Unzipping mechanism of the double-stranded DNA unwinding by a hexameric helicase: the effect of the 3' arm and the stability of the dsDNA on the unwinding activity of the Escherichia coli DnaB helicase

Journal of Molecular Biology
Roberto GallettoW Bujalowski

Abstract

The effect of two structural elements of a replication DNA fork substrate, the length of the 3' arm of the fork and the stability of the double-stranded DNA (dsDNA) part, on the kinetics of the dsDNA unwinding by the Escherichia coli hexameric helicase DnaB protein has been examined under single turnover conditions using the rapid quench-flow technique. The length of the 3' arm of the replication fork, i.e. the number of nucleotides in the arm, is a major structural factor that controls the unwinding rate and processivity of the helicase. The data show the existence of an optimal length of the 3' arm where there is the highest unwinding rate and processivity, indicating that during the unwinding process, the helicase transiently interacts with the 3' arm at a specific distance on the arm with respect to the duplex part of the DNA. Moreover, the area on the enzyme that engages in interactions has also a discrete size. For DNA substrates with the 3' arm containing 14, or less, nucleotide residues, the DnaB helicase becomes a completely distributive enzyme. However, the 3' arm is not a "specific activating cofactor" in the unwinding reaction. Rather, the 3' arm plays a role as a mechanical fulcrum for the enzyme, necessary to prov...Continue Reading

References

Jan 1, 1990·Annual Review of Biochemistry·S W Matson, K A Kaiser-Rogers
May 1, 1995·Journal of Structural Biology·M C San MartinJ M Carazo
Apr 25, 1995·Proceedings of the National Academy of Sciences of the United States of America·E H EgelmanS S Patel
Jan 1, 1996·Annual Review of Biochemistry·T M Lohman, K P Bjornson
Mar 6, 1999·The Journal of Biological Chemistry·D L Kaplan, T A Steitz
Aug 31, 2000·Annual Review of Biochemistry·S S Patel, K M Picha
Sep 11, 2002·Journal of Molecular Biology·Shixin YangEdward H Egelman
Nov 2, 2002·Proceedings of the National Academy of Sciences of the United States of America·Bindu NanduriKevin D Raney

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Citations

Nov 17, 2009·Nature Structural & Molecular Biology·Annie SchwartzMarc Boudvillain
Nov 3, 2009·The Journal of Biological Chemistry·Milind K GuptaPeter McGlynn
Aug 16, 2011·The Journal of Biological Chemistry·Ajit K SatapathyCharles C Richardson
May 23, 2012·PloS One·Adeyemi O AdedejiStefan G Sarafianos
Aug 22, 2007·Proceedings of the National Academy of Sciences of the United States of America·Wei ChengCarlos Bustamante
Mar 13, 2012·Annual Review of Biophysics·Taekjip HaTimothy M Lohman
Aug 26, 2011·Current Opinion in Chemical Biology·Smita S PatelDivya Nandakumar
Apr 14, 2016·Methods : a Companion to Methods in Enzymology·Sean M Carney, Michael A Trakselis
Jul 15, 2015·DNA Repair·Irfan KhanRobert M Brosh
Oct 7, 2010·Biophysical Journal·Noah RibeckOmar A Saleh
Aug 27, 2016·Frontiers in Molecular Biosciences·Katarzyna E WegrzynIgor Konieczny
Sep 25, 2017·The Journal of Biological Chemistry·Sean M CarneyMichael A Trakselis
Feb 14, 2006·Nature Structural & Molecular Biology·Robert L Eoff, Kevin D Raney
May 24, 2008·The EMBO Journal·Ilker Donmez, Smita S Patel
Nov 30, 2005·Journal of Physics. Condensed Matter : an Institute of Physics Journal·M D Betterton, F Jülicher
Sep 12, 2019·Angewandte Chemie·Akira OnoJiro Kondo
Oct 23, 2004·International Journal of Cancer. Journal International Du Cancer·David ChinWilliam B Coman
May 17, 2007·The Journal of Biological Chemistry·Ilker DonmezSmita S Patel
Sep 22, 2007·The Journal of Biological Chemistry·Eli RothenbergTaekjip Ha
Aug 12, 2019·Biophysical Journal·Shaon ChakrabartiD Thirumalai
Aug 19, 2021·Critical Reviews in Biochemistry and Molecular Biology·Amy J Fernandez, James M Berger

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