Structure of Csd3 from Helicobacter pylori, a cell shape-determining metallopeptidase

Acta Crystallographica. Section D, Biological Crystallography
Doo Ri AnSe Won Suh

Abstract

Helicobacter pylori is associated with various gastrointestinal diseases such as gastritis, ulcers and gastric cancer. Its colonization of the human gastric mucosa requires high motility, which depends on its helical cell shape. Seven cell shape-determining genes (csd1, csd2, csd3/hdpA, ccmA, csd4, csd5 and csd6) have been identified in H. pylori. Their proteins play key roles in determining the cell shape through modifications of the cell-wall peptidoglycan by the alteration of cross-linking or by the trimming of peptidoglycan muropeptides. Among them, Csd3 (also known as HdpA) is a bifunctional enzyme. Its D,D-endopeptidase activity cleaves the D-Ala(4)-mDAP(3) peptide bond between cross-linked muramyl tetrapeptides and pentapeptides. It is also a D,D-carboxypeptidase that cleaves off the terminal D-Ala(5) from the muramyl pentapeptide. Here, the crystal structure of this protein has been determined, revealing the organization of its three domains in a latent and inactive state. The N-terminal domain 1 and the core of domain 2 share the same fold despite a very low level of sequence identity, and their surface-charge distributions are different. The C-terminal LytM domain contains the catalytic site with a Zn(2+) ion, like th...Continue Reading

References

Mar 22, 1979·Nature·H C Berg, L Turner
Dec 1, 1979·Computer Programs in Biomedicine·G D Knott
Mar 16, 2002·Infection and Immunity·Karen M Ottemann, Andrew C Lowenthal
Dec 25, 2002·Acta Crystallographica. Section D, Biological Crystallography·Thomas C Terwilliger
Dec 23, 2003·Journal of Molecular Biology·Sergey G OdintsovMatthias Bochtler
Mar 27, 2004·Proceedings of the National Academy of Sciences of the United States of America·Sören SchreiberSebastian Suerbaum
Jun 25, 2004·Nucleic Acids Research·Matthias Heinig, Dmitrij Frishman
Nov 5, 2005·Journal of Molecular Biology·Małgorzata FirczukMatthias Bochtler
Dec 13, 2005·Microbiology and Molecular Biology Reviews : MMBR·Dirk-Jan Scheffers, Mariana G Pinho
Mar 16, 2006·Proceedings of the National Academy of Sciences of the United States of America·Samy O MerouehShahriar Mobashery
Jul 19, 2006·Clinical Microbiology Reviews·Johannes G KustersErnst J Kuipers
Jul 31, 2007·Biochimica Et Biophysica Acta·Waldemar Vollmer, Ute Bertsche
Nov 6, 2007·Current Opinion in Microbiology·Kevin D Young
Jan 16, 2008·FEMS Microbiology Reviews·Waldemar VollmerMiguel A de Pedro
Feb 13, 2008·FEMS Microbiology Reviews·Waldemar VollmerSimon Foster
May 24, 2008·Proteins·Sugadev RagumaniSubramanyam Swaminathan
Jan 9, 2010·Acta Crystallographica. Section D, Biological Crystallography·Vincent B ChenDavid C Richardson
Jan 9, 2010·Acta Crystallographica. Section D, Biological Crystallography·Alexei Vagin, Alexei Teplyakov
Feb 4, 2010·Acta Crystallographica. Section D, Biological Crystallography·Paul D AdamsPeter H Zwart
Apr 13, 2010·Acta Crystallographica. Section D, Biological Crystallography·P EmsleyK Cowtan
May 12, 2010·Nucleic Acids Research·Liisa Holm, Päivi Rosenström
Apr 5, 2011·Acta Crystallographica. Section D, Biological Crystallography·Garib N MurshudovAlexei A Vagin
Sep 24, 2011·Annual Review of Microbiology·Paphavee LertsethtakarnDavid R Hendrixson
Jun 22, 2012·Molecular Microbiology·Desirée C YangThomas G Bernhardt
Sep 5, 2012·Trends in Microbiology·Timna J WyckoffNina R Salama
Sep 27, 2012·Current Opinion in Gastroenterology·Peter MalfertheinerJan Bornschein
Dec 25, 2012·BMC Bioinformatics·Jose M DuarteGuido Capitani
Sep 18, 2013·Helicobacter·Claire Roubaud BaudronAntonio Gasbarrini
Oct 3, 2013·Proceedings of the National Academy of Sciences of the United States of America·Lisandro H OteroJuan A Hermoso
Apr 20, 2014·Nucleic Acids Research·Homa GhaleiMarkus C Wahl
May 17, 2014·Clinical Medicine Insights. Gastroenterology·Bruna M RoeslerJosé M R Zeitune
Jun 11, 2014·World Journal of Gastroenterology : WJG·Luigina Cellini
Jul 22, 2014·The FEBS Journal·Izabela SabalaMatthias Bochtler
Nov 6, 2014·Acta Crystallographica. Section D, Biological Crystallography·Hyoun Sook KimSe Won Suh
Jan 1, 1997·Methods in Enzymology·Zbyszek Otwinowski, Wladek Minor

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Citations

Sep 16, 2015·Helicobacter·Dionyssios N SgourasYoshio Yamaoka
Jul 26, 2017·Frontiers in Microbiology·Muriel C F van TeeselingFelipe Cava
May 13, 2020·Proceedings of the National Academy of Sciences of the United States of America·Jung-Ho ShinTobias Dörr
May 19, 2018·Chemical Reviews·Joan L ArolasF Xavier Gomis-Rüth
Sep 8, 2021·Frontiers in Microbiology·Wanda M Figueroa-CuilanPamela J B Brown

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Methods Mentioned

BETA
gel filtration
X-ray
equilibrium sedimentation

Software Mentioned

CCP
2000
MLAB
HKL
MolProbity
MOLREP
AutoSol
R
REFMAC
PHENIX

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