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Title: Protection of abasic sites during DNA replication by a stable thiazolidine protein-DNA cross-link

Abstract

Abasic (AP) sites are one of the most common DNA lesions that block replicative polymerases. 5-hydroxymethylcytosine binding, embryonic stem cell-specific protein (HMCES) recognizes and processes these lesions in the context of single-stranded DNA (ssDNA). A HMCES DNA-protein cross-link (DPC) intermediate is thought to shield the AP site from endonucleases and error-prone polymerases. The highly evolutionarily conserved SOS-response associated peptidase (SRAP) domain of HMCES and its Escherichia coli ortholog YedK mediate lesion recognition. Here we uncover the basis of AP site protection by SRAP domains from a crystal structure of the YedK DPC. We report YedK forms a stable thiazolidine linkage between a ring-opened AP site and the α-amino and sulfhydryl substituents of its amino-terminal cysteine residue. The thiazolidine linkage explains the remarkable stability of the HMCES DPC, its resistance to strand cleavage and the proteolysis requirement for resolution. Furthermore, its structure reveals that HMCES has specificity for AP sites in ssDNA at junctions found when replicative polymerases encounter the AP lesion.

Authors:
 [1]; ORCiD logo [2];  [1]; ORCiD logo [1]; ORCiD logo [3]
  1. Vanderbilt Univ. School of Medicine, Nashville, TN (United States)
  2. Vanderbilt Univ., Nashville, TN (United States)
  3. Vanderbilt Univ. School of Medicine, Nashville, TN (United States); Vanderbilt Univ., Nashville, TN (United States)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
National Institutes of Health (NIH); Vanderbilt Molecular Biophysics Training Program; Vanderbilt-Ingram Cancer Center; USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22); Michigan Economic Development Corporation and the Michigan Technology Tri-Corridor
OSTI Identifier:
1544876
Grant/Contract Number:  
R01ES030575; R01GM117299; P01CA092584; AC02-06CH11357; 085P1000817
Resource Type:
Accepted Manuscript
Journal Name:
Nature Structural & Molecular Biology
Additional Journal Information:
Journal Volume: 26; Journal Issue: 7; Journal ID: ISSN 1545-9993
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES; Biochemistry; DNA; Enzyme mechanisms; Structural biology

Citation Formats

Thompson, Petria S., Amidon, Katherine M., Mohni, Kareem N., Cortez, David, and Eichman, Brandt F. Protection of abasic sites during DNA replication by a stable thiazolidine protein-DNA cross-link. United States: N. p., 2019. Web. doi:10.1038/s41594-019-0255-5.
Thompson, Petria S., Amidon, Katherine M., Mohni, Kareem N., Cortez, David, & Eichman, Brandt F. Protection of abasic sites during DNA replication by a stable thiazolidine protein-DNA cross-link. United States. doi:10.1038/s41594-019-0255-5.
Thompson, Petria S., Amidon, Katherine M., Mohni, Kareem N., Cortez, David, and Eichman, Brandt F. Mon . "Protection of abasic sites during DNA replication by a stable thiazolidine protein-DNA cross-link". United States. doi:10.1038/s41594-019-0255-5.
@article{osti_1544876,
title = {Protection of abasic sites during DNA replication by a stable thiazolidine protein-DNA cross-link},
author = {Thompson, Petria S. and Amidon, Katherine M. and Mohni, Kareem N. and Cortez, David and Eichman, Brandt F.},
abstractNote = {Abasic (AP) sites are one of the most common DNA lesions that block replicative polymerases. 5-hydroxymethylcytosine binding, embryonic stem cell-specific protein (HMCES) recognizes and processes these lesions in the context of single-stranded DNA (ssDNA). A HMCES DNA-protein cross-link (DPC) intermediate is thought to shield the AP site from endonucleases and error-prone polymerases. The highly evolutionarily conserved SOS-response associated peptidase (SRAP) domain of HMCES and its Escherichia coli ortholog YedK mediate lesion recognition. Here we uncover the basis of AP site protection by SRAP domains from a crystal structure of the YedK DPC. We report YedK forms a stable thiazolidine linkage between a ring-opened AP site and the α-amino and sulfhydryl substituents of its amino-terminal cysteine residue. The thiazolidine linkage explains the remarkable stability of the HMCES DPC, its resistance to strand cleavage and the proteolysis requirement for resolution. Furthermore, its structure reveals that HMCES has specificity for AP sites in ssDNA at junctions found when replicative polymerases encounter the AP lesion.},
doi = {10.1038/s41594-019-0255-5},
journal = {Nature Structural & Molecular Biology},
number = 7,
volume = 26,
place = {United States},
year = {2019},
month = {6}
}

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Works referenced in this record:

Recent advances in the structural mechanisms of DNA glycosylases
journal, January 2013

  • Brooks, Sonja C.; Adhikary, Suraj; Rubinson, Emily H.
  • Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Vol. 1834, Issue 1
  • DOI: 10.1016/j.bbapap.2012.10.005

Dynamic Readers for 5-(Hydroxy)Methylcytosine and Its Oxidized Derivatives
journal, February 2013


Base Excision Repair
journal, April 2013


Rapid DNA-protein cross-linking and strand scission by an abasic site in a nucleosome core particle
journal, December 2010

  • Sczepanski, J. T.; Wong, R. S.; McKnight, J. N.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 52
  • DOI: 10.1073/pnas.1012860108

Mechanism of thiazolidine hydrolysis. Ring opening and hydrolysis of 1,3-thiazolidine derivatives of p-(dimethylamino)cinnamaldehyde
journal, April 1991

  • Fife, Thomas H.; Natarajan, R.; Shen, C. C.
  • Journal of the American Chemical Society, Vol. 113, Issue 8
  • DOI: 10.1021/ja00008a041

Rate and equilibrium constants for oxazolidine and thiazolidine ring-opening reactions
journal, January 1996


Reactions of oxygen and sulphur anions with oxazolidine and thiazolidine derivatives of 2-mesyloxymethylglyceraldehyde acetonide
journal, July 1976

  • Just, George; Chung, Bong Young; Kim, Sunggak
  • Canadian Journal of Chemistry, Vol. 54, Issue 13
  • DOI: 10.1139/v76-299

Coot model-building tools for molecular graphics
journal, November 2004

  • Emsley, Paul; Cowtan, Kevin
  • Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132
  • DOI: 10.1107/S0907444904019158

Collaboration gets the most out of software
journal, September 2013


Error-free versus mutagenic processing of genomic uracil—Relevance to cancer
journal, July 2014


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

Recognition but no repair of abasic site in single-stranded DNA by human ribosomal uS3 protein residing within intact 40S subunit
journal, January 2017

  • Grosheva, Anastasia S.; Zharkov, Dmitry O.; Stahl, Joachim
  • Nucleic Acids Research, Vol. 45, Issue 7
  • DOI: 10.1093/nar/gkx052

The cutting edges in DNA repair, licensing, and fidelity: DNA and RNA repair nucleases sculpt DNA to measure twice, cut once
journal, July 2014


Erasure of Tet-Oxidized 5-Methylcytosine by a SRAP Nuclease
journal, October 2017


Suicidal cross-linking of PARP-1 to AP site intermediates in cells undergoing base excision repair
journal, April 2014

  • Prasad, Rajendra; Horton, Julie K.; Chastain, Paul D.
  • Nucleic Acids Research, Vol. 42, Issue 10
  • DOI: 10.1093/nar/gku288

Mechanism of reactions involving Schiff base intermediates. Thiazolidine formation from L-cysteine and formaldehyde
journal, November 1971

  • Kallen, Roland G.
  • Journal of the American Chemical Society, Vol. 93, Issue 23
  • DOI: 10.1021/ja00752a040

Infidelity of DNA synthesis associated with bypass of apurinic sites.
journal, January 1983

  • Schaaper, R. M.; Kunkel, T. A.; Loeb, L. A.
  • Proceedings of the National Academy of Sciences, Vol. 80, Issue 2
  • DOI: 10.1073/pnas.80.2.487

HMCES Maintains Genome Integrity by Shielding Abasic Sites in Single-Strand DNA
journal, January 2019


Repair pathway for PARP-1 DNA-protein crosslinks
journal, January 2019


ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules
journal, May 2016

  • Ashkenazy, Haim; Abadi, Shiran; Martz, Eric
  • Nucleic Acids Research, Vol. 44, Issue W1
  • DOI: 10.1093/nar/gkw408

Excision of cytosine and thymine from DNA by mutants of human uracil-DNA glycosylase.
journal, July 1996


The Action of Formaldehyde upon Cysteine
journal, January 1937

  • Ratner, Sarah; Clarke, H. T.
  • Journal of the American Chemical Society, Vol. 59, Issue 1
  • DOI: 10.1021/ja01280a050

Reduction of Schiff Bases with Sodium Borohydride
journal, September 1957

  • Billman, John H.; Diesing, Arthur C.
  • The Journal of Organic Chemistry, Vol. 22, Issue 9
  • DOI: 10.1021/jo01360a019

Structure and Mechanism of DNA Polymerase β
journal, February 2006

  • Beard, William A.; Wilson, Samuel H.
  • Chemical Reviews, Vol. 106, Issue 2
  • DOI: 10.1021/cr0404904

The intricate structural chemistry of base excision repair machinery: Implications for DNA damage recognition, removal, and repair
journal, April 2007