ArticleJournal of molecular biology2011
Variation in mutation rates caused by RB69pol fidelity mutants can be rationalized on the basis of their kinetic behavior and crystal structures.
Article in Journal of molecular biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Structure of New Binary and Ternary DNA Polymerase Complexes From Bacteriophage RB69.Frontiers in molecular biosciences · 2021Article
- John W. (Jan) Drake: A Biochemical View of a GeneticistGenetics · 2020Article
- Environmental Effects on Guanine-Thymine Mispair Tautomerization Explored with Quantum Mechanical/Molecular Mechanical Free Energy Simulations.Journal of the American Chemical Society · 2020Article
- RB69 DNA polymerase structure, kinetics, and fidelity.Biochemistry · 2014Review
- Alteration in the cavity size adjacent to the active site of RB69 DNA polymerase changes its conformational dynamics.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
- 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
- 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
- Contrasting mutation rates from specific-locus and long-term mutation-accumulation procedures.G3 (Bethesda, Md.) · 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
- Antimutator variants of DNA polymerases.Critical reviews in biochemistry and molecular biology · 2011Review
- 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
- Reversal of a mutator activity by a nearby fidelity-neutral substitution in the RB69 DNA polymerase binding pocket.Journal of molecular biology · 2010Article
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8 authors.
Funding
Abstract
We have previously observed that stepwise replacement of amino acid residues in the nascent base-pair binding pocket of RB69 DNA polymerase (RB69pol) with Ala or Gly expanded the space in this pocket, resulting in a progressive increase in misincorporation. However, in vivo results with similar RB69pol nascent base-pair binding pocket mutants showed that mutation rates, as determined by the T4 phage rI forward assay and rII reversion assay, were significantly lower for the RB69pol S565G/Y567A double mutant than for the Y567A single mutant, the opposite of what we would have predicted. To investigate the reasons for this unexpected result, we have determined the pre-steady-state kinetic parameters and crystal structures of relevant ternary complexes. We found that the S565G/Y567A mutant generally had greater base selectivity than the Y567A mutant and that the kinetic parameters for dNMP insertion, excision of the 3'-terminal nucleotide residue, and primer extension beyond a mispair differed not only between these two mutants but also between the two highly mutable sequences in the T4 rI complementary strand. Comparison of the crystal structures of these two mutants with correct and incorrect incoming dNTPs provides insight into the unexpected increase in the fidelity of the S565G/Y567A double mutant. Taken together, the kinetic and structural results provide a basis for integrating and interpreting in vivo and in vitro observations.
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