An intermolecular binding mechanism involving multiple LysM domains mediates carbohydrate recognition by an endopeptidase

Acta Crystallographica. Section D, Biological Crystallography
Jaslyn E M M WongMickaël Blaise

Abstract

LysM domains, which are frequently present as repetitive entities in both bacterial and plant proteins, are known to interact with carbohydrates containing N-acetylglucosamine (GlcNAc) moieties, such as chitin and peptidoglycan. In bacteria, the functional significance of the involvement of multiple LysM domains in substrate binding has so far lacked support from high-resolution structures of ligand-bound complexes. Here, a structural study of the Thermus thermophilus NlpC/P60 endopeptidase containing two LysM domains is presented. The crystal structure and small-angle X-ray scattering solution studies of this endopeptidase revealed the presence of a homodimer. The structure of the two LysM domains co-crystallized with N-acetyl-chitohexaose revealed a new intermolecular binding mode that may explain the differential interaction between LysM domains and short or long chitin oligomers. By combining the structural information with the three-dimensional model of peptidoglycan, a model suggesting how protein dimerization enhances the recognition of peptidoglycan is proposed.

References

Sep 1, 1995·Journal of Bacteriology·J C QuintelaM A de Pedro
Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
Mar 16, 2006·Proceedings of the National Academy of Sciences of the United States of America·Samy O MerouehShahriar Mobashery
Aug 8, 2007·Journal of Molecular Biology·Evgeny Krissinel, Kim Henrick
Dec 18, 2007·The Journal of Biological Chemistry·Takayuki OhnumaEtsuko Katoh
Jan 16, 2008·FEMS Microbiology Reviews·Waldemar VollmerMiguel A de Pedro
Feb 13, 2008·FEMS Microbiology Reviews·Waldemar VollmerSimon Foster
Oct 15, 2009·Chemical Communications : Chem Comm·W Mei KokCraig A Hutton
Jan 9, 2010·Acta Crystallographica. Section D, Biological Crystallography·Vincent B ChenDavid C Richardson
Apr 13, 2010·Acta Crystallographica. Section D, Biological Crystallography·P EmsleyK Cowtan
May 12, 2010·Nucleic Acids Research·Liisa Holm, Päivi Rosenström
Oct 15, 2010·Acta Crystallographica. Section F, Structural Biology and Crystallization Communications·Qingping XuIan A Wilson
Jul 29, 2011·Applied Microbiology and Biotechnology·Jan Reith, Christoph Mayer
Aug 9, 2011·Methods : a Companion to Methods in Enzymology·Paul D AdamsPeter H Zwart
Dec 29, 2011·Nature Reviews. Microbiology·Athanasios TypasWaldemar Vollmer
Feb 4, 2012·The Journal of Biological Chemistry·Matthew B Frankel, Olaf Schneewind
Mar 14, 2012·Biochemistry·Marc A BoudreauShahriar Mobashery
Jun 2, 2012·Science·Tingting LiuJijie Chai
Aug 4, 2012·Proceedings of the National Academy of Sciences of the United States of America·Angelique BroghammerJens Stougaard
Nov 21, 2012·Annals of the New York Academy of Sciences·Jarrod W JohnsonShahriar Mobashery
Dec 12, 2012·Annals of the New York Academy of Sciences·Alexander J F Egan, Waldemar Vollmer
Dec 29, 2012·Methods : a Companion to Methods in Enzymology·Susanne A I SeidelStefan Duhr
Jun 15, 2013·Journal of Synchrotron Radiation·Thomas UrsbyMarjolein M G M Thunnissen
Nov 7, 2013·Acta Crystallographica. Section F, Structural Biology and Crystallization Communications·Jaslyn E M M Wong, Mickael Blaise
Dec 7, 2013·Acta Crystallographica. Section D, Biological Crystallography·Atul KumarBhupesh Taneja
Jan 8, 2014·Proceedings of the National Academy of Sciences of the United States of America·Masahiro HayafuneNaoto Shibuya
Jan 18, 2014·Chembiochem : a European Journal of Chemical Biology·Nicolai N MaolanonKnud J Jensen
Jun 11, 2014·Biochimica Et Biophysica Acta·Sung Joon KimManmilan Singh
Jul 1, 2014·Nature Communications·Stéphane MesnageMichael P Williamson
Nov 28, 2014·Journal of the American Chemical Society·Paul SchandaJean-Pierre Simorre
Apr 1, 2012·Journal of Applied Crystallography·Maxim V PetoukhovDmitri I Svergun

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Citations

Oct 13, 2015·Structure·Leonardus M I KoharudinAngela M Gronenborn
Aug 4, 2015·Glycoconjugate Journal·Judith Fliegmann, Jean-Jacques Bono
Dec 19, 2015·PLoS Pathogens·Andrea A Gust
Jan 27, 2017·Annual Review of Plant Biology·Ulrich HohmannMichael Hothorn
Mar 3, 2018·The Journal of Biological Chemistry·Christine C YokoyamaHerbert W Virgin
May 23, 2018·Molecular Plant-microbe Interactions : MPMI·Ekaterina GubaevaBruno M Moerschbacher
Sep 7, 2017·Proceedings of the National Academy of Sciences of the United States of America·Zoltan BozsokiJens Stougaard
Jun 27, 2019·Proceedings of the National Academy of Sciences of the United States of America·Jaslyn E M M WongJens Stougaard
May 29, 2020·International Journal of Biological Macromolecules·Abid AliAsad U Khan
Oct 17, 2021·World Journal of Microbiology & Biotechnology·Adriana López-ArvizuIsrael García-Cano

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Methods Mentioned

BETA
NMR
size-exclusion chromatography
Gel Filtration
X-ray
microscale thermophoresis
PISA

Software Mentioned

BsxCuBE
CRYSOL
Coot
CORAL
MolProbity
PHENIX
DALI
ATSAS
GraphPad Prism

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