4Q6O
Structural analysis of the mDAP-bound form of Helicobacter pylori Csd4, a D,L-carboxypeptidase
Summary for 4Q6O
| Entry DOI | 10.2210/pdb4q6o/pdb |
| Related | 4Q6M 4Q6N 4Q6P 4Q6Q |
| Descriptor | Conserved hypothetical secreted protein, CALCIUM ION, 2,6-DIAMINOPIMELIC ACID, ... (5 entities in total) |
| Functional Keywords | m14 metallopeptidase, d, l-carboxypeptidase, peptidoglycan, csd5, hydrolase |
| Biological source | Helicobacter pylori |
| Total number of polymer chains | 1 |
| Total formula weight | 50593.08 |
| Authors | |
| Primary citation | Kim, H.S.,Kim, J.,Im, H.N.,An, D.R.,Lee, M.,Hesek, D.,Mobashery, S.,Kim, J.Y.,Cho, K.,Yoon, H.J.,Han, B.W.,Lee, B.I.,Suh, S.W. Structural basis for the recognition of muramyltripeptide by Helicobacter pylori Csd4, a D,L-carboxypeptidase controlling the helical cell shape Acta Crystallogr.,Sect.D, 70:2800-2812, 2014 Cited by PubMed Abstract: 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. PubMed: 25372672DOI: 10.1107/S1399004714018732 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.41 Å) |
Structure validation
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