Structure of human DNA polymerase κ inserting dATP opposite an 8-OxoG DNA lesion

Rodrigo Vasquez-Del Carpio, Timothy D. Silverstein, Samer Lone, Michael K. Swan, Jayati R. Choudhury, Robert E. Johnson, Satya Prakash, Louise Prakash, Aneel K. Aggarwal

Research output: Contribution to journalArticle

37 Citations (Scopus)

Abstract

Background: Oxygen-free radicals formed during normal aerobic cellular metabolism attack bases in DNA and 7,8-dihydro-8-oxoguanine (8-oxoG) is one of the major lesions formed. It is amongst the most mutagenic lesions in cells because of its dual coding potential, wherein 8-oxoG(syn) can pair with an A in addition to normal base pairing of 8-oxoG(anti) with a C. Human DNA polymerase κ (Polk) is a member of the newly discovered Y-family of DNA polymerases that possess the ability to replicate through DNA lesions. To understand the basis of Polk's preference for insertion of an A opposite 8-oxoG lesion, we have solved the structure of Polk in ternary complex with a template-primer presenting 8-oxoG in the active site and with dATP as the incoming nucleotide. Methodology and Principal Findings: We show that the Polk active site is well-adapted to accommodate 8-oxoG in the syn conformation. That is, the polymerase and the bound template-primer are almost identical in their conformations to that in the ternary complex with undamaged DNA. There is no steric hindrance to accommodating 8-oxoG in the syn conformation for Hoogsteen base-paring with incoming dATP. Conclusions and Significance: The structure we present here is the first for a eukaryotic translesion synthesis (TLS) DNA polymerase with an 8-oxoG:A base pair in the active site. The structure shows why Polk is more efficient at inserting an A opposite the 8-oxoG lesion than a C. The structure also provides a basis for why Polk is more efficient at inserting an A opposite the lesion than other Y-family DNA polymerases.

Original languageEnglish (US)
Article numbere5766
JournalPLoS One
Volume4
Issue number6
DOIs
StatePublished - Jun 2 2009

Fingerprint

DNA-directed DNA polymerase
DNA-Directed DNA Polymerase
lesions (animal)
Catalytic Domain
Conformations
Base Pairing
DNA
active sites
Free Radicals
Reactive Oxygen Species
Nucleotides
Metabolism
Oxygen
nucleotides
oxygen
metabolism
synthesis
cells

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Vasquez-Del Carpio, R., Silverstein, T. D., Lone, S., Swan, M. K., Choudhury, J. R., Johnson, R. E., ... Aggarwal, A. K. (2009). Structure of human DNA polymerase κ inserting dATP opposite an 8-OxoG DNA lesion. PLoS One, 4(6), [e5766]. https://doi.org/10.1371/journal.pone.0005766

Structure of human DNA polymerase κ inserting dATP opposite an 8-OxoG DNA lesion. / Vasquez-Del Carpio, Rodrigo; Silverstein, Timothy D.; Lone, Samer; Swan, Michael K.; Choudhury, Jayati R.; Johnson, Robert E.; Prakash, Satya; Prakash, Louise; Aggarwal, Aneel K.

In: PLoS One, Vol. 4, No. 6, e5766, 02.06.2009.

Research output: Contribution to journalArticle

Vasquez-Del Carpio, R, Silverstein, TD, Lone, S, Swan, MK, Choudhury, JR, Johnson, RE, Prakash, S, Prakash, L & Aggarwal, AK 2009, 'Structure of human DNA polymerase κ inserting dATP opposite an 8-OxoG DNA lesion', PLoS One, vol. 4, no. 6, e5766. https://doi.org/10.1371/journal.pone.0005766
Vasquez-Del Carpio R, Silverstein TD, Lone S, Swan MK, Choudhury JR, Johnson RE et al. Structure of human DNA polymerase κ inserting dATP opposite an 8-OxoG DNA lesion. PLoS One. 2009 Jun 2;4(6). e5766. https://doi.org/10.1371/journal.pone.0005766
Vasquez-Del Carpio, Rodrigo ; Silverstein, Timothy D. ; Lone, Samer ; Swan, Michael K. ; Choudhury, Jayati R. ; Johnson, Robert E. ; Prakash, Satya ; Prakash, Louise ; Aggarwal, Aneel K. / Structure of human DNA polymerase κ inserting dATP opposite an 8-OxoG DNA lesion. In: PLoS One. 2009 ; Vol. 4, No. 6.
@article{20789f4c25d24edda6ec0f65bbe3dab4,
title = "Structure of human DNA polymerase κ inserting dATP opposite an 8-OxoG DNA lesion",
abstract = "Background: Oxygen-free radicals formed during normal aerobic cellular metabolism attack bases in DNA and 7,8-dihydro-8-oxoguanine (8-oxoG) is one of the major lesions formed. It is amongst the most mutagenic lesions in cells because of its dual coding potential, wherein 8-oxoG(syn) can pair with an A in addition to normal base pairing of 8-oxoG(anti) with a C. Human DNA polymerase κ (Polk) is a member of the newly discovered Y-family of DNA polymerases that possess the ability to replicate through DNA lesions. To understand the basis of Polk's preference for insertion of an A opposite 8-oxoG lesion, we have solved the structure of Polk in ternary complex with a template-primer presenting 8-oxoG in the active site and with dATP as the incoming nucleotide. Methodology and Principal Findings: We show that the Polk active site is well-adapted to accommodate 8-oxoG in the syn conformation. That is, the polymerase and the bound template-primer are almost identical in their conformations to that in the ternary complex with undamaged DNA. There is no steric hindrance to accommodating 8-oxoG in the syn conformation for Hoogsteen base-paring with incoming dATP. Conclusions and Significance: The structure we present here is the first for a eukaryotic translesion synthesis (TLS) DNA polymerase with an 8-oxoG:A base pair in the active site. The structure shows why Polk is more efficient at inserting an A opposite the 8-oxoG lesion than a C. The structure also provides a basis for why Polk is more efficient at inserting an A opposite the lesion than other Y-family DNA polymerases.",
author = "{Vasquez-Del Carpio}, Rodrigo and Silverstein, {Timothy D.} and Samer Lone and Swan, {Michael K.} and Choudhury, {Jayati R.} and Johnson, {Robert E.} and Satya Prakash and Louise Prakash and Aggarwal, {Aneel K.}",
year = "2009",
month = "6",
day = "2",
doi = "10.1371/journal.pone.0005766",
language = "English (US)",
volume = "4",
journal = "PLoS One",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "6",

}

TY - JOUR

T1 - Structure of human DNA polymerase κ inserting dATP opposite an 8-OxoG DNA lesion

AU - Vasquez-Del Carpio, Rodrigo

AU - Silverstein, Timothy D.

AU - Lone, Samer

AU - Swan, Michael K.

AU - Choudhury, Jayati R.

AU - Johnson, Robert E.

AU - Prakash, Satya

AU - Prakash, Louise

AU - Aggarwal, Aneel K.

PY - 2009/6/2

Y1 - 2009/6/2

N2 - Background: Oxygen-free radicals formed during normal aerobic cellular metabolism attack bases in DNA and 7,8-dihydro-8-oxoguanine (8-oxoG) is one of the major lesions formed. It is amongst the most mutagenic lesions in cells because of its dual coding potential, wherein 8-oxoG(syn) can pair with an A in addition to normal base pairing of 8-oxoG(anti) with a C. Human DNA polymerase κ (Polk) is a member of the newly discovered Y-family of DNA polymerases that possess the ability to replicate through DNA lesions. To understand the basis of Polk's preference for insertion of an A opposite 8-oxoG lesion, we have solved the structure of Polk in ternary complex with a template-primer presenting 8-oxoG in the active site and with dATP as the incoming nucleotide. Methodology and Principal Findings: We show that the Polk active site is well-adapted to accommodate 8-oxoG in the syn conformation. That is, the polymerase and the bound template-primer are almost identical in their conformations to that in the ternary complex with undamaged DNA. There is no steric hindrance to accommodating 8-oxoG in the syn conformation for Hoogsteen base-paring with incoming dATP. Conclusions and Significance: The structure we present here is the first for a eukaryotic translesion synthesis (TLS) DNA polymerase with an 8-oxoG:A base pair in the active site. The structure shows why Polk is more efficient at inserting an A opposite the 8-oxoG lesion than a C. The structure also provides a basis for why Polk is more efficient at inserting an A opposite the lesion than other Y-family DNA polymerases.

AB - Background: Oxygen-free radicals formed during normal aerobic cellular metabolism attack bases in DNA and 7,8-dihydro-8-oxoguanine (8-oxoG) is one of the major lesions formed. It is amongst the most mutagenic lesions in cells because of its dual coding potential, wherein 8-oxoG(syn) can pair with an A in addition to normal base pairing of 8-oxoG(anti) with a C. Human DNA polymerase κ (Polk) is a member of the newly discovered Y-family of DNA polymerases that possess the ability to replicate through DNA lesions. To understand the basis of Polk's preference for insertion of an A opposite 8-oxoG lesion, we have solved the structure of Polk in ternary complex with a template-primer presenting 8-oxoG in the active site and with dATP as the incoming nucleotide. Methodology and Principal Findings: We show that the Polk active site is well-adapted to accommodate 8-oxoG in the syn conformation. That is, the polymerase and the bound template-primer are almost identical in their conformations to that in the ternary complex with undamaged DNA. There is no steric hindrance to accommodating 8-oxoG in the syn conformation for Hoogsteen base-paring with incoming dATP. Conclusions and Significance: The structure we present here is the first for a eukaryotic translesion synthesis (TLS) DNA polymerase with an 8-oxoG:A base pair in the active site. The structure shows why Polk is more efficient at inserting an A opposite the 8-oxoG lesion than a C. The structure also provides a basis for why Polk is more efficient at inserting an A opposite the lesion than other Y-family DNA polymerases.

UR - http://www.scopus.com/inward/record.url?scp=66849126006&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=66849126006&partnerID=8YFLogxK

U2 - 10.1371/journal.pone.0005766

DO - 10.1371/journal.pone.0005766

M3 - Article

VL - 4

JO - PLoS One

JF - PLoS One

SN - 1932-6203

IS - 6

M1 - e5766

ER -