1ZRS
wild-type LD-carboxypeptidase
Summary for 1ZRS
| Entry DOI | 10.2210/pdb1zrs/pdb |
| Descriptor | hypothetical protein (2 entities in total) |
| Functional Keywords | ld-carboxypeptidase, peptidoglycan hydrolase, serine peptidase, serine-histidine-glutamate triad, nucleophilic elbow, hydrolase |
| Biological source | Pseudomonas aeruginosa |
| Cellular location | Cytoplasm (By similarity): Q9HTZ1 |
| Total number of polymer chains | 2 |
| Total formula weight | 69274.70 |
| Authors | Korza, H.J.,Bochtler, M. (deposition date: 2005-05-21, release date: 2005-09-20, Last modification date: 2024-02-14) |
| Primary citation | Korza, H.J.,Bochtler, M. Pseudomonas aeruginosa LD-carboxypeptidase, a serine peptidase with a Ser-His-Glu triad and a nucleophilic elbow. J.Biol.Chem., 280:40802-40812, 2005 Cited by PubMed Abstract: LD-Carboxypeptidases (EC 3.4.17.13) are named for their ability to cleave amide bonds between l- and d-amino acids, which occur naturally in bacterial peptidoglycan. They are specific for the link between meso-diaminopimelic acid and d-alanine and therefore degrade GlcNAc-MurNAc tetrapeptides to the corresponding tripeptides. As only the tripeptides can be reused as peptidoglycan building blocks, ld-carboxypeptidases are thought to play a role in peptidoglycan recycling. Despite the pharmaceutical interest in peptidoglycan biosynthesis, the fold and catalytic type of ld-carboxypeptidases are unknown. Here, we show that a previously uncharacterized open reading frame in Pseudomonas aeruginosa has ld-carboxypeptidase activity and present the crystal structure of this enzyme. The structure shows that the enzyme consists of an N-terminal beta-sheet and a C-terminal beta-barrel domain. At the interface of the two domains, Ser(115) adopts a highly strained conformation in the context of a strand-turn-helix motif that is similar to the "nucleophilic elbow" in alphabeta-hydrolases. Ser(115) is hydrogen-bonded to a histidine residue, which is oriented by a glutamate residue. All three residues, which occur in the order Ser-Glu-His in the amino acid sequence, are strictly conserved in naturally occurring ld-carboxypeptidases and cannot be mutated to alanines without loss of activity. We conclude that ld-carboxypeptidases are serine peptidases with Ser-His-Glu catalytic triads. PubMed: 16162494DOI: 10.1074/jbc.M506328200 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.5 Å) |
Structure validation
Download full validation report
