Literature DB >> 26002198

New structural snapshots provide molecular insights into the mechanism of high fidelity DNA synthesis.

Bret D Freudenthal1, William A Beard1, Samuel H Wilson2.   

Abstract

Time-lapse X-ray crystallography allows visualization of intermediate structures during the DNA polymerase catalytic cycle. Employing time-lapse crystallography with human DNA polymerase β has recently allowed us to capture and solve novel intermediate structures that are not stable enough to be analyzed by traditional crystallography. The structures of these intermediates reveals exciting surprises about active site metal ions and enzyme conformational changes as the reaction proceeds from the ground state to product release. In this perspective, we provide an overview of recent advances in understanding the DNA polymerase nucleotidyl transferase reaction and highlight both the significance and mysteries of enzyme efficiency and specificity that remain to be solved. Published by Elsevier B.V.

Entities:  

Keywords:  Base excision repair; DNA polymerase; DNA repair; Fidelity; Function; Genome instability; Structure; X-family; X-ray crystallography

Mesh:

Substances:

Year:  2015        PMID: 26002198      PMCID: PMC4522352          DOI: 10.1016/j.dnarep.2015.04.007

Source DB:  PubMed          Journal:  DNA Repair (Amst)        ISSN: 1568-7856


  29 in total

Review 1.  Structure and mechanism of DNA polymerase Beta.

Authors:  William A Beard; Samuel H Wilson
Journal:  Chem Rev       Date:  2006-02       Impact factor: 60.622

2.  Purification and domain-mapping of mammalian DNA polymerase beta.

Authors:  W A Beard; S H Wilson
Journal:  Methods Enzymol       Date:  1995       Impact factor: 1.600

3.  Efficiency of correct nucleotide insertion governs DNA polymerase fidelity.

Authors:  William A Beard; David D Shock; Brian J Vande Berg; Samuel H Wilson
Journal:  J Biol Chem       Date:  2002-10-04       Impact factor: 5.157

4.  Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal.

Authors:  J R Kiefer; C Mao; J C Braman; L S Beese
Journal:  Nature       Date:  1998-01-15       Impact factor: 49.962

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

Authors:  M R Sawaya; R Prasad; S H Wilson; J Kraut; H Pelletier
Journal:  Biochemistry       Date:  1997-09-16       Impact factor: 3.162

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

Authors:  Vinod K Batra; William A Beard; David D Shock; Joseph M Krahn; Lars C Pedersen; Samuel H Wilson
Journal:  Structure       Date:  2006-04       Impact factor: 5.006

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

Authors:  H Pelletier; M R Sawaya; W Wolfle; S H Wilson; J Kraut
Journal:  Biochemistry       Date:  1996-10-01       Impact factor: 3.162

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

Authors:  M R Sawaya; H Pelletier; A Kumar; S H Wilson; J Kraut
Journal:  Science       Date:  1994-06-24       Impact factor: 47.728

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

Authors:  H Pelletier; M R Sawaya; A Kumar; S H Wilson; J Kraut
Journal:  Science       Date:  1994-06-24       Impact factor: 47.728

10.  Structural basis for the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism.

Authors:  L S Beese; T A Steitz
Journal:  EMBO J       Date:  1991-01       Impact factor: 11.598

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  8 in total

Review 1.  Structure and function relationships in mammalian DNA polymerases.

Authors:  Nicole M Hoitsma; Amy M Whitaker; Matthew A Schaich; Mallory R Smith; Max S Fairlamb; Bret D Freudenthal
Journal:  Cell Mol Life Sci       Date:  2019-11-13       Impact factor: 9.261

2.  Mechanism of Deoxyguanosine Diphosphate Insertion by Human DNA Polymerase β.

Authors:  Fausto A Varela; Bret D Freudenthal
Journal:  Biochemistry       Date:  2021-01-21       Impact factor: 3.162

Review 3.  Recent Advances in Understanding the Structures of Translesion Synthesis DNA Polymerases.

Authors:  Justin A Ling; Zach Frevert; M Todd Washington
Journal:  Genes (Basel)       Date:  2022-05-20       Impact factor: 4.141

4.  Apurinic/apyrimidinic (AP) endonuclease 1 processing of AP sites with 5' mismatches.

Authors:  Max S Fairlamb; Amy M Whitaker; Bret D Freudenthal
Journal:  Acta Crystallogr D Struct Biol       Date:  2018-07-24       Impact factor: 7.652

5.  Capturing a mammalian DNA polymerase extending from an oxidized nucleotide.

Authors:  Amy M Whitaker; Mallory R Smith; Matthew A Schaich; Bret D Freudenthal
Journal:  Nucleic Acids Res       Date:  2017-06-20       Impact factor: 16.971

6.  A non-natural nucleotide uses a specific pocket to selectively inhibit telomerase activity.

Authors:  Wilnelly Hernandez-Sanchez; Wei Huang; Brian Plucinsky; Nelson Garcia-Vazquez; Nathaniel J Robinson; William P Schiemann; Anthony J Berdis; Emmanuel Skordalakes; Derek J Taylor
Journal:  PLoS Biol       Date:  2019-04-05       Impact factor: 8.029

7.  Determinants of adenine-mutagenesis in diversity-generating retroelements.

Authors:  Sumit Handa; Andres Reyna; Timothy Wiryaman; Partho Ghosh
Journal:  Nucleic Acids Res       Date:  2021-01-25       Impact factor: 16.971

8.  A guardian residue hinders insertion of a Fapy•dGTP analog by modulating the open-closed DNA polymerase transition.

Authors:  Mallory R Smith; David D Shock; William A Beard; Marc M Greenberg; Bret D Freudenthal; Samuel H Wilson
Journal:  Nucleic Acids Res       Date:  2019-04-08       Impact factor: 16.971

  8 in total

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