PDBsum entry 3beb

Hydrolase

PDB id: 3beb

Contents

Protein chain

354 a.a. *

Ligands

HJ3

GOL

Waters ×188

* Residue conservation analysis

PDB id:

3beb

Name:

Hydrolase

Title:

Crystal structure of e. Coli penicillin-binding protein 5 in complex with a peptide-mimetic penicillin

Structure:

Penicillin-binding protein 5. Chain: a. Fragment: sequence database residues 30-386. Synonym: dd- peptidase, dd-carboxypeptidase, beta-lactamase, d- alanyl-d-alanine carboxypeptidase daca, pbp-5. Engineered: yes

Source:

Escherichia coli. Gene: daca, pfv. Expressed in: escherichia coli.

Resolution:

2.00Å R-factor: 0.238 R-free: 0.296

Authors:

J.Heilemann,A.J.Powell,C.Davies

Key ref:

E.Sauvage et al. (2008). Crystal structures of complexes of bacterial DD-peptidases with peptidoglycan-mimetic ligands: the substrate specificity puzzle. J Mol Biol, 381, 383-393. PubMed id: 18602645 DOI: 10.1016/j.jmb.2008.06.012

Date:

16-Nov-07 Release date: 26-Aug-08

Protein chain

P0AEB2  (DACA_ECOLI) -  D-alanyl-D-alanine carboxypeptidase DacA from Escherichia coli (strain K12)

Seq: 403 a.a.

Struc: 354 a.a.

Enzyme reactions

• Enzyme class 1: E.C.3.4.16.4 - serine-type D-Ala-D-Ala carboxypeptidase.
• Reaction: D-alanyl-D-alanine + H₂O = 2 D-alanine

(Bound ligand (Het Group name = HJ3) matches with 52.00% similarity) + = 2 × (Bound ligand (Het Group name = GOL) matches with 50.00% similarity)

• Enzyme class 2: E.C.3.5.2.6 - beta-lactamase.

Pathway:

• Reaction: a beta-lactam + H2O = a substituted beta-amino acid
• Cofactor: Zn(2+)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

Added reference

DOI no: 10.1016/j.jmb.2008.06.012

J Mol Biol 381:383-393 (2008)

PubMed id: 18602645

Crystal structures of complexes of bacterial DD-peptidases with peptidoglycan-mimetic ligands: the substrate specificity puzzle.

E.Sauvage, A.J.Powell, J.Heilemann, H.R.Josephine, P.Charlier, C.Davies, R.F.Pratt.

ABSTRACT

The X-ray crystal structures of covalent complexes of the Actinomadura R39 dd-peptidase and Escherichia coli penicillin-binding protein (PBP) 5 with beta-lactams bearing peptidoglycan-mimetic side chains have been determined. The structure of the hydrolysis product of an analogous peptide bound noncovalently to the former enzyme has also been obtained. The R39 DD-peptidase structures reveal the presence of a specific binding site for the D-alpha-aminopimelyl side chain, characteristic of the stem peptide of Actinomadura R39. This binding site features a hydrophobic cleft for the pimelyl methylene groups and strong hydrogen bonding to the polar terminus. Both of these active site elements are provided by amino acid side chains from two separate domains of the protein. In contrast, no clear electron density corresponding to the terminus of the peptidoglycan-mimetic side chains is present when these beta-lactams are covalently bound to PBP5. There is, therefore, no indication of a specific side-chain binding site in this enzyme. These results are in agreement with those from kinetics studies published earlier and support the general prediction made at the time of a direct correlation between kinetics and structural evidence. The essential high-molecular-mass PBPs have demonstrated, to date, no specific reactivity with peptidoglycan-mimetic peptide substrates and beta-lactam inhibitors and, thus, probably do not possess a specific substrate-binding site of the type demonstrated here with the R39 DD-peptidase. This striking deficiency may represent a sophisticated defense mechanism against low-molecular-mass substrate-analogue inhibitors/antibiotics; its discovery should focus new inhibitor design.

Selected figure(s)

Figure 1.
Fig. 1. Crystal structures of the R39 dd-peptidase in complex with (a) the cephalosporin 6 and (b) the peptide 7, and crystal structures of PBP5 from E. coli in complex with (c) the cephalosporin 6 and (d) the penicillin 5. In these stereoviews of the respective active sites, the electron density is a |F[o]| − |F[c]| difference map calculated from the final coordinates of each model refined in the absence of the ligand. The resulting positive density is shown in blue and is contoured at 2.0σ. Carbon atoms of each ligand that are visible in the electron density and have been included in the final model are in green. Those that could not be modeled (in PBP5) due to weak density are in gray and are included to show the approximate positions of these groups. The carbon atoms of amino acids that form each active site are in yellow. Oxygen atoms are in red, nitrogen atoms are in blue, and sulfur atoms are in orange. Potential hydrogen bonds are shown as dashed lines, and the distances are noted in angstroms. Some distances beyond hydrogen-bonding range are shown in (d) for comparison with the equivalent distances in (c). This figure was generated using PYMOL (www.pymol.sourceforge.net).

Figure 2.
Fig. 2. Interaction between Arg248 and the cephalosporin carboxylate. The backbones of wild-type (green), penicillin-5-bound (purple), and cephalosporin-6-bound (yellow) structures of PBP5 are superimposed, showing conformational differences in a loop comprising residues 242–248. In the cephalosporin structure, Arg248 interacts with the carboxylate of the cephalosporin (in yellow), whereas in the penicillin-bound structure, Arg248 occupies a position similar to that in wild-type PBP5. There are also differences in the respective positions of Phe245.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 381, 383-393) copyright 2008.