Structural basis for proofreading during replication of the Escherichia coli chromosome

Samir Hamdan; Paul D. Carr; Susan E. Brown; David L. Ollis; Nicholas E. Dixon

doi:10.1016/S0969-2126(02)00738-4

Structural basis for proofreading during replication of the Escherichia coli chromosome

Samir Hamdan, Paul D. Carr, Susan E. Brown, David L. Ollis, Nicholas E. Dixon^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

128 Scopus citations

Abstract

The ε subunit of the Escherichia coli replicative DNA polymerase III is the proofreading 3′-5′ exonuclease. Structures of its catalytic N-terminal domain (ε186) were determined at two pH values (5.8 and 8.5) at resolutions of 1.7-1.8 Å, in complex with two Mn(II) ions and a nucleotide product of its reaction, thymidine 5′-monophosphate. The protein structure is built around a core five-stranded β sheet that is a common feature of members of the DnaQ superfamily. The structures were identical, except for differences in the way TMP and water molecules are coordinated to the binuclear metal center in the active site. These data are used to develop a mechanism for ε and to produce a plausible model of the complex of ε186 with DNA.

Original language	English (US)
Pages (from-to)	535-546
Number of pages	12
Journal	Structure
Volume	10
Issue number	4
DOIs	https://doi.org/10.1016/S0969-2126(02)00738-4
State	Published - 2002
Externally published	Yes

Bibliographical note

Funding Information:
Philippe Carpentier and the support staff at the FIP beamline, ESRF are thanked for their support during data collection at that facility. Harry Tong and the support staff at the BioCARS beamline are thanked for their support during data collection at the Advanced Photon Source. This work, including use of the BioCARS sector, was supported by the Australian Synchrotron Research Program, which is funded by the Commonwealth of Australia under the Major National Research Facilities Program. Use of the APS was supported by the U.S. Department of Energy, Basic Energy Sciences, and Office of Energy Research, under Contract Number W-31-109-Eng-38. S.E.B. was a recipient of an Australian Postdoctoral Fellowship (Australian Research Council).

Keywords

Binuclear metallohydrolase
DNA polymerase III
DNA replication
DnaQ
Exonuclease (3′-5′)
Manganese metalloenzyme
X-ray crystallography

ASJC Scopus subject areas

Structural Biology
Molecular Biology

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10.1016/S0969-2126(02)00738-4

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title = "Structural basis for proofreading during replication of the Escherichia coli chromosome",

abstract = "The ε subunit of the Escherichia coli replicative DNA polymerase III is the proofreading 3′-5′ exonuclease. Structures of its catalytic N-terminal domain (ε186) were determined at two pH values (5.8 and 8.5) at resolutions of 1.7-1.8 {\AA}, in complex with two Mn(II) ions and a nucleotide product of its reaction, thymidine 5′-monophosphate. The protein structure is built around a core five-stranded β sheet that is a common feature of members of the DnaQ superfamily. The structures were identical, except for differences in the way TMP and water molecules are coordinated to the binuclear metal center in the active site. These data are used to develop a mechanism for ε and to produce a plausible model of the complex of ε186 with DNA.",

keywords = "Binuclear metallohydrolase, DNA polymerase III, DNA replication, DnaQ, Exonuclease (3′-5′), Manganese metalloenzyme, X-ray crystallography",

author = "Samir Hamdan and Carr, {Paul D.} and Brown, {Susan E.} and Ollis, {David L.} and Dixon, {Nicholas E.}",

note = "Funding Information: Philippe Carpentier and the support staff at the FIP beamline, ESRF are thanked for their support during data collection at that facility. Harry Tong and the support staff at the BioCARS beamline are thanked for their support during data collection at the Advanced Photon Source. This work, including use of the BioCARS sector, was supported by the Australian Synchrotron Research Program, which is funded by the Commonwealth of Australia under the Major National Research Facilities Program. Use of the APS was supported by the U.S. Department of Energy, Basic Energy Sciences, and Office of Energy Research, under Contract Number W-31-109-Eng-38. S.E.B. was a recipient of an Australian Postdoctoral Fellowship (Australian Research Council). ",

year = "2002",

doi = "10.1016/S0969-2126(02)00738-4",

language = "English (US)",

volume = "10",

pages = "535--546",

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AU - Carr, Paul D.

AU - Brown, Susan E.

AU - Ollis, David L.

AU - Dixon, Nicholas E.

N1 - Funding Information: Philippe Carpentier and the support staff at the FIP beamline, ESRF are thanked for their support during data collection at that facility. Harry Tong and the support staff at the BioCARS beamline are thanked for their support during data collection at the Advanced Photon Source. This work, including use of the BioCARS sector, was supported by the Australian Synchrotron Research Program, which is funded by the Commonwealth of Australia under the Major National Research Facilities Program. Use of the APS was supported by the U.S. Department of Energy, Basic Energy Sciences, and Office of Energy Research, under Contract Number W-31-109-Eng-38. S.E.B. was a recipient of an Australian Postdoctoral Fellowship (Australian Research Council).

PY - 2002

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N2 - The ε subunit of the Escherichia coli replicative DNA polymerase III is the proofreading 3′-5′ exonuclease. Structures of its catalytic N-terminal domain (ε186) were determined at two pH values (5.8 and 8.5) at resolutions of 1.7-1.8 Å, in complex with two Mn(II) ions and a nucleotide product of its reaction, thymidine 5′-monophosphate. The protein structure is built around a core five-stranded β sheet that is a common feature of members of the DnaQ superfamily. The structures were identical, except for differences in the way TMP and water molecules are coordinated to the binuclear metal center in the active site. These data are used to develop a mechanism for ε and to produce a plausible model of the complex of ε186 with DNA.

AB - The ε subunit of the Escherichia coli replicative DNA polymerase III is the proofreading 3′-5′ exonuclease. Structures of its catalytic N-terminal domain (ε186) were determined at two pH values (5.8 and 8.5) at resolutions of 1.7-1.8 Å, in complex with two Mn(II) ions and a nucleotide product of its reaction, thymidine 5′-monophosphate. The protein structure is built around a core five-stranded β sheet that is a common feature of members of the DnaQ superfamily. The structures were identical, except for differences in the way TMP and water molecules are coordinated to the binuclear metal center in the active site. These data are used to develop a mechanism for ε and to produce a plausible model of the complex of ε186 with DNA.

KW - Binuclear metallohydrolase

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KW - DNA replication

KW - DnaQ

KW - Exonuclease (3′-5′)

KW - Manganese metalloenzyme

KW - X-ray crystallography

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Structural basis for proofreading during replication of the Escherichia coli chromosome

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

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