensional spectral processing system based on UNIX pipes Delaglio, Frank; Grzesiek, Stephan; Vuister, GeertenW. Journal of Biomolecular NMR, Vol. 6, Issue 3 https://doi.org/10.1007/BF00197809	journal	November 1995
Physiological concentrations of purines and pyrimidines Traut, Thomas W. Molecular and Cellular Biochemistry, Vol. 140, Issue 1 https://doi.org/10.1007/BF00928361	journal	January 1994
[20] Processing of X-ray diffraction data collected in oscillation mode Otwinowski, Zbyszek; Minor, Wladek Macromolecular Crystallography Part A, 307-326 https://doi.org/10.1016/S0076-6879(97)76066-X	book	January 1997
Enzymatic Removal of Ribonucleotides from DNA Is Essential for Mammalian Genome Integrity and Development Reijns, Martin A. M.; Rabe, Björn; Rigby, Rachel E. Cell, Vol. 149, Issue 5 https://doi.org/10.1016/j.cell.2012.04.011	journal	May 2012
Ribonucleotide incorporation, proofreading and bypass by human DNA polymerase δ Clausen, Anders R.; Zhang, Sufang; Burgers, Peter M. DNA Repair, Vol. 12, Issue 2 https://doi.org/10.1016/j.dnarep.2012.11.006	journal	February 2013
Redundancy in ribonucleotide excision repair: Competition, compensation, and cooperation Vaisman, Alexandra; Woodgate, Roger DNA Repair, Vol. 29 https://doi.org/10.1016/j.dnarep.2015.02.008	journal	May 2015
Unlocking the steric gate of DNA polymerase η leads to increased genomic instability in Saccharomyces cerevisiae Donigan, Katherine A.; Cerritelli, Susana M.; McDonald, John P. DNA Repair, Vol. 35 https://doi.org/10.1016/j.dnarep.2015.07.002	journal	November 2015
Structural Mechanism of Ribonucleotide Discrimination by a Y-Family DNA Polymerase Kirouac, Kevin N.; Suo, Zucai; Ling, Hong Journal of Molecular Biology, Vol. 407, Issue 3 https://doi.org/10.1016/j.jmb.2011.01.037	journal	April 2011
RNase H2-Initiated Ribonucleotide Excision Repair Sparks, Justin L.; Chon, Hyongi; Cerritelli, Susana M. Molecular Cell, Vol. 47, Issue 6 https://doi.org/10.1016/j.molcel.2012.06.035	journal	September 2012
DNA replication fidelity. Kunkel, T. A. Journal of Biological Chemistry, Vol. 267, Issue 26 https://doi.org/10.1016/s0021-9258(19)36949-2	journal	September 1992
Efficient Translesion Replication Past Oxaliplatin and Cisplatin GpG Adducts by Human DNA Polymerase η ^† Vaisman, Alexandra; Masutani, Chikahide; Hanaoka, Fumio Biochemistry, Vol. 39, Issue 16 https://doi.org/10.1021/bi000130k	journal	April 2000
A Conserved Tyr Residue Is Required for Sugar Selectivity in a Pol α DNA Polymerase ^† Yang, Guangwei; Franklin, Matthew; Li, Jing Biochemistry, Vol. 41, Issue 32 https://doi.org/10.1021/bi0202171	journal	August 2002
An Overview of Y-Family DNA Polymerases and a Case Study of Human DNA Polymerase η Yang, Wei Biochemistry, Vol. 53, Issue 17 https://doi.org/10.1021/bi500019s	journal	April 2014
The Steric Gate Amino Acid Tyrosine 112 Is Required for Efficient Mismatched-Primer Extension by Human DNA Polymerase κ Niimi, Naoko; Sassa, Akira; Katafuchi, Atsushi Biochemistry, Vol. 48, Issue 20 https://doi.org/10.1021/bi900153t	journal	May 2009
Kinetics of RNA Degradation by Specific Base Catalysis of Transesterification Involving the 2‘-Hydroxyl Group Li, Yingfu; Breaker, Ronald R. Journal of the American Chemical Society, Vol. 121, Issue 23 https://doi.org/10.1021/ja990592p	journal	June 1999
The XPV (xeroderma pigmentosum variant) gene encodes human DNA polymerase η Masutani, Chikahide; Kusumoto, Rika; Yamada, Ayumi Nature, Vol. 399, Issue 6737 https://doi.org/10.1038/21447	journal	June 1999
Efficient and accurate replication in the presence of 7,8-dihydro-8-oxoguanine by DNA polymerase η Haracska, Lajos; Yu, Sung-Lim; Johnson, Robert E. Nature Genetics, Vol. 25, Issue 4 https://doi.org/10.1038/78169	journal	August 2000
Xeroderma Pigmentosum-Variant Patients from America, Europe, and Asia Inui, Hiroki; Oh, Kyu-Seon; Nadem, Carine Journal of Investigative Dermatology, Vol. 128, Issue 8 https://doi.org/10.1038/jid.2008.48	journal	August 2008
Structure and mechanism of human DNA polymerase η Biertümpfel, Christian; Zhao, Ye; Kondo, Yuji Nature, Vol. 465, Issue 7301 https://doi.org/10.1038/nature09196	journal	June 2010
Genome instability due to ribonucleotide incorporation into DNA McElhinny, Stephanie A. Nick; Kumar, Dinesh; Clark, Alan B. Nature Chemical Biology, Vol. 6, Issue 10 https://doi.org/10.1038/nchembio.424	journal	August 2010
Y-family DNA polymerases and their role in tolerance of cellular DNA damage Sale, Julian E.; Lehmann, Alan R.; Woodgate, Roger Nature Reviews Molecular Cell Biology, Vol. 13, Issue 3 https://doi.org/10.1038/nrm3289	journal	February 2012
PARP1 exhibits enhanced association and catalytic efficiency with γH2A.X-nucleosome Sharma, Deepti; De Falco, Louis; Padavattan, Sivaraman Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-13641-0	journal	December 2019
Cavin1 intrinsically disordered domains are essential for fuzzy electrostatic interactions and caveola formation Tillu, Vikas A.; Rae, James; Gao, Ya Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-021-21035-4	journal	February 2021
Multi-functionality of a tryptophan residue conserved in substrate-binding groove of GH19 chitinases Nagata, Takuya; Shinya, Shoko; Ohnuma, Takayuki Scientific Reports, Vol. 11, Issue 1 https://doi.org/10.1038/s41598-021-81903-3	journal	January 2021
Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis Vaisman, Alexandra; Ling, Hong; Woodgate, Roger The EMBO Journal, Vol. 24, Issue 17 https://doi.org/10.1038/sj.emboj.7600786	journal	August 2005
Constitutively high dNTP concentration inhibits cell cycle progression and the DNA damage checkpoint in yeast Saccharomyces cerevisiae Chabes, A.; Stillman, B. Proceedings of the National Academy of Sciences, Vol. 104, Issue 4 https://doi.org/10.1073/pnas.0610585104	journal	January 2007
Abundant ribonucleotide incorporation into DNA by yeast replicative polymerases Nick McElhinny, S. A.; Watts, B. E.; Kumar, D. Proceedings of the National Academy of Sciences, Vol. 107, Issue 11 https://doi.org/10.1073/pnas.0914857107	journal	March 2010
Structural basis of human DNA polymerase -mediated chemoresistance to cisplatin Zhao, Y.; Biertumpfel, C.; Gregory, M. T. Proceedings of the National Academy of Sciences, Vol. 109, Issue 19 https://doi.org/10.1073/pnas.1202681109	journal	April 2012
Structure-function analysis of ribonucleotide bypass by B family DNA replicases Clausen, A. R.; Murray, M. S.; Passer, A. R. Proceedings of the National Academy of Sciences, Vol. 110, Issue 42 https://doi.org/10.1073/pnas.1309119110	journal	September 2013
Structural and mechanistic studies of polymerase bypass of phenanthriplatin DNA damage Gregory, M. T.; Park, G. Y.; Johnstone, T. C. Proceedings of the National Academy of Sciences, Vol. 111, Issue 25 https://doi.org/10.1073/pnas.1405739111	journal	June 2014
Excision of misincorporated ribonucleotides in DNA by RNase H (type 2) and FEN-1 in cell-free extracts Rydberg, B.; Game, J. Proceedings of the National Academy of Sciences, Vol. 99, Issue 26 https://doi.org/10.1073/pnas.262591699	journal	December 2002
Choosing the right sugar: How polymerases select a nucleotide substrate Joyce, C. M. Proceedings of the National Academy of Sciences, Vol. 94, Issue 5 https://doi.org/10.1073/pnas.94.5.1619	journal	March 1997
Inefficient Bypass of an Abasic Site by DNA Polymerase η Haracska, Lajos; Washington, M. Todd; Prakash, Satya Journal of Biological Chemistry, Vol. 276, Issue 9 https://doi.org/10.1074/jbc.M008021200	journal	December 2000
DNA Polymerase β Ribonucleotide Discrimination: INSERTION, MISINSERTION, EXTENSION, AND CODING Cavanaugh, Nisha A.; Beard, William A.; Wilson, Samuel H. Journal of Biological Chemistry, Vol. 285, Issue 32 https://doi.org/10.1074/jbc.M110.132407	journal	June 2010
Molecular Insights into DNA Polymerase Deterrents for Ribonucleotide Insertion Cavanaugh, Nisha A.; Beard, William A.; Batra, Vinod K. Journal of Biological Chemistry, Vol. 286, Issue 36 https://doi.org/10.1074/jbc.M111.253401	journal	July 2011
The Steric Gate of DNA Polymerase ι Regulates Ribonucleotide Incorporation and Deoxyribonucleotide Fidelity Donigan, Katherine A.; McLenigan, Mary P.; Yang, Wei Journal of Biological Chemistry, Vol. 289, Issue 13 https://doi.org/10.1074/jbc.M113.545442	journal	February 2014
Kinetics, Structure, and Mechanism of 8-Oxo-7,8-dihydro-2′-deoxyguanosine Bypass by Human DNA Polymerase η Patra, Amritraj; Nagy, Leslie D.; Zhang, Qianqian Journal of Biological Chemistry, Vol. 289, Issue 24 https://doi.org/10.1074/jbc.M114.551820	journal	April 2014
Structural and Kinetic Analysis of Nucleoside Triphosphate Incorporation Opposite an Abasic Site by Human Translesion DNA Polymerase η Patra, Amritaj; Zhang, Qianqian; Lei, Li Journal of Biological Chemistry, Vol. 290, Issue 13 https://doi.org/10.1074/jbc.M115.637561	journal	February 2015
Roles of Residues Arg-61 and Gln-38 of Human DNA Polymerase η in Bypass of Deoxyguanosine and 7,8-Dihydro-8-oxo-2′-deoxyguanosine Su, Yan; Patra, Amritraj; Harp, Joel M. Journal of Biological Chemistry, Vol. 290, Issue 26 https://doi.org/10.1074/jbc.M115.653691	journal	May 2015
The Properties of Steric Gate Mutants Reveal Different Constraints within the Active Sites of Y-family and A-family DNA Polymerases DeLucia, Angela M.; Chaudhuri, Santanov; Potapova, Olga Journal of Biological Chemistry, Vol. 281, Issue 37 https://doi.org/10.1074/jbc.M604393200	journal	July 2006
DNA Replication Fidelity Kunkel, Thomas A. Journal of Biological Chemistry, Vol. 279, Issue 17 https://doi.org/10.1074/jbc.R400006200	journal	February 2004
An error-prone family Y DNA polymerase (DinB homolog from Sulfolobus solfataricus) uses a 'steric gate' residue for discrimination against ribonucleotides DeLucia, A. M. Nucleic Acids Research, Vol. 31, Issue 14 https://doi.org/10.1093/nar/gkg417	journal	July 2003
Critical amino acids in Escherichia coli UmuC responsible for sugar discrimination and base-substitution fidelity Vaisman, Alexandra; Kuban, Wojciech; McDonald, John P. Nucleic Acids Research, Vol. 40, Issue 13 https://doi.org/10.1093/nar/gks233	journal	March 2012
The catalytic cycle for ribonucleotide incorporation by human DNA Pol λ Gosavi, Rajendrakumar A.; Moon, Andrea F.; Kunkel, Thomas A. Nucleic Acids Research, Vol. 40, Issue 15 https://doi.org/10.1093/nar/gks413	journal	May 2012
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
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
REFMAC 5 for the refinement of macromolecular crystal structures Murshudov, Garib N.; Skubák, Pavol; Lebedev, Andrey A. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444911001314	journal	March 2011
Visual automated macromolecular model building Langer, Gerrit G.; Hazledine, Saul; Wiegels, Tim Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 4 https://doi.org/10.1107/S0907444913000565	journal	March 2013
hRAD30 Mutations in the Variant Form of Xeroderma Pigmentosum Johnson, R. E. Science, Vol. 285, Issue 5425 https://doi.org/10.1126/science.285.5425.263	journal	July 1999
The Role of DNA Polymerase η in Translesion Synthesis Past Platinum–DNA Adducts in Human Fibroblasts Bassett, Ekaterina; King, Nicole M.; Bryant, Miriam F. Cancer Research, Vol. 64, Issue 18 https://doi.org/10.1158/0008-5472.CAN-04-1328	journal	September 2004
A Role for Polymerase η in the Cellular Tolerance to Cisplatin-Induced Damage Albertella, Mark R.; Green, Catherine M.; Lehmann, Alan R. Cancer Research, Vol. 65, Issue 21 https://doi.org/10.1158/0008-5472.CAN-05-1095	journal	November 2005
A Novel Role of DNA Polymerase in Modulating Cellular Sensitivity to Chemotherapeutic Agents Chen, Y. -w. Molecular Cancer Research, Vol. 4, Issue 4 https://doi.org/10.1158/1541-7786.MCR-05-0118	journal	April 2006
Structure of Human DNA Polymerase κ Inserting dATP Opposite an 8-OxoG DNA Lesion Carpio, Rodrigo Vasquez-Del; Silverstein, Timothy D.; Lone, Samer PLoS ONE, Vol. 4, Issue 6 https://doi.org/10.1371/journal.pone.0005766	journal	June 2009
Molecular Insights into DNA Polymerase Deterrents for Ribonucleotide Insertion A., Cavanaugh, Nisha; H., Wilson, Samuel; G., Pedersen, Lee The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/be8d-zy22	text	January 2011
PHENIX: a comprehensive Python-based system for macromolecular structure solution. Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.45787	text	January 2010

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