Human DNA Polymerase ν Catalyzes Correct and Incorrect DNA Synthesis with High Catalytic Efficiency

• Published in: The Journal of biological chemistry Vol. 290; no. 26; pp. 16292 - 16303
• Main Authors: Gowda, A.S. Prakasha, Moldovan, George-Lucian, Spratt, Thomas E.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 26.06.2015; American Society for Biochemistry and Molecular Biology
• Subjects: Base Pair Mismatch; Base Sequence; Biocatalysis; DNA - genetics; DNA - metabolism; DNA and Chromosomes; DNA polymerase; DNA repair; DNA Replication; DNA-Directed DNA Polymerase - chemistry; DNA-Directed DNA Polymerase - genetics; DNA-Directed DNA Polymerase - metabolism; enzyme kinetics; enzyme mechanism; Humans; Kinetics; Molecular Sequence Data; Oligodeoxyribonucleotides - genetics; Oligodeoxyribonucleotides - metabolism; DNA replication; DNA polymerase; enzyme mechanism; DNA repair; enzyme kinetics
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1074/jbc.M115.653287

DNA polymerase ν (pol ν) is a low fidelity A-family polymerase with a putative role in interstrand cross-link repair and homologous recombination. We carried out pre-steady-state kinetic analysis to elucidate the kinetic mechanism of this enzyme. We found that the mechanism consists of seven steps, similar that of other A-family polymerases. pol ν binds to DNA with a Kd for DNA of 9.2 nm, with an off-rate constant of 0.013 s−1and an on-rate constant of 14 μm−1 s−1. dNTP binding is rapid with Kd values of 20 and 476 μm for the correct and incorrect dNTP, respectively. Pyrophosphorylation occurs with a Kd value for PPi of 3.7 mm and a maximal rate constant of 11 s−1. Pre-steady-state kinetics, examination of the elemental effect using dNTPαS, and pulse-chase experiments indicate that a rapid phosphodiester bond formation step is flanked by slow conformational changes for both correct and incorrect base pair formation. These experiments in combination with computer simulations indicate that the first conformational change occurs with rate constants of 75 and 20 s−1; rapid phosphodiester bond formation occurs with a Keq of 2.2 and 1.7, and the second conformational change occurs with rate constants of 2.1 and 0.5 s−1, for correct and incorrect base pair formation, respectively. The presence of a mispair does not induce the polymerase to adopt a low catalytic conformation. pol ν catalyzes both correct and mispair formation with high catalytic efficiency. Background: DNA polymerase ν is a low fidelity polymerase with an unknown function. Results: The kinetic mechanism of correct and incorrect base pair formation was determined. Conclusion: Phosphodiester bond formation is rapid for both correct and mispair formation. Significance: The presence of a mispair does not induce the polymerase to adopt a low catalytic conformation.