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Mechanism of anchoring of OmpA protein to the cell wall peptidoglycan of the gram‐negative bacterial outer membrane

Park, Jeong Soon,Lee, Woo Cheol,Yeo, Kwon Joo,Ryu, Kyoung‐,Seok,Kumarasiri, Malika,Hesek, Dusan,Lee, Mijoon,Mobashery, Shahriar,Song, Jung Hyun,Kim, Seung Il,Lee, Je Chul,Cheong, Chaejoon,Jeon, Federation of American Society for Experimental Bi 2012 The FASEB Journal Vol.26 No.1
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The outer membrane protein A (OmpA) plays important roles in anchoring of the outer membrane to the bacterial cell wall. The C-terminal periplasmic domain of OmpA (OmpA-like domain) associates with the peptidoglycan (PGN) layer noncovalently. However, there is a paucity of information on the structural aspects of the mechanism of PGN recognition by OmpA-like domains. To elucidate this molecular recognition process, we solved the high-resolution crystal structure of an OmpA-like domain from Acinetobacter baumannii bound to diaminopimelate (DAP), a unique bacterial amino acid from the PGN. The structure clearly illustrates that two absolutely conserved Asp271 and Arg286 residues are the key to the binding to DAP of PGN. Identification of DAP as the central anchoring site of PGN to OmpA is further supported by isothermal titration calorimetry and a pulldown assay with PGN. An NMR-based computational model for complexation between the PGN and OmpA emerged, and this model is validated by determining the crystal structure in complex with a synthetic PGN fragment. These structural data provide a detailed glimpse of how the anchoring of OmpA to the cell wall of gram-negative bacteria takes place in a DAP-dependent manner.
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The Cell Shape-determining Csd6 Protein from Helicobacter pylori Constitutes a New Family of L,D -Carboxypeptidase

Kim, Hyoun Sook,Im, Ha Na,An, Doo Ri,Yoon, Ji Young,Jang, Jun Young,Mobashery, Shahriar,Hesek, Dusan,Lee, Mijoon,Yoo, Jakyung,Cui, Minghua,Choi, Sun,Kim, Cheolhee,Lee, Nam Ki,Kim, Soon-Jong,Kim, Jin Y American Society for Biochemistry and Molecular Bi 2015 The Journal of biological chemistry Vol.290 No.41
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<▼1>Background: Csd6 is one of the cell shape-determining proteins in H. pylori.Results: The active site of Csd6 is tailored to function as an L,D-carboxypeptidase in the peptidoglycan-trimming process.Conclusion: Csd6 constitutes a new family of L,D-carboxypeptidase.Significance: The substrate limitation of Csd6 is a strategy that H. pylori uses to regulate its helical cell shape and motility.</▼1><▼2>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.</▼2>

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