Mismatched dNTP incorporation by DNA polymerase does not proceed via globally different conformational pathways (Q27650213)

1

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Marc Niebuhr

2

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Chang-Shung Tung

3

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Hsiu-Chien Chan

4

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Chia-Cheng Chou

5

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Ming-Daw Tsai

Crystal structure of a DinB family error-prone DNA polymerase from Sulfolobus solfataricus

6

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language of work or name

English

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publication date

May 2008

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published in

Nucleic Acids Research

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volume

36

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issue

9

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page(s)

2948-57

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cites work

1 reference

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Crystal structure of a DinB lesion bypass DNA polymerase catalytic fragment reveals a classic polymerase catalytic domain

20 March 2017

1 reference

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Determination of domain structure of proteins from X-ray solution scattering

20 March 2017

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Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing

20 March 2017

1 reference

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

20 March 2017

1 reference

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Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis

20 March 2017

1 reference

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

20 March 2017

1 reference

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The Amber biomolecular simulation programs

20 March 2017

1 reference

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Refinement of macromolecular structures by the maximum-likelihood method

20 March 2017

1 reference

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XtalView/Xfit--A versatile program for manipulating atomic coordinates and electron density

20 March 2017

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Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination

20 March 2017

1 reference

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Structures of mismatch replication errors observed in a DNA polymerase

20 March 2017

1 reference

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Solution structures of 2 : 1 and 1 : 1 DNA polymerase-DNA complexes probed by ultracentrifugation and small-angle X-ray scattering

20 March 2017

1 reference

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Structure and mechanism of DNA polymerase Beta.

29 September 2017

1 reference

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Mechanistic comparison of high-fidelity and error-prone DNA polymerases and ligases involved in DNA repair

29 September 2017

1 reference

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

29 September 2017

1 reference

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A closed conformation for the Pol lambda catalytic cycle.

29 September 2017

1 reference

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DNA polymerase fidelity: kinetics, structure, and checkpoints

29 September 2017

1 reference

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Use of 2-aminopurine fluorescence to examine conformational changes during nucleotide incorporation by DNA polymerase I (Klenow fragment).

29 September 2017

1 reference

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A reexamination of the nucleotide incorporation fidelity of DNA polymerases

29 September 2017

1 reference

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High affinity hormone binding to the extracellular N-terminal exodomain of the follicle-stimulating hormone receptor is critically modulated by exoloop 3.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396427

Simulating the effect of DNA polymerase mutations on transition-state energetics and fidelity: evaluating amino acid group contribution and allosteric coupling for ionized residues in human pol beta

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396427

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

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396427

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

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396427

A geometrical approach in folding a pseudoknot motif within the E. coli 16S-RNA.

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396427

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

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396427

Investigation of the conformational states of Wzz and the Wzz.O-antigen complex under near-physiological conditions.

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396427

The hydrophobic hinge region of rat DNA polymerase beta is critical for substrate binding pocket geometry

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396427

Use of viscogens, dNTPalphaS, and rhodium(III) as probes in stopped-flow experiments to obtain new evidence for the mechanism of catalysis by DNA polymerase beta.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396427

Hinge residue Ile260 of DNA polymerase beta is important for enzyme activity and fidelity

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396427

The BioCAT undulator beamline 18ID: a facility for biological non-crystalline diffraction and X-ray absorption spectroscopy at the Advanced Photon Source.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396427

Dpo4 is hindered in extending a G.T mismatch by a reverse wobble

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396427

Global Conformations, Hydrodynamics, and X-ray Scattering Properties of Taq and Escherichia coli DNA Polymerases in Solution

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396427

Use of 2-aminopurine and tryptophan fluorescence as probes in kinetic analyses of DNA polymerase beta

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396427

Structural study of homeodomain protein-DNA complexes using a homology modeling approach.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396427

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

27 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18385153

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A new paradigm for DNA polymerase specificity

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18385153

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Processing of X-ray diffraction data collected in oscillation mode

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18385153