Quantum mechanics/molecular mechanics investigation of the chemical reaction in Dpo4 reveals water-dependent pathways and requirements for active site reorganization (Q38731525)

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scientific article published on 12 September 2008

Language	Label	Description	Also known as
English	Quantum mechanics/molecular mechanics investigation of the chemical reaction in Dpo4 reveals water-dependent pathways and requirements for active site reorganization	scientific article published on 12 September 2008

Statements

scholarly article

1 reference

Europe PubMed Central

5 September 2017

Quantum mechanics/molecular mechanics investigation of the chemical reaction in Dpo4 reveals water-dependent pathways and requirements for active site reorganization (English)

1 reference

Europe PubMed Central

5 September 2017

quantum mechanics

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2

object named as

Tamar Schlick

1 reference

Europe PubMed Central

5 September 2017

author name string

Yanli Wang

1

1 reference

Europe PubMed Central

5 September 2017

language of work or name

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publication date

12 September 2008

1 reference

Europe PubMed Central

5 September 2017

Journal of the American Chemical Society

1 reference

Europe PubMed Central

5 September 2017

130

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Europe PubMed Central

5 September 2017

13240-13250

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Europe PubMed Central

5 September 2017

40

1 reference

Europe PubMed Central

5 September 2017

Incorrect nucleotide insertion at the active site of a G:A mismatch catalyzed by DNA polymerase beta

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195406

6 September 2017

Structure and activity of Y-class DNA polymerase DPO4 from Sulfolobus solfataricus with templates containing the hydrophobic thymine analog 2,4-difluorotoluene

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3195406

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Exploring the role of large conformational changes in the fidelity of DNA polymerase beta

1 reference

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Hydrogen bonding of 7,8-dihydro-8-oxodeoxyguanosine with a charged residue in the little finger domain determines miscoding events in Sulfolobus solfataricus DNA polymerase Dpo4

1 reference

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6 September 2017

A water-mediated and substrate-assisted catalytic mechanism for Sulfolobus solfataricus DNA polymerase IV.

1 reference

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Two proton transfers in the transition state for nucleotidyl transfer catalyzed by RNA- and DNA-dependent RNA and DNA polymerases

1 reference

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Modifying the beta,gamma leaving-group bridging oxygen alters nucleotide incorporation efficiency, fidelity, and the catalytic mechanism of DNA polymerase beta

1 reference

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Regulation of DNA repair fidelity by molecular checkpoints: "gates" in DNA polymerase beta's substrate selection

1 reference

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Correct and incorrect nucleotide incorporation pathways in DNA polymerase beta

1 reference

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Energy analysis of chemistry for correct insertion by DNA polymerase beta

1 reference

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On possible pitfalls in ab initio quantum mechanics/molecular mechanics minimization approaches for studies of enzymatic reactions

1 reference

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

1 reference

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Stepwise translocation of Dpo4 polymerase during error-free bypass of an oxoG lesion

1 reference

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Efficient and high fidelity incorporation of dCTP opposite 7,8-dihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA polymerase Dpo4.

1 reference

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

1 reference

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

1 reference

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Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis

1 reference

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DNA adduct bypass polymerization by Sulfolobus solfataricus DNA polymerase Dpo4: analysis and crystal structures of multiple base pair substitution and frameshift products with the adduct 1,N2-ethenoguanine.

1 reference

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1 reference

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

1 reference

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The spacious active site of a Y-family DNA polymerase facilitates promiscuous nucleotide incorporation opposite a bulky carcinogen-DNA adduct: elucidating the structure-function relationship through experimental and computational approaches

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

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Crystal structure of a benzo[a]pyrene diol epoxide adduct in a ternary complex with a DNA polymerase

1 reference

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Replication of a cis-syn thymine dimer at atomic resolution

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DNA damage and repair

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Studies of polymer surfaces by sum frequency generation vibrational spectroscopy.

1 reference

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Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4): an archaeal DinB-like DNA polymerase with lesion-bypass properties akin to eukaryotic poleta

1 reference

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

1 reference

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The Y-family of DNA polymerases

1 reference

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DNA polymerases: structural diversity and common mechanisms

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1 reference

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31 August 2018

Subtle but variable conformational rearrangements in the replication cycle of Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) may accommodate lesion bypass

1 reference

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1 reference

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Sulfolobus solfataricus DNA polymerase Dpo4 is partially inhibited by "wobble" pairing between O6-methylguanine and cytosine, but accurate bypass is preferred

1 reference

https://pubmed.ncbi.nlm.nih.gov/18785738

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1021/JA802215C

1 reference

Europe PubMed Central

5 September 2017

1 reference

Europe PubMed Central

5 September 2017

1 reference

Europe PubMed Central

5 September 2017

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