The C-terminal region of translesion synthesis DNA polymerase η is partially unstructured and has high conformational flexibility

Powers, Kyle T.; Elcock, Adrian H.; Washington, M. Todd

doi:10.1093/nar/gky031

Title: The C-terminal region of translesion synthesis DNA polymerase η is partially unstructured and has high conformational flexibility

Journal Article · Mon Jan 29 00:00:00 EST 2018 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gky031· OSTI ID:1478096

Powers, Kyle T. ^[1];

^[1]; Washington, M. Todd ^[1]

Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA 52242-1109, USA

Cite

Export

Save

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

Sponsoring Organization:: National Institutes of Health (NIH)

OSTI ID:: 1478096

Journal Information:: Nucleic Acids Research, Vol. 46, Issue 4; ISSN 0305-1048

Publisher:: Oxford University Press

Country of Publication:: United States

Language:: ENGLISH

References (64)

A novel mode of ubiquitin recognition by the ubiquitin-binding zinc finger domain of WRNIP1 Suzuki, Nobuhiro; Rohaim, Ahmed; Kato, Ryuichi The FEBS Journal, Vol. 283, Issue 11 https://doi.org/10.1111/febs.13734	journal	April 2016
Acidic Residues Critical for the Activity and Biological Function of Yeast DNA Polymerase Kondratick, C. M.; Washington, M. T.; Prakash, S. Molecular and Cellular Biology, Vol. 21, Issue 6 https://doi.org/10.1128/MCB.21.6.2018-2025.2001	journal	March 2001
Replication of damaged DNA by translesion synthesis in human cells Lehmann, Alan R. FEBS Letters, Vol. 579, Issue 4 https://doi.org/10.1016/j.febslet.2004.11.029	journal	November 2004
Eukaryotic Translesion Polymerases and Their Roles and Regulation in DNA Damage Tolerance Waters, L. S.; Minesinger, B. K.; Wiltrout, M. E. Microbiology and Molecular Biology Reviews, Vol. 73, Issue 1 https://doi.org/10.1128/MMBR.00034-08	journal	March 2009
Mechanism of nucleotide incorporation opposite a thymine-thymine dimer by yeast DNA polymerase Washington, M. T.; Prakash, L.; Prakash, S. Proceedings of the National Academy of Sciences, Vol. 100, Issue 21 https://doi.org/10.1073/pnas.2134223100	journal	October 2003
Y-family DNA polymerases in mammalian cells Guo, Caixia; Kosarek-Stancel, J. Nicole; Tang, Tie-Shan Cellular and Molecular Life Sciences, Vol. 66, Issue 14 https://doi.org/10.1007/s00018-009-0024-4	journal	April 2009
R.I.P. to the PIP: PCNA-binding motif no longer considered specific: PIP motifs and other related sequences are not distinct entities and can bind multiple proteins involved in genome maintenance Boehm, Elizabeth M.; Washington, M. Todd BioEssays, Vol. 38, Issue 11 https://doi.org/10.1002/bies.201600116	journal	August 2016
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
CRYSOL – a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates Svergun, D.; Barberato, C.; Koch, M. H. J. Journal of Applied Crystallography, Vol. 28, Issue 6 https://doi.org/10.1107/S0021889895007047	journal	December 1995
Determination of the regularization parameter in indirect-transform methods using perceptual criteria Svergun, D. I. Journal of Applied Crystallography, Vol. 25, Issue 4, p. 495-503 https://doi.org/10.1107/S0021889892001663	journal	August 1992
Bypass of DNA Lesions Generated During Anticancer Treatment with Cisplatin by DNA Polymerase Alt, A.; Lammens, K.; Chiocchini, C. Science, Vol. 318, Issue 5852 https://doi.org/10.1126/science.1148242	journal	November 2007
PRIMUS: a Windows PC-based system for small-angle scattering data analysis Konarev, Petr V.; Volkov, Vladimir V.; Sokolova, Anna V. Journal of Applied Crystallography, Vol. 36, Issue 5, p. 1277-1282 https://doi.org/10.1107/S0021889803012779	journal	September 2003
The Proliferating Cell Nuclear Antigen (PCNA)-interacting Protein (PIP) Motif of DNA Polymerase η Mediates Its Interaction with the C-terminal Domain of Rev1 Boehm, Elizabeth M.; Powers, Kyle T.; Kondratick, Christine M. Journal of Biological Chemistry, Vol. 291, Issue 16 https://doi.org/10.1074/jbc.M115.697938	journal	February 2016
ATSAS 2.1 – towards automated and web-supported small-angle scattering data analysis Petoukhov, Maxim V.; Konarev, Peter V.; Kikhney, Alexey G. Journal of Applied Crystallography, Vol. 40, Issue s1 https://doi.org/10.1107/S0021889807002853	journal	April 2007
A Cartesian treecode for screened coulomb interactions Li, Peijun; Johnston, Hans; Krasny, Robert Journal of Computational Physics, Vol. 228, Issue 10 https://doi.org/10.1016/j.jcp.2009.02.022	journal	June 2009
The Phyre2 web portal for protein modeling, prediction and analysis Kelley, Lawrence A.; Mezulis, Stefans; Yates, Christopher M. Nature Protocols, Vol. 10, Issue 6 https://doi.org/10.1038/nprot.2015.053	journal	May 2015
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
Mechanism of Efficient and Accurate Nucleotide Incorporation Opposite 7,8-Dihydro-8-Oxoguanine by Saccharomyces cerevisiae DNA Polymerase Carlson, K. D.; Washington, M. T. Molecular and Cellular Biology, Vol. 25, Issue 6 https://doi.org/10.1128/MCB.25.6.2169-2176.2005	journal	March 2005
Structural Basis of Rev1-mediated Assembly of a Quaternary Vertebrate Translesion Polymerase Complex Consisting of Rev1, Heterodimeric Polymerase (Pol) ζ, and Pol κ Wojtaszek, Jessica; Lee, Chul-Jin; D'Souza, Sanjay Journal of Biological Chemistry, Vol. 287, Issue 40 https://doi.org/10.1074/jbc.M112.394841	journal	August 2012
PHENIX : building new software for automated crystallographic structure determination Adams, Paul D.; Grosse-Kunstleve, Ralf W.; Hung, Li-Wei Acta Crystallographica Section D Biological Crystallography, Vol. 58, Issue 11 https://doi.org/10.1107/S0907444902016657	journal	October 2002
Coarse grained simulations of a small peptide: Effects of finite damping and hydrodynamic interactions Winter, Uwe; Geyer, Tihamér The Journal of Chemical Physics, Vol. 131, Issue 10 https://doi.org/10.1063/1.3216573	journal	January 2009
Ubiquitin-Binding Domains in Y-Family Polymerases Regulate Translesion Synthesis Bienko, M. Science, Vol. 310, Issue 5755 https://doi.org/10.1126/science.1120615	journal	December 2005
Accurate SAXS Profile Computation and its Assessment by Contrast Variation Experiments Schneidman-Duhovny, Dina; Hammel, Michal; Tainer, John A. Biophysical Journal, Vol. 105, Issue 4 https://doi.org/10.1016/j.bpj.2013.07.020	journal	August 2013
Structure of the Catalytic Core of S. cerevisiae DNA Polymerase η Trincao, Jose; Johnson, Robert E.; Escalante, Carlos R. Molecular Cell, Vol. 8, Issue 2 https://doi.org/10.1016/S1097-2765(01)00306-9	journal	August 2001
Multifaceted Recognition of Vertebrate Rev1 by Translesion Polymerases ζ and κ Wojtaszek, Jessica; Liu, Jiangxin; D'Souza, Sanjay Journal of Biological Chemistry, Vol. 287, Issue 31 https://doi.org/10.1074/jbc.M112.380998	journal	June 2012
Theoretical Studies of Protein Folding Go, N. Annual Review of Biophysics and Bioengineering, Vol. 12, Issue 1 https://doi.org/10.1146/annurev.bb.12.060183.001151	journal	June 1983
BioXTAS RAW , a software program for high-throughput automated small-angle X-ray scattering data reduction and preliminary analysis Nielsen, S. S.; Toft, K. Noergaard; Snakenborg, D. Journal of Applied Crystallography, Vol. 42, Issue 5 https://doi.org/10.1107/S0021889809023863	journal	August 2009
Validation of protein models from Cα coordinates alone Kleywegt, Gerard J. Journal of Molecular Biology, Vol. 273, Issue 2 https://doi.org/10.1006/jmbi.1997.1309	journal	October 1997
The CCP4 suite programs for protein crystallography Acta Crystallographica Section D Biological Crystallography, Vol. 50, Issue 5, p. 760-763 https://doi.org/10.1107/S0907444994003112	journal	September 1994
Translesion synthesis: Y-family polymerases and the polymerase switch Lehmann, A.; Niimi, A.; Ogi, T. DNA Repair, Vol. 6, Issue 7 https://doi.org/10.1016/j.dnarep.2007.02.003	journal	July 2007
Requirement of DNA Polymerase Activity of Yeast Rad30 Protein for Its Biological Function Johnson, Robert E.; Prakash, Satya; Prakash, Louise Journal of Biological Chemistry, Vol. 274, Issue 23 https://doi.org/10.1074/jbc.274.23.15975	journal	June 1999
Molecular architecture of the Ub-PCNA/Pol η complex bound to DNA Lau, Wilson C. Y.; Li, Yinyin; Zhang, Qinfen Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep15759	journal	October 2015
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/S0907444909047337	journal	January 2010
Striking Effects of Hydrodynamic Interactions on the Simulated Diffusion and Folding of Proteins Frembgen-Kesner, Tamara; Elcock, Adrian H. Journal of Chemical Theory and Computation, Vol. 5, Issue 2 https://doi.org/10.1021/ct800499p	journal	January 2009
Control of spontaneous and damage-induced mutagenesis by SUMO and ubiquitin conjugation Stelter, Philipp; Ulrich, Helle D. Nature, Vol. 425, Issue 6954 https://doi.org/10.1038/nature01965	journal	September 2003
Prediction of disordered regions in proteins based on the meta approach Ishida, T.; Kinoshita, K. Bioinformatics, Vol. 24, Issue 11 https://doi.org/10.1093/bioinformatics/btn195	journal	April 2008
EUKARYOTIC TRANSLESION SYNTHESIS DNA POLYMERASES: Specificity of Structure and Function Prakash, Satya; Johnson, Robert E.; Prakash, Louise Annual Review of Biochemistry, Vol. 74, Issue 1 https://doi.org/10.1146/annurev.biochem.74.082803.133250	journal	June 2005
Structure of the ubiquitin-binding zinc finger domain of human DNA Y-polymerase η Bomar, Martha G.; Pai, Ming-Tao; Tzeng, Shiou-Ru EMBO reports, Vol. 8, Issue 3 https://doi.org/10.1038/sj.embor.7400901	journal	February 2007
RAD6-dependent DNA repair is linked to modification of PCNA by ubiquitin and SUMO Hoege, Carsten; Pfander, Boris; Moldovan, George-Lucian Nature, Vol. 419, Issue 6903 https://doi.org/10.1038/nature00991	journal	September 2002
Mechanism of replication blocking and bypass of Y-family polymerase by bulky acetylaminofluorene DNA adducts Schorr, S.; Schneider, S.; Lammens, K. Proceedings of the National Academy of Sciences, Vol. 107, Issue 48 https://doi.org/10.1073/pnas.1008894107	journal	November 2010
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
Insights from Coarse-Grained Gō Models for Protein Folding and Dynamics Hills, Ronald; Brooks, Charles International Journal of Molecular Sciences, Vol. 10, Issue 3 https://doi.org/10.3390/ijms10030889	journal	March 2009
Structural Basis for Error-free Replication of Oxidatively Damaged DNA by Yeast DNA Polymerase η Silverstein, Timothy D.; Jain, Rinku; Johnson, Robert E. Structure, Vol. 18, Issue 11 https://doi.org/10.1016/j.str.2010.08.019	journal	November 2010
Translesion Synthesis: Insights into the Selection and Switching of DNA Polymerases Zhao, Linlin; Washington, M. Genes, Vol. 8, Issue 1 https://doi.org/10.3390/genes8010024	journal	January 2017
Interaction with PCNA Is Essential for Yeast DNA Polymerase η Function Haracska, Lajos; Kondratick, Christine M.; Unk, Ildiko Molecular Cell, Vol. 8, Issue 2 https://doi.org/10.1016/S1097-2765(01)00319-7	journal	August 2001
Translesion DNA synthesis in eukaryotes: A one- or two-polymerase affair Prakash, S. Genes & Development, Vol. 16, Issue 15 https://doi.org/10.1101/gad.1009802	journal	August 2002
Coot model-building tools for molecular graphics Emsley, Paul; Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132 https://doi.org/10.1107/S0907444904019158	journal	November 2004
Efficient Bypass of a Thymine-Thymine Dimer by Yeast DNA Polymerase, Pol Johnson, R. E.; Prakash, S.; Prakash, L. Science, Vol. 283, Issue 5404 https://doi.org/10.1126/science.283.5404.1001	journal	February 1999
Evaluating conformational free energies: The colony energy and its application to the problem of loop prediction Xiang, Z.; Soto, C. S.; Honig, B. Proceedings of the National Academy of Sciences, Vol. 99, Issue 11 https://doi.org/10.1073/pnas.102179699	journal	May 2002
Brownian dynamics with hydrodynamic interactions Ermak, Donald L.; McCammon, J. A. The Journal of Chemical Physics, Vol. 69, Issue 4 https://doi.org/10.1063/1.436761	journal	August 1978
Transport Properties of Polymer Chains in Dilute Solution: Hydrodynamic Interaction Yamakawa, Hiromi The Journal of Chemical Physics, Vol. 53, Issue 1 https://doi.org/10.1063/1.1673799	journal	July 1970
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
PCNA tool belts and polymerase bridges form during translesion synthesis Boehm, Elizabeth M.; Spies, Maria; Washington, M. Todd Nucleic Acids Research, Vol. 44, Issue 17 https://doi.org/10.1093/nar/gkw563	journal	June 2016
Polarizable atomic multipole X-ray refinement: weighting schemes for macromolecular diffraction Fenn, T. D.; Schnieders, M. J. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 11 https://doi.org/10.1107/S0907444911039060	journal	October 2011
SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information Biasini, Marco; Bienert, Stefan; Waterhouse, Andrew Nucleic Acids Research, Vol. 42, Issue W1 https://doi.org/10.1093/nar/gku340	journal	April 2014
Absolute Protein-Protein Association Rate Constants from Flexible, Coarse-Grained Brownian Dynamics Simulations: The Role of Intermolecular Hydrodynamic Interactions in Barnase-Barstar Association Frembgen-Kesner, Tamara; Elcock, Adrian H. Biophysical Journal, Vol. 99, Issue 9 https://doi.org/10.1016/j.bpj.2010.09.006	journal	November 2010
A practical guide to small angle X-ray scattering (SAXS) of flexible and intrinsically disordered proteins Kikhney, Alexey G.; Svergun, Dmitri I. FEBS Letters, Vol. 589, Issue 19PartA https://doi.org/10.1016/j.febslet.2015.08.027	journal	August 2015
Structure and flexibility within proteins as identified through small angle X-ray scattering Pelikan, M.; Hura, G.; Hammel, M. General Physiology and Biophysics, Vol. 28, Issue 2 https://doi.org/10.4149/gpb_2009_02_174	journal	January 2009
New yeast-Escherichia coli shuttle vectors constructed with in vitro mutagenized yeast genes lacking six-base pair restriction sites Gietz, R. Daniel; Akio, Sugino Gene, Vol. 74, Issue 2 https://doi.org/10.1016/0378-1119(88)90185-0	journal	December 1988
Molecular Simulations of Cotranslational Protein Folding: Fragment Stabilities, Folding Cooperativity, and Trapping in the Ribosome Elcock, Adrian H. PLoS Computational Biology, Vol. 2, Issue 7 https://doi.org/10.1371/journal.pcbi.0020098	journal	January 2006
Variational Treatment of Hydrodynamic Interaction in Polymers Rotne, Jens; Prager, Stephen The Journal of Chemical Physics, Vol. 50, Issue 11 https://doi.org/10.1063/1.1670977	journal	June 1969
Variations on a theme: Eukaryotic Y-family DNA polymerases Washington, M. Todd; Carlson, Karissa D.; Freudenthal, Bret D. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Vol. 1804, Issue 5 https://doi.org/10.1016/j.bbapap.2009.07.004	journal	May 2010
Pre-steady state kinetic studies show that an abasic site is a cognate lesion for the yeast Rev1 protein Pryor, John M.; Washington, M. Todd DNA Repair, Vol. 10, Issue 11 https://doi.org/10.1016/j.dnarep.2011.08.011	journal	November 2011
Structural basis for the suppression of skin cancers by DNA polymerase η Silverstein, Timothy D.; Johnson, Robert E.; Jain, Rinku Nature, Vol. 465, Issue 7301 https://doi.org/10.1038/nature09104	journal	June 2010

Similar Records

Structural and Kinetic Analysis of Miscoding Opposite the DNA Adduct 1,N⁶ -Ethenodeoxyadenosine by Human Translesion DNA Polymerase $η$

Journal Article · Mon May 16 00:00:00 EDT 2016 · Journal of Biological Chemistry · OSTI ID:1478096

Patra, Amritraj; Su, Yan; Zhang, Qianqian; +3 more

Structural and Kinetic Analysis of Nucleoside Triphosphate Incorporation Opposite an Abasic Site by Human Translesion DNA Polymerase η

Journal Article · Mon Feb 09 00:00:00 EST 2015 · Journal of Biological Chemistry · OSTI ID:1478096

Patra, Amritaj; Zhang, Qianqian; Lei, Li; +3 more

Metal-ion dependence of the active-site conformation of the translesion DNA polymerase Dpo4 from Sulfolobus solfataricus

Journal Article · Wed Jul 18 00:00:00 EDT 2012 · Acta Crystallogr. F · OSTI ID:1478096

Irimia, Adriana; Loukachevitch, Lioudmila V; Eoff, Robert L; +2 more

Title: The C-terminal region of translesion synthesis DNA polymerase η is partially unstructured and has high conformational flexibility

Citation Formats

References (64)

Similar Records

Related Subjects