Identification of a single HNH active site in type IIS restriction endonuclease Eco31I

Journal of Molecular Biology
Arturas JakubauskasArvydas Janulaitis

Abstract

Type IIS restriction endonuclease Eco31I is a "short-distance cutter", which cleaves DNA strands close to its recognition sequence, 5'-GGTCTC(1/5). Previously, it has been proposed that related endonucleases recognizing a common sequence core GTCTC possess two active sites for cleavage of both strands in the DNA substrate. Here, we present bioinformatic identification and experimental evidence for a single nuclease active site. We identified a short region of homology between Eco31I and HNH nucleases, constructed a three-dimensional model of the putative catalytic domain and validated our predictions by random and site-specific mutagenesis. The restriction mechanism of Eco31I is suggested by analogy to the mechanisms of phage T4 endonuclease VII and homing endonuclease I-PpoI. We propose that residues D311 and N334 coordinate the cofactor. H312 acts as a general base-activating water molecule for the nucleophilic attack. K337 together with R340 and D345 are located in close proximity to the active center and are essential for correct folding of catalytic motif, while D345 together with R264 and D273 could be directly involved in DNA binding. We also predict that the Eco31I catalytic domain contains a putative Zn-binding site, w...Continue Reading

References

May 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·L LiS Chandrasegaran
Dec 18, 1985·Biochimica Et Biophysica Acta·V ButkusA Janulaitis
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Sep 2, 1998·Proceedings of the National Academy of Sciences of the United States of America·J BitinaiteI Schildkraut
Nov 11, 1998·Molecular Cell·M S JuricaB L Stoddard
Mar 13, 1999·Nature Structural Biology·C KleanthousA M Hemmings
Sep 10, 1999·The Journal of Biological Chemistry·A J PommerC Kleanthous
Dec 3, 1999·Nature Structural Biology·E A GalburtB L Stoddard
Mar 1, 2000·Trends in Biochemical Sciences·C CombetG Deléage
Dec 1, 2001·The Journal of Biological Chemistry·Abigail J BathStephen E Halford
Mar 26, 2003·Nucleic Acids Research·Richard J RobertsShuang-yong Xu
Jun 26, 2003·Nucleic Acids Research·Michal A Kurowski, Janusz M Bujnicki
Sep 13, 2003·BMC Bioinformatics·Roman L TatusovDarren A Natale
Dec 19, 2003·Nucleic Acids Research·Martin MaderaJulian Gough
Jun 11, 2004·The Journal of Biological Chemistry·María J Maté, Colin Kleanthous
Jun 25, 2004·Nucleic Acids Research·Aron Marchler-Bauer, Stephen H Bryant
Jul 13, 2004·Nucleic Acids Research·James C SamuelsonShuang-yong Xu
Aug 18, 2004·Journal of Molecular Biology·Betty W ShenBarry L Stoddard
Nov 9, 2004·Bioinformatics·Johannes Söding
Nov 25, 2004·Nucleic Acids Research·Matheshwaran SaravananValakunja Nagaraja
Dec 21, 2004·Nucleic Acids Research·Aron Marchler-BauerStephen H Bryant
Dec 21, 2004·Nucleic Acids Research·Nicola J MulderCathy H Wu
Jul 19, 2005·Biochimica Et Biophysica Acta·Edita KriukieneArvydas Lubys
Dec 31, 2005·Nucleic Acids Research·Robert D FinnAlex Bateman
Dec 31, 2005·Nucleic Acids Research·Ivica LetunicPeer Bork

❮ Previous
Next ❯

Citations

Sep 22, 2010·Quarterly Reviews of Biophysics·Wei Yang
May 10, 2011·Nature Reviews. Microbiology·Kira S MakarovaEugene V Koonin
Dec 19, 2007·Nucleic Acids Research·Giedrius GasiunasVirginijus Siksnys
Feb 9, 2010·PloS One·Siu-Hong ChanShuang-Yong Xu
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
Oct 19, 2017·Nucleic Acids Research·Jagoda JablonskaKrzysztof Ginalski
Nov 17, 2009·Cellular and Molecular Life Sciences : CMLS·Maria J MarcaidaGuillermo Montoya
Jun 12, 2017·European Journal of Clinical Microbiology & Infectious Diseases : Official Publication of the European Society of Clinical Microbiology·P GholizadehH S Kafil
Jul 23, 2008·Biochemistry·Arturas JakubauskasArvydas Janulaitis
Aug 26, 2010·Biochemistry·Kommireddy VasuValakunja Nagaraja

❮ Previous
Next ❯

Related Concepts

Related Feeds

Antifungals (ASM)

An antifungal, also known as an antimycotic medication, is a pharmaceutical fungicide or fungistatic used to treat and prevent mycosis such as athlete's foot, ringworm, candidiasis, cryptococcal meningitis, and others. Discover the latest research on antifungals here.

Antifungals

An antifungal, also known as an antimycotic medication, is a pharmaceutical fungicide or fungistatic used to treat and prevent mycosis such as athlete's foot, ringworm, candidiasis, cryptococcal meningitis, and others. Discover the latest research on antifungals here.