ArticleBiochemistry2009
RB69 DNA polymerase mutants with expanded nascent base-pair-binding pockets are highly efficient but have reduced base selectivity.
Article in Biochemistry, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed, 24 citations in OpenAlex.
- Molecular events during translocation and proofreading extracted from 200 static structures of DNA polymerase.Nucleic acids research · 2016Article
- RB69 DNA polymerase structure, kinetics, and fidelity.Biochemistry · 2014Review
- Structure-function analysis of ribonucleotide bypass by B family DNA replicases.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- A strategically located serine residue is critical for the mutator activity of DNA polymerase IV from Escherichia coli.Nucleic acids research · 2013Article
- DNA mismatch synthesis complexes provide insights into base selectivity of a B family DNA polymerase.Journal of the American Chemical Society · 2013Article
- Utility of the bacteriophage RB69 polymerase gp43 as a surrogate enzyme for herpesvirus orthologs.Viruses · 2013Review
- A remote palm domain residue of RB69 DNA polymerase is critical for enzyme activity and influences the conformation of the active site.PloS one · 2013Article
- Contribution of partial charge interactions and base stacking to the efficiency of primer extension at and beyond abasic sites in DNA.Biochemistry · 2012Article
- Using a fluorescent cytosine analogue tC(o) to probe the effect of the Y567 to Ala substitution on the preinsertion steps of dNMP incorporation by RB69 DNA polymerase.Biochemistry · 2012Article
- Probing minor groove hydrogen bonding interactions between RB69 DNA polymerase and DNA.Biochemistry · 2012Article
- Bidentate and tridentate metal-ion coordination states within ternary complexes of RB69 DNA polymerase.Protein science : a publication of the Protein Society · 2012Article
- Structural basis for differential insertion kinetics of dNMPs opposite a difluorotoluene nucleotide residue.Biochemistry · 2012Article
- Structure of the 2-aminopurine-cytosine base pair formed in the polymerase active site of the RB69 Y567A-DNA polymerase.Biochemistry · 2011Article
- Structural insights into complete metal ion coordination from ternary complexes of B family RB69 DNA polymerase.Biochemistry · 2011Article
- Hydrogen-bonding capability of a templating difluorotoluene nucleotide residue in an RB69 DNA polymerase ternary complex.Journal of the American Chemical Society · 2011Article
- Variation in mutation rates caused by RB69pol fidelity mutants can be rationalized on the basis of their kinetic behavior and crystal structures.Journal of molecular biology · 2011Article
- Insights into base selectivity from the 1.8 Å resolution structure of an RB69 DNA polymerase ternary complex.Biochemistry · 2011Article
- Reversal of a mutator activity by a nearby fidelity-neutral substitution in the RB69 DNA polymerase binding pocket.Journal of molecular biology · 2010Article
- Substitution of Ala for Tyr567 in RB69 DNA polymerase allows dAMP and dGMP to be inserted opposite Guanidinohydantoin .Biochemistry · 2010Article
- Substitution of Ala for Tyr567 in RB69 DNA polymerase allows dAMP to be inserted opposite 7,8-dihydro-8-oxoguanine .Biochemistry · 2010Article
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4 authors at 1 institution in 1 country.
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Abstract
We have investigated the effect of systematically enlarging the nascent base-pair-binding pocket (NBP) of a replicative DNA polymerase from bacteriophage RB69 (RB69 pol) on the incorporation efficiency (k(pol)/K(d,app)) for both correct and incorrect dNMPs. Accordingly, we replaced residues L561, Y567, and S565 in the NBP with Ala, Ala, and Gly, respectively. We combined L561A and Y567A to give a double mutant and then introduced the S565G mutation to give a triple mutant. The efficiency of incorrect dNMP insertion increased markedly relative to the wild type with the single mutants and increased further as the number of substitutions in the NBP increased. The difference in incorporation efficiency for mispairs between the mutants and the wild-type RB69 pol was due mainly to k(pol). Unexpectedly, enlarging the NBP had a minimal effect on the incorporation efficiency of correct dNMPs. Our kinetic data suggest that replicative DNA pols exert base discrimination via "negative selection" against mispairs by using residues in the NBP, particularly the three residues analyzed in this study, to allow rapid incorporation of only correct base pairs. This proposal differs from how geometry and "tightness of fit" of the NBP is often invoked to account for rapid incorporation of correct base pairs, namely, that a tighter fit within the NBP leads to an increase in insertion rates [Kool, E. T. (2002) Annu. Rev. Biochem. 71, 191-219]. We related our findings to that of a model translesion DNA pol, Sulfolobus solfataricus Dpo4. We concur with the main conclusion of a previous study [Mizukami, S., et al. (2006) Biochemistry 45, 2772-2778], namely, that lesion bypass pols exhibit low incorporation efficiencies for correct dNMPs (leading to relative promiscuity) not because of a more open NBP but because of a loose fit of substrates bound in the catalytic centers. This is a property not shared by RB69 pol and its mutants.
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