Cryo-EM structure and dynamics of eukaryotic DNA polymerase δ holoenzyme

Rinku Jain, William J. Rice, Radhika Malik, Robert E. Johnson, Louise Prakash, Satya Prakash, Iban Ubarretxena-Belandia, Aneel K. Aggarwal

Research output: Contribution to journalArticle

Abstract

DNA polymerase δ (Polδ) plays pivotal roles in eukaryotic DNA replication and repair. Polδ is conserved from yeast to humans, and mutations in human Polδ have been implicated in various cancers. Saccharomyces cerevisiae Polδ consists of catalytic Pol3 and the regulatory Pol31 and Pol32 subunits. Here, we present the near atomic resolution (3.2 Å) cryo-EM structure of yeast Polδ holoenzyme in the act of DNA synthesis. The structure reveals an unexpected arrangement in which the regulatory subunits (Pol31 and Pol32) lie next to the exonuclease domain of Pol3 but do not engage the DNA. The Pol3 C-terminal domain contains a 4Fe−4S cluster and emerges as the keystone of Polδ assembly. We also show that the catalytic and regulatory subunits rotate relative to each other and that this is an intrinsic feature of the Polδ architecture. Collectively, the structure provides a framework for understanding DNA transactions at the replication fork.

Original languageEnglish (US)
Pages (from-to)955-962
Number of pages8
JournalNature Structural and Molecular Biology
Volume26
Issue number10
DOIs
StatePublished - Oct 1 2019

Fingerprint

Holoenzymes
DNA-Directed DNA Polymerase
DNA
Yeasts
Exonucleases
DNA Replication
DNA Repair
Saccharomyces cerevisiae
Catalytic Domain
Mutation
Neoplasms

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

Cite this

Cryo-EM structure and dynamics of eukaryotic DNA polymerase δ holoenzyme. / Jain, Rinku; Rice, William J.; Malik, Radhika; Johnson, Robert E.; Prakash, Louise; Prakash, Satya; Ubarretxena-Belandia, Iban; Aggarwal, Aneel K.

In: Nature Structural and Molecular Biology, Vol. 26, No. 10, 01.10.2019, p. 955-962.

Research output: Contribution to journalArticle

Jain, R, Rice, WJ, Malik, R, Johnson, RE, Prakash, L, Prakash, S, Ubarretxena-Belandia, I & Aggarwal, AK 2019, 'Cryo-EM structure and dynamics of eukaryotic DNA polymerase δ holoenzyme', Nature Structural and Molecular Biology, vol. 26, no. 10, pp. 955-962. https://doi.org/10.1038/s41594-019-0305-z
Jain, Rinku ; Rice, William J. ; Malik, Radhika ; Johnson, Robert E. ; Prakash, Louise ; Prakash, Satya ; Ubarretxena-Belandia, Iban ; Aggarwal, Aneel K. / Cryo-EM structure and dynamics of eukaryotic DNA polymerase δ holoenzyme. In: Nature Structural and Molecular Biology. 2019 ; Vol. 26, No. 10. pp. 955-962.
@article{d62e190257a84bcea7d809f6721cf2cc,
title = "Cryo-EM structure and dynamics of eukaryotic DNA polymerase δ holoenzyme",
abstract = "DNA polymerase δ (Polδ) plays pivotal roles in eukaryotic DNA replication and repair. Polδ is conserved from yeast to humans, and mutations in human Polδ have been implicated in various cancers. Saccharomyces cerevisiae Polδ consists of catalytic Pol3 and the regulatory Pol31 and Pol32 subunits. Here, we present the near atomic resolution (3.2 {\AA}) cryo-EM structure of yeast Polδ holoenzyme in the act of DNA synthesis. The structure reveals an unexpected arrangement in which the regulatory subunits (Pol31 and Pol32) lie next to the exonuclease domain of Pol3 but do not engage the DNA. The Pol3 C-terminal domain contains a 4Fe−4S cluster and emerges as the keystone of Polδ assembly. We also show that the catalytic and regulatory subunits rotate relative to each other and that this is an intrinsic feature of the Polδ architecture. Collectively, the structure provides a framework for understanding DNA transactions at the replication fork.",
author = "Rinku Jain and Rice, {William J.} and Radhika Malik and Johnson, {Robert E.} and Louise Prakash and Satya Prakash and Iban Ubarretxena-Belandia and Aggarwal, {Aneel K.}",
year = "2019",
month = "10",
day = "1",
doi = "10.1038/s41594-019-0305-z",
language = "English (US)",
volume = "26",
pages = "955--962",
journal = "Nature Structural and Molecular Biology",
issn = "1545-9993",
publisher = "Nature Publishing Group",
number = "10",

}

TY - JOUR

T1 - Cryo-EM structure and dynamics of eukaryotic DNA polymerase δ holoenzyme

AU - Jain, Rinku

AU - Rice, William J.

AU - Malik, Radhika

AU - Johnson, Robert E.

AU - Prakash, Louise

AU - Prakash, Satya

AU - Ubarretxena-Belandia, Iban

AU - Aggarwal, Aneel K.

PY - 2019/10/1

Y1 - 2019/10/1

N2 - DNA polymerase δ (Polδ) plays pivotal roles in eukaryotic DNA replication and repair. Polδ is conserved from yeast to humans, and mutations in human Polδ have been implicated in various cancers. Saccharomyces cerevisiae Polδ consists of catalytic Pol3 and the regulatory Pol31 and Pol32 subunits. Here, we present the near atomic resolution (3.2 Å) cryo-EM structure of yeast Polδ holoenzyme in the act of DNA synthesis. The structure reveals an unexpected arrangement in which the regulatory subunits (Pol31 and Pol32) lie next to the exonuclease domain of Pol3 but do not engage the DNA. The Pol3 C-terminal domain contains a 4Fe−4S cluster and emerges as the keystone of Polδ assembly. We also show that the catalytic and regulatory subunits rotate relative to each other and that this is an intrinsic feature of the Polδ architecture. Collectively, the structure provides a framework for understanding DNA transactions at the replication fork.

AB - DNA polymerase δ (Polδ) plays pivotal roles in eukaryotic DNA replication and repair. Polδ is conserved from yeast to humans, and mutations in human Polδ have been implicated in various cancers. Saccharomyces cerevisiae Polδ consists of catalytic Pol3 and the regulatory Pol31 and Pol32 subunits. Here, we present the near atomic resolution (3.2 Å) cryo-EM structure of yeast Polδ holoenzyme in the act of DNA synthesis. The structure reveals an unexpected arrangement in which the regulatory subunits (Pol31 and Pol32) lie next to the exonuclease domain of Pol3 but do not engage the DNA. The Pol3 C-terminal domain contains a 4Fe−4S cluster and emerges as the keystone of Polδ assembly. We also show that the catalytic and regulatory subunits rotate relative to each other and that this is an intrinsic feature of the Polδ architecture. Collectively, the structure provides a framework for understanding DNA transactions at the replication fork.

UR - http://www.scopus.com/inward/record.url?scp=85072913798&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85072913798&partnerID=8YFLogxK

U2 - 10.1038/s41594-019-0305-z

DO - 10.1038/s41594-019-0305-z

M3 - Article

C2 - 31582849

AN - SCOPUS:85072913798

VL - 26

SP - 955

EP - 962

JO - Nature Structural and Molecular Biology

JF - Nature Structural and Molecular Biology

SN - 1545-9993

IS - 10

ER -