ArticleThe Journal of biological chemistry2008
Kinetic analysis of correct nucleotide insertion by a Y-family DNA polymerase reveals conformational changes both prior to and following phosphodiester bond formation as detected by tryptophan fluorescence.
Article in The Journal of biological chemistry, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Ribonucleotide errors, RNase HII, and ribonucleotide excision repair.Critical reviews in biochemistry and molecular biology · 2026Review
- Kinetic Evidence for an Induced Fit Mechanism in the Binding of the Substrate Camphor by Cytochrome P450ACS catalysis · 2021Article
- Impact of 1,The Journal of biological chemistry · 2020Article
- DNA binding strength increases the processivity and activity of a Y-Family DNA polymerase.Scientific reports · 2017Article
- Investigation of Intradomain Motions of a Y-Family DNA Polymerase during Substrate Binding and Catalysis.Biochemistry · 2016Article
- Pre-Steady-State Kinetic Analysis of Single-Nucleotide Incorporation by DNA Polymerases.Current protocols in nucleic acid chemistry · 2016Article
- Cooperative motion of a key positively charged residue and metal ions for DNA replication catalyzed by human DNA Polymerase-η.Nucleic acids research · 2016Article
- Noncognate DNA damage prevents the formation of the active conformation of the Y-family DNA polymerases DinB and DNA polymerase κ.The FEBS journal · 2015Article
- Human DNA Polymerase ν Catalyzes Correct and Incorrect DNA Synthesis with High Catalytic Efficiency.The Journal of biological chemistry · 2015Article
- Elucidation of kinetic mechanisms of human translesion DNA polymerase κ using tryptophan mutants.The FEBS journal · 2014Article
- Dynamic conformational change regulates the protein-DNA recognition: an investigation on binding of a Y-family polymerase to its target DNA.PLoS computational biology · 2014Article
- Recent insight into the kinetic mechanisms and conformational dynamics of Y-Family DNA polymerases.Biochemistry · 2014Review
- Conformational dynamics of a Y-family DNA polymerase during substrate binding and catalysis as revealed by interdomain Förster resonance energy transfer.Biochemistry · 2014Article
- Nucleotide selection by the Y-family DNA polymerase Dpo4 involves template translocation and misalignment.Nucleic acids research · 2014Article
- Leukotriene biosynthesis inhibitor MK886 impedes DNA polymerase activity.Chemical research in toxicology · 2013Article
- Enhancement of human DNA polymerase η activity and fidelity is dependent upon a bipartite interaction with the Werner syndrome protein.The Journal of biological chemistry · 2012Article
- Differential temperature-dependent multimeric assemblies of replication and repair polymerases on DNA increase processivity.Biochemistry · 2012Article
- Enhancing the anti-lymphoma potential of 3,4-methylenedioxymethamphetamine ('ecstasy') through iterative chemical redesign: mechanisms and pathways to cell death.Investigational new drugs · 2012Article
- Unlocking the sugar "steric gate" of DNA polymerases.Biochemistry · 2011Review
- Techniques used to study the DNA polymerase reaction pathway.Biochimica et biophysica acta · 2010Review
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3 authors.
Funding
Abstract
The Sulfolobus solfataricus Y-family DNA polymerase Dpo4 is a model for translesion replication and has been used in the analysis of individual steps involved in catalysis. The role of conformational changes has not been clear. Introduction of Trp residues into the Trp-devoid wild-type protein provided fluorescence probes of these events, particularly in the case of mutants T239W and N188W. With both mutants, a rapid increase in Trp fluorescence was observed only in the case of normal base pairing (G:C), was saturable with respect to dCTP concentration, and occurred in the absence of phosphodiester bond formation. A subsequent decrease in the Trp fluorescence occurred when phosphodiester bond formation was permitted, and these rates were independent of the dCTP concentration. This step is relatively slow and is attributed to a conformational relaxation step occurring after pyrophosphate release, which was measured and shown to be fast in a separate experiment. The measured rate of release of DNA from Dpo4 was rapid and is not rate-limiting. Overall, the measurements provide a kinetic scheme for Dpo4 different than generally accepted for replicative polymerases or proposed for Dpo4 and other Y-family polymerases: the initial enzyme.DNA.dNTP complex undergoes a rapid (18 s(-1)), reversible (21 s(-1)) conformational change, followed by relatively rapid phosphodiester bond formation (11 s(-1)) and then fast release of pyrophosphate, followed by a rate-limiting relaxation of the active conformation (2 s(-1)) and then rapid DNA release, yielding an overall steady-state kcat of <1 s(-1).
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