Structure-specific DNA-induced conformational changes in Taq polymerase revealed by small angle neutron scattering.

The Journal of Biological Chemistry
Derek L HoZimei Bu

Abstract

The DNA polymerase I from Thermus aquaticus (Taq polymerase) performs lagging-strand DNA synthesis and DNA repair. Taq polymerase contains a polymerase domain for synthesizing a new DNA strand and a 5'-nuclease domain for cleaving RNA primers or damaged DNA strands. The extended crystal structure of Taq polymerase poses a puzzle on how this enzyme coordinates its polymerase and the nuclease activities to generate only a nick. Using contrast variation solution small angle neutron scattering, we have examined the conformational changes that occur in Taq polymerase upon binding "overlap flap" DNA, a structure-specific DNA substrate that mimics the substrate in strand replacement reactions. In solution, apoTaq polymerase has an overall expanded equilibrium conformation similar to that in the crystal structure. Upon binding to the DNA substrate, both the polymerase and the nuclease domains adopt more compact overall conformations, but these changes are not enough to bring the two active sites close enough to generate a nick. Reconstruction of the three-dimensional molecular envelope from small angle neutron scattering data shows that in the DNA-bound form, the nuclease domain is lifted up relative to its position in the non-DNA-boun...Continue Reading

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Citations

Aug 29, 2012·The Journal of Biological Chemistry·Jayant James JayasundarZimei Bu
Jul 26, 2013·The European Physical Journal. E, Soft Matter·David J E CallawayZimei Bu
Nov 25, 2005·Proceedings of the National Academy of Sciences of the United States of America·Zimei BuDavid J E Callaway
Feb 11, 2005·Proceedings of the National Academy of Sciences of the United States of America·Igor ZwirEduardo A Groisman
Oct 29, 2010·Journal of Nucleic Acids·Rihito MoritaSeiki Kuramitsu
Jul 14, 2009·Journal of Molecular Biology·Jianquan LiZimei Bu
Aug 12, 2014·Colloids and Surfaces. B, Biointerfaces·Frank D ScheragJürgen Rühe
Jun 17, 2014·Journal of Molecular Biology·Cuiling XuZucai Suo
Apr 3, 2013·Current Protocols in Protein Science·John F AnknerDean A A Myles
Aug 8, 2018·Acta Crystallographica. Section D, Structural Biology·Max S FairlambBret D Freudenthal
Apr 9, 2008·Journal of Cellular Physiology·Kuo-Hsiang Tang, Ming-Daw Tsai
Mar 13, 2017·Journal of Molecular Biology·David J E CallawayZimei Bu
Jun 6, 2009·Chemical Reviews·Anthony J Berdis

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