PDBsum entry 1zrs

Hydrolase

PDB id: 1zrs

Contents

Protein chains

294 a.a. *

Waters ×313

* Residue conservation analysis

PDB id:

1zrs

Name:

Hydrolase

Title:

Wild-type ld-carboxypeptidase

Structure:

Hypothetical protein. Chain: a, b. Engineered: yes

Source:

Pseudomonas aeruginosa. Organism_taxid: 287. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PQS)

Resolution:

1.50Å R-factor: 0.164 R-free: 0.177

Authors:

H.J.Korza,M.Bochtler

Key ref:

H.J.Korza and M.Bochtler (2005). Pseudomonas aeruginosa LD-carboxypeptidase, a serine peptidase with a Ser-His-Glu triad and a nucleophilic elbow. J Biol Chem, 280, 40802-40812. PubMed id: 16162494 DOI: 10.1074/jbc.M506328200

Date:

21-May-05 Release date: 20-Sep-05

Protein chains

Q9HTZ1  (LDC_PSEAE) -  Murein tetrapeptide carboxypeptidase from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)

Seq: 307 a.a.

Struc: 294 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.4.17.13 - muramoyltetrapeptide carboxypeptidase.
• Reaction: N-acetyl-D-glucosaminyl-N-acetylmuramoyl-L-alanyl-meso-2,6- diaminoheptanedioyl-D-alanine + H2O = N-acetyl-D-glucosaminyl-N- acetylmuramoyl-L-alanyl-meso-2,6-diaminoheptanedioate + D-alanine

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Key reference

DOI no: 10.1074/jbc.M506328200

J Biol Chem 280:40802-40812 (2005)

PubMed id: 16162494

Pseudomonas aeruginosa LD-carboxypeptidase, a serine peptidase with a Ser-His-Glu triad and a nucleophilic elbow.

H.J.Korza, M.Bochtler.

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.

Selected figure(s)

Figure 1.
FIGURE 1. Schematic representation of the disaccharide tri- and tetrapeptide fragments resulting from digestion of P. putida peptidoglycan with lysozyme. The calculated and experimentally measured monoisotopic masses of the most abundant species are indicated. Stereochemical information was taken from Refs. 8 and 15, and the glycosidic linkage was placed between C-1 of GlcNAc and C-4 of MurNAc and not between C-1 of MurNAc and C-4 of GlcNAc. This choice was based on the known preference of lysozyme for the glycosidic link that connects C-1 of MurNAc to C-4 of GlcNAc (16). S and P stand for substrate and product of the enzymatic reaction.

Figure 9.
FIGURE 9. Comparison of the nucleophilic elbows in LD-carboxypeptidase (A and B) and the lipase from G. candidum as a representative of -hydrolases (C and D). A and C show C- traces in monorepresentation, and B and D show all atom representations in stereo. The solid green lines show hydrogen bonds that match the pattern for 3[10]-helices, and dashed green lines show hydrogen bonds in regular -helices. The figure was made with the MolScript program (54).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 40802-40812) copyright 2005.

Figures were selected by an automated process.