4y4v | pdb_00004y4v

Structure of Helicobacter pylori Csd6 in the D-Ala-bound state

spinqualitylabelsall models 4y4v, resolution 2.04Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 4y4v is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: DAL, GOL NonStd Res: CSO Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum Publication Abstract from PubMed 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-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 L,D-carboxypeptidase but not as 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. The Cell-Shape Determining Csd6 Protein from Helicobacter pylori Constitutes a New Family of L,D-Carboxypeptidase.,Kim HS, Im HN, An DR, Yoon JY, Jang JY, Mobashery S, Hesek D, Lee M, Yoo J, Cui M, Choi S, Kim C, Lee NK, Kim SJ, Kim JY, Bang G, Han BW, Lee BI, Yoon HJ, Suh SW J Biol Chem. 2015 Aug 25. pii: jbc.M115.658781. PMID:26306031 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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