title: Structural Basis of the Heterodimer Formation between Cell Shape-Determining Proteins Csd1 and Csd2 from Helicobacter pylori.
abstract: Colonization of the human gastric mucosa by Helicobacter pylori requires its high motility, which depends on the helical cell shape. In H. pylori, several genes (csd1, csd2, csd3/hdpA, ccmA, csd4, csd5, and csd6) play key roles in determining the cell shape by alteration of cross-linking or by trimming of peptidoglycan stem peptides. H. pylori Csd1, Csd2, and Csd3/HdpA are M23B metallopeptidase family members and may act as d,d-endopeptidases to cleave the d-Ala4-mDAP3 peptide bond of cross-linked dimer muropeptides. Csd3 functions also as the d,d-carboxypeptidase to cleave the d-Ala4-d-Ala5 bond of the muramyl pentapeptide. To provide a basis for understanding molecular functions of Csd1 and Csd2, we have carried out their structural characterizations. We have discovered that (i) Csd2 exists in monomer-dimer equilibrium and (ii) Csd1 and Csd2 form a heterodimer. We have determined crystal structures of the Csd2121-308 homodimer and the heterodimer between Csd1125-312 and Csd2121-308. Overall structures of Csd1125-312 and Csd2121-308 monomers are similar to each other, consisting of a helical domain and a LytM domain. The helical domains of both Csd1 and Csd2 play a key role in the formation of homodimers or heterodimers. The Csd1 LytM domain contains a catalytic site with a Zn2+ ion, which is coordinated by three conserved ligands and two water molecules, whereas the Csd2 LytM domain has incomplete metal ligands and no metal ion is bound. Structural knowledge of these proteins sheds light on the events that regulate the cell wall in H. pylori.
authors.affiliation: Department of Biophysics and Chemical Biology, College of Natural Sciences, Seoul National University, Seoul, Korea.
authors.forename: Doo Ri
authors.initials: DR
authors.lastname: An
authors.affiliation: Department of Biophysics and Chemical Biology, College of Natural Sciences, Seoul National University, Seoul, Korea.
authors.forename: Ha Na
authors.initials: HN
authors.lastname: Im
authors.affiliation: Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, Korea.
authors.forename: Jun Young
authors.initials: JY
authors.lastname: Jang
authors.affiliation: Biomolecular Function Research Branch, Division of Precision Medicine and Cancer Informatics, Research Institute, National Cancer Center, Gyeonggi, Korea.
authors.forename: Hyoun Sook
authors.initials: HS
authors.lastname: Kim
authors.affiliation: Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, Korea.
authors.forename: Jieun
authors.initials: J
authors.lastname: Kim
authors.affiliation: Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, Korea.
authors.forename: Hye Jin
authors.initials: HJ
authors.lastname: Yoon
authors.affiliation: Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America.
authors.forename: Dusan
authors.initials: D
authors.lastname: Hesek
authors.affiliation: Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America.
authors.forename: Mijoon
authors.initials: M
authors.lastname: Lee
authors.affiliation: Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America.
authors.forename: Shahriar
authors.initials: S
authors.lastname: Mobashery
authors.affiliation: Department of Chemistry, Mokpo National University, Chonnam, Korea.
authors.forename: Soon-Jong
authors.initials: SJ
authors.lastname: Kim
authors.affiliation: Department of Biophysics and Chemical Biology, College of Natural Sciences, Seoul National University, Seoul, Korea.|Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, Korea.
authors.forename: Se Won
authors.identifier: http://orcid.org/0000-0002-1768-4635
authors.initials: SW
authors.lastname: Suh
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D020134:Catalytic Domain; D048430:Cell Shape / Q000502:physiology*; D018360:Crystallography, X-Ray; D019281:Dimerization; D016480:Helicobacter pylori / Q000378:metabolism*; D006639:Histidine / Q000235:genetics / Q000378:metabolism; D045726:Metalloproteases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D008969:Molecular Sequence Data; D009842:Oligopeptides / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding; D020836:Protein Structure, Quaternary; D011993:Recombinant Fusion Proteins / Q000096:biosynthesis / Q000737:chemistry / Q000302:isolation & purification; D016415:Sequence Alignment; D013379:Substrate Specificity; D015032:Zinc / Q000737:chemistry / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; C471213:His-His-His-His-His-His; D009842:Oligopeptides; D011993:Recombinant Fusion Proteins; D006639:Histidine; D045726:Metalloproteases; D015032:Zinc