Dual role for Zn2+ in maintaining structural integrity and inducing DNA sequence specificity in a promiscuous endonuclease

The Journal of Biological Chemistry
Matheshwaran SaravananValakunja Nagaraja

Abstract

We describe two uncommon roles for Zn2+ in enzyme KpnI restriction endonuclease (REase). Among all of the REases studied, KpnI REase is unique in its DNA binding and cleavage characteristics. The enzyme is a poor discriminator of DNA sequences, cleaving DNA in a promiscuous manner in the presence of Mg2+. Unlike most Type II REases, the active site of the enzyme comprises an HNH motif, which can accommodate Mg2+, Mn2+, or Ca2+. Among these metal ions, Mg2+ and Mn2+ induce promiscuous cleavage by the enzyme, whereas Ca2+-bound enzyme exhibits site-specific cleavage. Examination of the sequence of the protein revealed the presence of a zinc finger CCCH motif rarely found in proteins of prokaryotic origin. The zinc binding motif tightly coordinates zinc to provide a rigid structural framework for the enzyme needed for its function. In addition to this structural scaffold, another atom of zinc binds to the active site to induce high fidelity cleavage and suppress the Mg2+- and Mn2+-mediated promiscuous behavior of the enzyme. This is the first demonstration of distinct structural and catalytic roles for zinc in an enzyme, suggesting the distinct origin of KpnI REase.

References

Dec 1, 1992·European Journal of Biochemistry·S Gite, V Shankar
Jan 1, 1997·Annual Review of Biophysics and Biomolecular Structure·J M Berg, H A Godwin
Jul 6, 2000·Nature Structural Biology·R SankaranarayananD Moras
Feb 13, 2001·The Journal of Peptide Research : Official Journal of the American Peptide Society·R I Boysen, M T Hearn
Feb 17, 2001·Current Opinion in Structural Biology·J H LaityP E Wright
May 9, 2001·The Journal of Biological Chemistry·K Komori, Y Ishino
Jul 8, 2003·The Journal of Biological Chemistry·Craig R CookMing Lei
Nov 19, 2003·Journal of Molecular Biology·Eva Scheuring VanameeAneel K Aggarwal
Sep 18, 2004·The Journal of Biological Chemistry·Siddamadappa ChandrashekaranValakunja Nagaraja
Nov 25, 2004·Nucleic Acids Research·Matheshwaran SaravananValakunja Nagaraja
Mar 17, 2005·Cellular and Molecular Life Sciences : CMLS·A PingoudW Wende
Sep 1, 1940·The Biochemical Journal·D Keilin, T Mann
Jan 5, 2007·Nucleic Acids Research·Richard J RobertsDana Macelis

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Citations

Jul 24, 2008·Proceedings of the National Academy of Sciences of the United States of America·Matheshwaran SaravananValakunja Nagaraja
Nov 6, 2012·Nucleic Acids Research·Shuang-yong Xu, Yogesh K Gupta
Mar 9, 2013·Microbiology and Molecular Biology Reviews : MMBR·Kommireddy Vasu, Valakunja Nagaraja
Oct 26, 2011·Future Medicinal Chemistry·Béla Gyurcsik, Anikó Czene
Jan 22, 2013·Journal of Biological Inorganic Chemistry : JBIC : a Publication of the Society of Biological Inorganic Chemistry·Anikó CzeneBéla Gyurcsik
Sep 15, 2009·Protein Expression and Purification·Penghua ZhangShuang-yong Xu
Aug 18, 2009·Journal of Molecular Biology·Vera PingoudAlfred Pingoud
Jan 8, 2015·Nucleic Acids Research·Tiesheng HanXinyi He

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