Modulation of DNA Polymerase Noncovalent Kinetic Transitions by Divalent Cations.

The Journal of Biological Chemistry
Joseph M DahlHongyun Wang

Abstract

Replicative DNA polymerases (DNAPs) require divalent metal cations for phosphodiester bond formation in the polymerase site and for hydrolytic editing in the exonuclease site. Me(2+) ions are intimate architectural components of each active site, where they are coordinated by a conserved set of amino acids and functional groups of the reaction substrates. Therefore Me(2+) ions can influence the noncovalent transitions that occur during each nucleotide addition cycle. Using a nanopore, transitions in individual Φ29 DNAP complexes are resolved with single-nucleotide spatial precision and sub-millisecond temporal resolution. We studied Mg(2+) and Mn(2+), which support catalysis, and Ca(2+), which supports deoxynucleoside triphosphate (dNTP) binding but not catalysis. We examined their effects on translocation, dNTP binding, and primer strand transfer between the polymerase and exonuclease sites. All three metals cause a concentration-dependent shift in the translocation equilibrium, predominantly by decreasing the forward translocation rate. Me(2+) also promotes an increase in the backward translocation rate that is dependent upon the primer terminal 3'-OH group. Me(2+) modulates the translocation rates but not their response to f...Continue Reading

References

Jul 15, 1993·Proceedings of the National Academy of Sciences of the United States of America·T A Steitz, J A Steitz
Apr 12, 1996·The Journal of Biological Chemistry·L Blanco, M Salas
Mar 22, 2003·Proceedings of the National Academy of Sciences of the United States of America·Sean J JohnsonLorena S Beese
Apr 18, 2006·Structure·Vinod K BatraSamuel H Wilson
Jul 7, 2007·Science·Zachary F PursellThomas A Kunkel
Apr 2, 2008·IUBMB Life·Margarita SalasMiguel de Vega
Sep 1, 2009·Nature Structural & Molecular Biology·Michael K SwanAneel K Aggarwal
Nov 12, 2009·Cold Spring Harbor Symposia on Quantitative Biology·T A Kunkel
Jan 19, 2010·Biochimica Et Biophysica Acta·Kenneth A Johnson
Feb 19, 2010·Trends in Biochemical Sciences·Erik Johansson, Stuart A Macneill
Dec 3, 2010·Journal of the American Chemical Society·Kate R LiebermanMark Akeson
Dec 16, 2011·Nucleic Acids Research·Thomas W KirbyRobert E London
Feb 16, 2012·Nature Biotechnology·Gerald M CherfMark Akeson
Mar 2, 2012·The Journal of Biological Chemistry·Joseph M DahlKate R Lieberman
May 11, 2012·Proceedings of the National Academy of Sciences of the United States of America·José A MorinBorja Ibarra
Oct 30, 2012·Journal of the American Chemical Society·Kate R LiebermanHongyun Wang
May 28, 2013·Journal of the American Chemical Society·Kate R LiebermanHongyun Wang
Jun 5, 2013·Cold Spring Harbor Perspectives in Biology·Erik Johansson, Nicholas Dixon
Dec 3, 2013·Nature Structural & Molecular Biology·Matthew HoggErik Johansson
Apr 26, 2014·Journal of the American Chemical Society·Kate R LiebermanHongyun Wang

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Citations

Jul 25, 2018·Current Protocols in Chemical Biology·Christopher Cozens, Vitor B Pinheiro
Jun 21, 2017·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Kherim WillemsGiovanni Maglia

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