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Literature DB >> 20823515

Metal-ion dependence of the active-site conformation of the translesion DNA polymerase Dpo4 from Sulfolobus solfataricus.

Adriana Irimia¹, Lioudmila V Loukachevitch, Robert L Eoff, F Peter Guengerich, Martin Egli.

Abstract

Crystal structures of a binary Mg2+-form Dpo4-DNA complex with 1,N2-etheno-dG in the template strand as well as of ternary Mg2+-form Dpo4-DNA-dCTP/dGTP complexes with 8-oxoG in the template strand have been determined. Comparison of their conformations and active-site geometries with those of the corresponding Ca2+-form complexes revealed that the DNA and polymerase undergo subtle changes as a result of the catalytically more active Mg2+ occupying both the A and B sites.

Entities: Chemical Species

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Year: 2010 PMID： 20823515 PMCID： PMC2935216 DOI： 10.1107/S1744309110029374

Source DB: PubMed Journal: Acta Crystallogr Sect F Struct Biol Cryst Commun ISSN： 1744-3091

27 in total

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

Authors: H Ling; F Boudsocq; R Woodgate; W Yang
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3. Snapshots of replication through an abasic lesion; structural basis for base substitutions and frameshifts.

Authors: Hong Ling; François Boudsocq; Roger Woodgate; Wei Yang
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4. 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.

Authors: Hong Zang; Angela K Goodenough; Jeong-Yun Choi; Adriana Irimia; Lioudmila V Loukachevitch; Ivan D Kozekov; Karen C Angel; Carmelo J Rizzo; Martin Egli; F Peter Guengerich
Journal: J Biol Chem Date: 2005-06-17 Impact factor: 5.157

5. Crystallography & NMR system: A new software suite for macromolecular structure determination.

Authors: A T Brünger; P D Adams; G M Clore; W L DeLano; P Gros; R W Grosse-Kunstleve; J S Jiang; J Kuszewski; M Nilges; N S Pannu; R J Read; L M Rice; T Simonson; G L Warren
Journal: Acta Crystallogr D Biol Crystallogr Date: 1998-09-01

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

Authors: Alexandra Vaisman; Hong Ling; Roger Woodgate; Wei Yang
Journal: EMBO J Date: 2005-08-18 Impact factor: 11.598

7. Structural and functional elucidation of the mechanism promoting error-prone synthesis by human DNA polymerase kappa opposite the 7,8-dihydro-8-oxo-2'-deoxyguanosine adduct.

Authors: Adriana Irimia; Robert L Eoff; F Peter Guengerich; Martin Egli
Journal: J Biol Chem Date: 2009-06-19 Impact factor: 5.157

8. Replication of a cis-syn thymine dimer at atomic resolution.

Authors: Hong Ling; François Boudsocq; Brian S Plosky; Roger Woodgate; Wei Yang
Journal: Nature Date: 2003-08-06 Impact factor: 49.962

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

Authors: Hong Ling; Jane M Sayer; Brian S Plosky; Haruhiko Yagi; François Boudsocq; Roger Woodgate; Donald M Jerina; Wei Yang
Journal: Proc Natl Acad Sci U S A Date: 2004-02-24 Impact factor: 11.205

10. Phaser crystallographic software.

Authors: Airlie J McCoy; Ralf W Grosse-Kunstleve; Paul D Adams; Martyn D Winn; Laurent C Storoni; Randy J Read
Journal: J Appl Crystallogr Date: 2007-07-13 Impact factor: 3.304

10 in total

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Authors: Karl E Zahn; Susan S Wallace; Sylvie Doublié
Journal: Curr Opin Struct Biol Date: 2011-04-07 Impact factor: 6.809

3. Mechanisms of Insertion of dCTP and dTTP Opposite the DNA Lesion O6-Methyl-2'-deoxyguanosine by Human DNA Polymerase η.

Authors: Amitraj Patra; Qianqian Zhang; F Peter Guengerich; Martin Egli
Journal: J Biol Chem Date: 2016-09-30 Impact factor: 5.157

Review 4. Different Divalent Cations Alter the Kinetics and Fidelity of DNA Polymerases.

Authors: Ashwani Kumar Vashishtha; Jimin Wang; William H Konigsberg
Journal: J Biol Chem Date: 2016-07-26 Impact factor: 5.157

5. Effect of Different Divalent Cations on the Kinetics and Fidelity of RB69 DNA Polymerase.

Authors: Ashwani Kumar Vashishtha; William H Konigsberg
Journal: Biochemistry Date: 2016-04-28 Impact factor: 3.162

6. Translesion DNA Synthesis.

Authors: Alexandra Vaisman; John P McDonald; Roger Woodgate
Journal: EcoSal Plus Date: 2012-11

7. Replication bypass of the trans-4-Hydroxynonenal-derived (6S,8R,11S)-1,N(2)-deoxyguanosine DNA adduct by the sulfolobus solfataricus DNA polymerase IV.

Authors: Surajit Banerjee; Plamen P Christov; Albena Kozekova; Carmelo J Rizzo; Martin Egli; Michael P Stone
Journal: Chem Res Toxicol Date: 2012-02-07 Impact factor: 3.739