(Q34185910)

English

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

scientific article

In more languages

Statements

scholarly article

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:15189842%20AND%20SRC:MED&resulttype=core&format=json

29 December 2019

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

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:15189842%20AND%20SRC:MED&resulttype=core&format=json

29 December 2019

Samuel H. Wilson

3

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:15189842%20AND%20SRC:MED&resulttype=core&format=json

29 December 2019

4

object named as

Suse Broyde

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:15189842%20AND%20SRC:MED&resulttype=core&format=json

29 December 2019

5

object named as

Tamar Schlick

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:15189842%20AND%20SRC:MED&resulttype=core&format=json

29 December 2019

author name string

Linjing Yang

1

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:15189842%20AND%20SRC:MED&resulttype=core&format=json

29 December 2019

William A Beard

2

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:15189842%20AND%20SRC:MED&resulttype=core&format=json

29 December 2019

language of work or name

0 references

publication date

1 June 2004

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:15189842%20AND%20SRC:MED&resulttype=core&format=json

29 December 2019

Biophysical Journal

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:15189842%20AND%20SRC:MED&resulttype=core&format=json

29 December 2019

86

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:15189842%20AND%20SRC:MED&resulttype=core&format=json

29 December 2019

6

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:15189842%20AND%20SRC:MED&resulttype=core&format=json

29 December 2019

3392-3408

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:15189842%20AND%20SRC:MED&resulttype=core&format=json

29 December 2019

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

Structural Insights into the Origins of DNA Polymerase Fidelity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

Efficiency of correct nucleotide insertion governs DNA polymerase fidelity.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

Local deformations revealed by dynamics simulations of DNA polymerase Beta with DNA mismatches at the primer terminus

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

Solution structure of a viral DNA polymerase X and evidence for a mutagenic function

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

Solution structure of a viral DNA repair polymerase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

The Y-family of DNA polymerases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

DNA polymerase lambda (Pol lambda), a novel eukaryotic DNA polymerase with a potential role in meiosis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 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=1304247

5 July 2018

Structural design of a eukaryotic DNA repair polymerase: DNA polymerase beta.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

Functional mutation of DNA polymerase beta found in human gastric cancer--inability of the base excision repair in vitro.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

Archaeal DNA replication: identifying the pieces to solve a puzzle.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

An open and closed case for all polymerases.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

Structure and functional implications of the polymerase active site region in a complex of HIV-1 RT with a double-stranded DNA template-primer and an antibody Fab fragment at 2.8 A resolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

DNA polymerase beta: effects of gapped DNA substrates on dNTP specificity, fidelity, processivity and conformational changes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 A resolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

Characterization of an African swine fever virus 20-kDa DNA polymerase involved in DNA repair

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

Hydrogen bonding revisited: geometric selection as a principal determinant of DNA replication fidelity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

Biomolecular dynamics at long timesteps: bridging the timescale gap between simulation and experimentation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

Crystal structure of a pol alpha family replication DNA polymerase from bacteriophage RB69

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

DNA polymerase beta: structure-fidelity relationship from Pre-steady-state kinetic analyses of all possible correct and incorrect base pairs for wild type and R283A mutant

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

DNA polymerase beta: pre-steady-state kinetic analysis and roles of arginine-283 in catalysis and fidelity.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

Structure of DNA polymerase I Klenow fragment bound to duplex DNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

Compilation, alignment, and phylogenetic relationships of DNA polymerases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

Function and structure relationships in DNA polymerases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

Kinetic mechanism whereby DNA polymerase I (Klenow) replicates DNA with high fidelity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

Infectious potential of human immunodeficiency virus type 1 reverse transcriptase mutants with altered inhibitor sensitivity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

Site-specific mutagenesis of AIDS virus reverse transcriptase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

Electrical potential of transfer RNAs: codon-anticodon recognition.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

Identification of residues critical for the polymerase activity of the Klenow fragment of DNA polymerase I from Escherichia coli

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

An attempt to unify the structure of polymerases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

Aspartic acid residues at positions 190 and 192 of rat DNA polymerase beta are involved in primer binding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

Fidelity mechanisms in DNA replication

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

Compilation and alignment of DNA polymerase sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

Pre-steady-state kinetic analysis of processive DNA replication including complete characterization of an exonuclease-deficient mutant

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

Kinetic mechanism of DNA polymerase I(Klenow fragment): identification of a second conformational change and evaluation of the internal equilibrium constant

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

Mechanism and fidelity of HIV reverse transcriptase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

5 July 2018

Loss of DNA polymerase beta stacking interactions with templating purines, but not pyrimidines, alters catalytic efficiency and fidelity.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

28 October 2018

Time-trimming tricks for dynamic simulations: splitting force updates to reduce computational work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

28 October 2018

Calculating the electrostatic properties of RNA provides new insights into molecular interactions and function.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

28 October 2018

Cloning, purification and characterization of DNA polymerase beta from Xenopus laevis--studies on its potential role in DNA-end joining.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

28 October 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

28 October 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

28 October 2018

The nucleotide analog 2-aminopurine as a spectroscopic probe of nucleotide incorporation by the Klenow fragment of Escherichia coli polymerase I and bacteriophage T4 DNA polymerase.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304247

28 October 2018

Structural insights into DNA polymerase beta fidelity: hold tight if you want it right

1 reference

https://pubmed.ncbi.nlm.nih.gov/15189842

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Mimicking the Structure and Function of DNA: Insights into DNA Stability and Replication

1 reference

https://pubmed.ncbi.nlm.nih.gov/15189842

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A unified DNA- and dNTP-binding mode for DNA polymerases

1 reference

https://pubmed.ncbi.nlm.nih.gov/15189842

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

DNA polymerase beta: multiple conformational changes in the mechanism of catalysis

1 reference

https://pubmed.ncbi.nlm.nih.gov/15189842

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Base substitution specificity of DNA polymerase beta depends on interactions in the DNA minor groove

1 reference

https://pubmed.ncbi.nlm.nih.gov/15189842

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The mechanism of action of T7 DNA polymerase

1 reference

https://pubmed.ncbi.nlm.nih.gov/15189842

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Mammalian base excision repair and DNA polymerase beta

1 reference

https://pubmed.ncbi.nlm.nih.gov/15189842

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1529/BIOPHYSJ.103.036012

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:15189842%20AND%20SRC:MED&resulttype=core&format=json

29 December 2019

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:15189842%20AND%20SRC:MED&resulttype=core&format=json

29 December 2019

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:15189842%20AND%20SRC:MED&resulttype=core&format=json

29 December 2019

ResearchGate publication ID

0 references

Sitelinks

Wikipedia(0 entries)

Wikibooks(0 entries)

Wikinews(0 entries)

Wikiquote(0 entries)

Wikisource(0 entries)

Wikiversity(0 entries)

Wikivoyage(0 entries)

Wiktionary(0 entries)

Multilingual sites(0 entries)

Retrieved from "https://www.wikidata.org/w/index.php?title=Q34185910&oldid=2033874442"