4XZZ

Structure of Helicobacter pylori Csd6 in the ligand-free state

Summary for 4XZZ

• Entry DOI: 10.2210/pdb4xzz/pdb
• Descriptor: Conserved hypothetical secreted protein, GLYCEROL (3 entities in total)
• Functional Keywords: csd6, cell shape, l, d-carboxypeptidase, helicobacter pylori, hp0518, flagellin, peptidoglycan, hydrolase
• Biological source: Helicobacter pylori 26695
• Total number of polymer chains: 2
• Total formula weight: 79558.35

Authors

Kim, H.S.,Im, H.N.,Yoon, H.J.,Suh, S.W. (deposition date: 2015-02-05, release date: 2015-09-02, Last modification date: 2024-05-29)

Primary citation

Kim, H.S.,Im, H.N.,An, D.R.,Yoon, J.Y.,Jang, J.Y.,Mobashery, S.,Hesek, D.,Lee, M.,Yoo, J.,Cui, M.,Choi, S.,Kim, C.,Lee, N.K.,Kim, S.J.,Kim, J.Y.,Bang, G.,Han, B.W.,Lee, B.I.,Yoon, H.J.,Suh, S.W.
The Cell Shape-determining Csd6 Protein from Helicobacter pylori Constitutes a New Family of l,d-Carboxypeptidase
J.Biol.Chem., 290:25103-25117, 2015

PubMed Abstract: Helicobacter pylori causes gastrointestinal diseases, including gastric cancer. Its high motility in the viscous gastric mucosa facilitates colonization of the human stomach and depends on the helical cell shape and the flagella. In H. pylori, Csd6 is one of the cell shape-determining proteins that play key roles in alteration of cross-linking or by trimming of peptidoglycan muropeptides. Csd6 is also involved in deglycosylation of the flagellar protein FlaA. To better understand its function, biochemical, biophysical, and structural characterizations were carried out. We show that Csd6 has a three-domain architecture and exists as a dimer in solution. The N-terminal domain plays a key role in dimerization. The middle catalytic domain resembles those of l,d-transpeptidases, but its pocket-shaped active site is uniquely defined by the four loops I to IV, among which loops I and III show the most distinct variations from the known l,d-transpeptidases. Mass analyses confirm that Csd6 functions only as an l,d-carboxypeptidase and not as an l,d-transpeptidase. The d-Ala-complexed structure suggests possible binding modes of both the substrate and product to the catalytic domain. The C-terminal nuclear transport factor 2-like domain possesses a deep pocket for possible binding of pseudaminic acid, and in silico docking supports its role in deglycosylation of flagellin. On the basis of these findings, it is proposed that H. pylori Csd6 and its homologs constitute a new family of l,d-carboxypeptidase. This work provides insights into the function of Csd6 in regulating the helical cell shape and motility of H. pylori.

PubMed: 26306031
DOI: 10.1074/jbc.M115.658781

Experimental method

X-RAY DIFFRACTION (2.03 Å)