(Q35037206)

5 August 2017

title

Energy analysis of chemistry for correct insertion by DNA polymerase beta (English)

1 reference

5 August 2017

Ping Lin

1

0 references

Lars C Pedersen

object named as

Lars C Pedersen

2

0 references

author name string

Vinod K Batra

3

1 reference

5 August 2017

William A Beard

4

1 reference

5 August 2017

Samuel H Wilson

5

1 reference

5 August 2017

Lee G Pedersen

6

1 reference

5 August 2017

language of work or name

English

0 references

publication date

28 August 2006

1 reference

Proceedings of the National Academy of Sciences of the United States of America

5 August 2017

published in

1 reference

5 August 2017

volume

103

1 reference

5 August 2017

issue

36

1 reference

5 August 2017

page(s)

13294-13299

1 reference

Magnesium-induced assembly of a complete DNA polymerase catalytic complex.

5 August 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

Structure and mechanism of DNA polymerase Beta.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

A thymine isostere in the templating position disrupts assembly of the closed DNA polymerase beta ternary complex

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

Mismatch-induced conformational distortions in polymerase beta support an induced-fit mechanism for fidelity.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

Nucleoside 5'-triphosphates: self-association, acid-base, and metal ion-binding properties in solution

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

Nucleotide-induced DNA polymerase active site motions accommodating a mutagenic DNA intermediate

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

Computer simulations of protein functions: searching for the molecular origin of the replication fidelity of DNA polymerases

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

DNA polymerase fidelity: kinetics, structure, and checkpoints

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

In silico evidence for DNA polymerase-beta's substrate-induced conformational change

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

Dynamic characterization of a DNA repair enzyme: NMR studies of [methyl-13C]methionine-labeled DNA polymerase beta.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

Critical role of magnesium ions in DNA polymerase beta's closing and active site assembly

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

Highly organized but pliant active site of DNA polymerase beta: compensatory mechanisms in mutant enzymes revealed by dynamics simulations and energy analyses.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

Development and testing of a general amber force field

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

Orchestration of cooperative events in DNA synthesis and repair mechanism unraveled by transition path sampling of DNA polymerase beta's closing

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

A structural solution for the DNA polymerase lambda-dependent repair of DNA gaps with minimal homology

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

How enzymes work: analysis by modern rate theory and computer simulations

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

Characterization of the active site of DNA polymerase β by molecular dynamics and quantum chemical calculation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

Computer simulation of the chemical catalysis of DNA polymerases: discriminating between alternative nucleotide insertion mechanisms for T7 DNA polymerase

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

Structural Insights into the Origins of DNA Polymerase Fidelity

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

The pentacovalent phosphorus intermediate of a phosphoryl transfer reaction

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

Computer simulations of enzyme catalysis: methods, progress, and insights

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

Structure of DNA polymerase beta with the mutagenic DNA lesion 8-oxodeoxyguanine reveals structural insights into its coding potential

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

Efficiency of correct nucleotide insertion governs DNA polymerase fidelity.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

Threonine 79 is a hinge residue that governs the fidelity of DNA polymerase beta by helping to position the DNA within the active site

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

Caught in the act: the structure of phosphorylated beta-phosphoglucomutase from Lactococcus lactis

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

Quantum mechanical methods for enzyme kinetics

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

Polymerase beta simulations suggest that Arg258 rotation is a slow step rather than large subdomain motions per se.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

A DNA polymerase beta mutator mutant with reduced nucleotide discrimination and increased protein stability

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

Insight into the catalytic mechanism of DNA polymerase beta: structures of intermediate complexes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

New developments in applying quantum mechanics to proteins.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

DNA structure and aspartate 276 influence nucleotide binding to human DNA polymerase beta. Implication for the identity of the rate-limiting conformational change

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

8 July 2018

DNA replication fidelity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

The E249K mutator mutant of DNA polymerase beta extends mispaired termini

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

Molecular dynamics simulations of biomolecules: long-range electrostatic effects

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

Structure-function analysis of the mammalian DNA polymerase beta active site: role of aspartic acid 256, arginine 254, and arginine 258 in nucleotidyl transfer

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

A general two-metal-ion mechanism for catalytic RNA

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

Crystal structure of rat DNA polymerase beta: evidence for a common polymerase mechanism

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

Crystal structure of the catalytic subunit of human protein phosphatase 1 and its complex with tungstate

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

Use of site-directed mutagenesis to elucidate the role of arginine-166 in the catalytic mechanism of alkaline phosphatase

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

Site-directed mutagenesis of recombinant rat DNA polymerase beta: involvement of arginine-183 in primer recognition

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

Reaction mechanism of alkaline phosphatase based on crystal structures. Two-metal ion catalysis

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

Rapid segmental and subdomain motions of DNA polymerase beta.

8 July 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0606006103

Computer simulation studies of the fidelity of DNA polymerases

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0606006103

Correlation of the kinetics of finger domain mutants in RB69 DNA polymerase with its structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0606006103

Conformational transition pathway of polymerase beta/DNA upon binding correct incoming substrate

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0606006103

Geometry optimization with QM/MM, ONIOM, and other combined methods. I. Microiterations and constraints.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0606006103

Chemical confirmation of a pentavalent phosphorane in complex with beta-phosphoglucomutase

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0606006103

Ab initio QM/MM study shows there is no general acid in the reaction catalyzed by 4-oxalocrotonate tautomerase

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0606006103

DNA polymerase beta: analysis of the contributions of tyrosine-271 and asparagine-279 to substrate specificity and fidelity of DNA replication by pre-steady-state kinetics

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0606006103

Enzyme-DNA interactions required for efficient nucleotide incorporation and discrimination in human DNA polymerase beta.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0606006103

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0606006103

MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0606006103

Mechanisms of signaling and related enzymes

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1569157

The D246V mutant of DNA polymerase beta misincorporates nucleotides: evidence for a role for the flexible loop in DNA positioning within the active site

25 October 2018

1 reference

12 December 2020

Function of arginine-166 in the active site of Escherichia coli alkaline phosphatase

1 reference

12 December 2020

DNA polymerase beta: contributions of template-positioning and dNTP triphosphate-binding residues to catalysis and fidelity

1 reference

12 December 2020

Structural insights into DNA polymerase beta deterrents for misincorporation support an induced-fit mechanism for fidelity

1 reference

12 December 2020

Involvement of phenylalanine 272 of DNA polymerase beta in discriminating between correct and incorrect deoxynucleoside triphosphates

1 reference

12 December 2020

Identifiers

DOI

10.1073/PNAS.0606006103

1 reference

5 August 2017

0 references

1 reference

5 August 2017

1 reference