Structural basis for the recognition of muramyltripeptide by Helicobacter pylori Csd4, a d,l-carboxypeptidase controlling the helical cell shape

Helicobacter pylori infection causes a variety of gastrointestinal diseases, including peptic ulcers and gastric cancer. Its colonization of the gastric mucosa of the human stomach is a prerequisite for survival in the stomach. Colonization depends on its motility, which is facilitated by the helical shape of the bacterium. In H. pylori, cross-linking relaxation or trimming of peptidoglycan muropeptides affects the helical cell shape. Csd4 has been identified as one of the cell shape-determining peptidoglycan hydrolases in H. pylori. It is a Zn(2+)-dependent d,l-carboxypeptidase that cleaves the bond between the γ-d-Glu and the mDAP of the non-cross-linked muramyl­tripeptide (muramyl-l-Ala-γ-d-Glu-mDAP) of the peptidoglycan to produce the muramyldipeptide (muramyl-l-Ala-γ-d-Glu) and mDAP. Here, the crystal structure of H. pylori Csd4 (HP1075 in strain 26695) is reported in three different states: the ligand-unbound form, the substrate-bound form and the product-bound form. H. pylori Csd4 consists of three domains: an N-terminal d,l-carboxypeptidase domain with a typical carboxy­peptidase fold, a central β-barrel domain with a novel fold and a C-terminal immunoglobulin-like domain. The d,l-carboxypeptidase domain recognizes the substrate by interacting primarily with the terminal mDAP moiety of the muramyltripeptide. It undergoes a significant structural change upon binding either mDAP or the mDAP-containing muramyl­tripeptide. It it also shown that Csd5, another cell-shape determinant in H. pylori, is capable of interacting not only with H. pylori Csd4 but also with the dipeptide product of the reaction catalyzed by Csd4.