How DNA polymerase X preferentially accommodates incoming dATP opposite 8-oxoguanine on the template

Benedetta Sampoli Benítez, Zachary R. Barbati, Karunesh Arora, Jasmina Bogdanovic, Tamar Schlick

Research output: Contribution to journalArticle

Abstract

The modified base 8-oxo-7,8-dihydro-2′-deoxyguanosine (oxoG) is a common DNA adduct produced by the oxidation of DNA by reactive oxygen species. Kinetic data reveal that DNA polymerase X (pol X) from the African swine fever virus incorporates adenine (dATP) opposite to oxoG with higher efficiency than the non-damaged G:C basepair. To help interpret the kinetic data, we perform molecular dynamics simulations of pol X/DNA complexes, in which the template base opposite to the incoming dNTP (dCTP, dATP, dGTP) is oxoG. Our results suggest that pol X accommodates the oxoGsyn:A mispair by sampling closed active conformations that mirror those observed in traditional Watson-Crick complexes. Moreover, for both the oxoGsyn:A and oxoG:C ternary complexes, conformational sampling of the polymerase follows previously described large subdomain movements, local residue motions, and active site reorganization. Interestingly, the oxoGsyn:A system exhibits superior active site geometry in comparison to the oxoG:C system. Simulations for the other mismatch basepair complexes reveal large protein subdomain movement for all systems, except for oxoG:G, which samples conformations close to the open state. In addition, active site geometry and basepairing of the template base with the incoming nucleotide, reveal distortions and misalignments that range from moderate (i.e., oxoG:Asyn) to extreme (i.e., oxoG anti/syn:G). These results agree with the available kinetic data for pol X and provide structural insights regarding the mechanism by which this polymerase can accommodate incoming nucleotides opposite oxoG. Our simulations also support the notion that α-helix E is involved both in DNA binding and active site stabilization. Our proposed mechanism by which pol X can preferentially accommodate dATP opposite template oxoG further underscores the role that enzyme dynamics and conformational sampling operate in polymerase fidelity and function.

Original languageEnglish (US)
Pages (from-to)2559-2568
Number of pages10
JournalBiophysical Journal
Volume105
Issue number11
DOIs
StatePublished - Dec 3 2013

Fingerprint

Catalytic Domain
Nucleotides
African Swine Fever Virus
DNA Adducts
DNA
Adenine
Molecular Dynamics Simulation
Reactive Oxygen Species
Binding Sites
8-hydroxyguanine
DNA polymerase X
Enzymes
Proteins

ASJC Scopus subject areas

  • Biophysics

Cite this

How DNA polymerase X preferentially accommodates incoming dATP opposite 8-oxoguanine on the template. / Sampoli Benítez, Benedetta; Barbati, Zachary R.; Arora, Karunesh; Bogdanovic, Jasmina; Schlick, Tamar.

In: Biophysical Journal, Vol. 105, No. 11, 03.12.2013, p. 2559-2568.

Research output: Contribution to journalArticle

Sampoli Benítez, Benedetta ; Barbati, Zachary R. ; Arora, Karunesh ; Bogdanovic, Jasmina ; Schlick, Tamar. / How DNA polymerase X preferentially accommodates incoming dATP opposite 8-oxoguanine on the template. In: Biophysical Journal. 2013 ; Vol. 105, No. 11. pp. 2559-2568.
@article{cc87a2b68abc4b6eb70581a18e3a6e3e,
title = "How DNA polymerase X preferentially accommodates incoming dATP opposite 8-oxoguanine on the template",
abstract = "The modified base 8-oxo-7,8-dihydro-2′-deoxyguanosine (oxoG) is a common DNA adduct produced by the oxidation of DNA by reactive oxygen species. Kinetic data reveal that DNA polymerase X (pol X) from the African swine fever virus incorporates adenine (dATP) opposite to oxoG with higher efficiency than the non-damaged G:C basepair. To help interpret the kinetic data, we perform molecular dynamics simulations of pol X/DNA complexes, in which the template base opposite to the incoming dNTP (dCTP, dATP, dGTP) is oxoG. Our results suggest that pol X accommodates the oxoGsyn:A mispair by sampling closed active conformations that mirror those observed in traditional Watson-Crick complexes. Moreover, for both the oxoGsyn:A and oxoG:C ternary complexes, conformational sampling of the polymerase follows previously described large subdomain movements, local residue motions, and active site reorganization. Interestingly, the oxoGsyn:A system exhibits superior active site geometry in comparison to the oxoG:C system. Simulations for the other mismatch basepair complexes reveal large protein subdomain movement for all systems, except for oxoG:G, which samples conformations close to the open state. In addition, active site geometry and basepairing of the template base with the incoming nucleotide, reveal distortions and misalignments that range from moderate (i.e., oxoG:Asyn) to extreme (i.e., oxoG anti/syn:G). These results agree with the available kinetic data for pol X and provide structural insights regarding the mechanism by which this polymerase can accommodate incoming nucleotides opposite oxoG. Our simulations also support the notion that α-helix E is involved both in DNA binding and active site stabilization. Our proposed mechanism by which pol X can preferentially accommodate dATP opposite template oxoG further underscores the role that enzyme dynamics and conformational sampling operate in polymerase fidelity and function.",
author = "{Sampoli Ben{\'i}tez}, Benedetta and Barbati, {Zachary R.} and Karunesh Arora and Jasmina Bogdanovic and Tamar Schlick",
year = "2013",
month = "12",
day = "3",
doi = "10.1016/j.bpj.2013.10.014",
language = "English (US)",
volume = "105",
pages = "2559--2568",
journal = "Biophysical Journal",
issn = "0006-3495",
publisher = "Biophysical Society",
number = "11",

}

TY - JOUR

T1 - How DNA polymerase X preferentially accommodates incoming dATP opposite 8-oxoguanine on the template

AU - Sampoli Benítez, Benedetta

AU - Barbati, Zachary R.

AU - Arora, Karunesh

AU - Bogdanovic, Jasmina

AU - Schlick, Tamar

PY - 2013/12/3

Y1 - 2013/12/3

N2 - The modified base 8-oxo-7,8-dihydro-2′-deoxyguanosine (oxoG) is a common DNA adduct produced by the oxidation of DNA by reactive oxygen species. Kinetic data reveal that DNA polymerase X (pol X) from the African swine fever virus incorporates adenine (dATP) opposite to oxoG with higher efficiency than the non-damaged G:C basepair. To help interpret the kinetic data, we perform molecular dynamics simulations of pol X/DNA complexes, in which the template base opposite to the incoming dNTP (dCTP, dATP, dGTP) is oxoG. Our results suggest that pol X accommodates the oxoGsyn:A mispair by sampling closed active conformations that mirror those observed in traditional Watson-Crick complexes. Moreover, for both the oxoGsyn:A and oxoG:C ternary complexes, conformational sampling of the polymerase follows previously described large subdomain movements, local residue motions, and active site reorganization. Interestingly, the oxoGsyn:A system exhibits superior active site geometry in comparison to the oxoG:C system. Simulations for the other mismatch basepair complexes reveal large protein subdomain movement for all systems, except for oxoG:G, which samples conformations close to the open state. In addition, active site geometry and basepairing of the template base with the incoming nucleotide, reveal distortions and misalignments that range from moderate (i.e., oxoG:Asyn) to extreme (i.e., oxoG anti/syn:G). These results agree with the available kinetic data for pol X and provide structural insights regarding the mechanism by which this polymerase can accommodate incoming nucleotides opposite oxoG. Our simulations also support the notion that α-helix E is involved both in DNA binding and active site stabilization. Our proposed mechanism by which pol X can preferentially accommodate dATP opposite template oxoG further underscores the role that enzyme dynamics and conformational sampling operate in polymerase fidelity and function.

AB - The modified base 8-oxo-7,8-dihydro-2′-deoxyguanosine (oxoG) is a common DNA adduct produced by the oxidation of DNA by reactive oxygen species. Kinetic data reveal that DNA polymerase X (pol X) from the African swine fever virus incorporates adenine (dATP) opposite to oxoG with higher efficiency than the non-damaged G:C basepair. To help interpret the kinetic data, we perform molecular dynamics simulations of pol X/DNA complexes, in which the template base opposite to the incoming dNTP (dCTP, dATP, dGTP) is oxoG. Our results suggest that pol X accommodates the oxoGsyn:A mispair by sampling closed active conformations that mirror those observed in traditional Watson-Crick complexes. Moreover, for both the oxoGsyn:A and oxoG:C ternary complexes, conformational sampling of the polymerase follows previously described large subdomain movements, local residue motions, and active site reorganization. Interestingly, the oxoGsyn:A system exhibits superior active site geometry in comparison to the oxoG:C system. Simulations for the other mismatch basepair complexes reveal large protein subdomain movement for all systems, except for oxoG:G, which samples conformations close to the open state. In addition, active site geometry and basepairing of the template base with the incoming nucleotide, reveal distortions and misalignments that range from moderate (i.e., oxoG:Asyn) to extreme (i.e., oxoG anti/syn:G). These results agree with the available kinetic data for pol X and provide structural insights regarding the mechanism by which this polymerase can accommodate incoming nucleotides opposite oxoG. Our simulations also support the notion that α-helix E is involved both in DNA binding and active site stabilization. Our proposed mechanism by which pol X can preferentially accommodate dATP opposite template oxoG further underscores the role that enzyme dynamics and conformational sampling operate in polymerase fidelity and function.

UR - http://www.scopus.com/inward/record.url?scp=84889585493&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84889585493&partnerID=8YFLogxK

U2 - 10.1016/j.bpj.2013.10.014

DO - 10.1016/j.bpj.2013.10.014

M3 - Article

VL - 105

SP - 2559

EP - 2568

JO - Biophysical Journal

JF - Biophysical Journal

SN - 0006-3495

IS - 11

ER -