PDBsum entry 1pwc

Hydrolase

PDB id: 1pwc

Contents

Protein chain

345 a.a. *

Ligands

PNM

Waters ×507

* Residue conservation analysis

PDB id:

1pwc

Name:

Hydrolase

Title:

Penicilloyl acyl enzyme complex of the streptomyces r61 dd-peptidase with penicillin g

Structure:

D-alanyl-d-alanine carboxypeptidase. Chain: a. Fragment: dd-peptidase. Synonym: dd-peptidase, dd-carboxypeptidase. Ec: 3.4.16.4

Source:

Streptomyces sp.. Organism_taxid: 31952. Strain: r61

Resolution:

1.10Å R-factor: 0.124 R-free: 0.148

Authors:

N.R.Silvaggi,H.R.Josephine,R.F.Pratt,J.A.Kelly

Key ref:

N.R.Silvaggi et al. (2005). Crystal structures of complexes between the R61 DD-peptidase and peptidoglycan-mimetic beta-lactams: a non-covalent complex with a "perfect penicillin". J Mol Biol, 345, 521-533. PubMed id: 15581896 DOI: 10.1016/j.jmb.2004.10.076

Date:

01-Jul-03 Release date: 13-Jul-04

Protein chain

P15555  (DAC_STRSR) -  D-alanyl-D-alanine carboxypeptidase from Streptomyces sp. (strain R61)

Seq: 406 a.a.

Struc: 345 a.a.

Enzyme reactions

• Enzyme class: 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 = PNM) matches with 41.00% similarity) + = 2 ×

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

Added reference

DOI no: 10.1016/j.jmb.2004.10.076

J Mol Biol 345:521-533 (2005)

PubMed id: 15581896

Crystal structures of complexes between the R61 DD-peptidase and peptidoglycan-mimetic beta-lactams: a non-covalent complex with a "perfect penicillin".

N.R.Silvaggi, H.R.Josephine, A.P.Kuzin, R.Nagarajan, R.F.Pratt, J.A.Kelly.

ABSTRACT

The bacterial D-alanyl-D-alanine transpeptidases (DD-peptidases) are the killing targets of beta-lactams, the most important clinical defense against bacterial infections. However, due to the constant development of antibiotic-resistance mechanisms by bacteria, there is an ever-present need for new, more effective antimicrobial drugs. While enormous numbers of beta-lactam compounds have been tested for antibiotic activity in over 50 years of research, the success of a beta-lactam structure in terms of antibiotic activity remains unpredictable. Tipper and Strominger suggested long ago that beta-lactams inhibit DD-peptidases because they mimic the D-alanyl-D-alanine motif of the peptidoglycan substrate of these enzymes. They also predicted that beta-lactams having a peptidoglycan-mimetic side-chain might be better antibiotics than their non-specific counterparts, but decades of research have not provided any evidence for this. We have recently described two such novel beta-lactams. The first is a penicillin having the glycyl-L-alpha-amino-epsilon-pimelyl side-chain of Streptomyces strain R61 peptidoglycan, making it the "perfect penicillin" for this organism. The other is a cephalosporin with the same side-chain. Here, we describe the X-ray crystal structures of the perfect penicillin in non-covalent and covalent complexes with the Streptomyces R61 DD-peptidase. The structure of the non-covalent enzyme-inhibitor complex is the first such complex to be trapped crystallographically with a DD-peptidase. In addition, the covalent complex of the peptidyl-cephalosporin with the R61 DD-peptidase is described. Finally, two covalent complexes with the traditional beta-lactams benzylpenicillin and cephalosporin C were determined for comparison with the peptidyl beta-lactams. These structures, together with relevant kinetics data, support Tipper and Strominger's assertion that peptidoglycan-mimetic side-chains should improve beta-lactams as inhibitors of DD-peptidases.

Selected figure(s)

Figure 3.
Figure 3. Representations of the active sites in the five complex structures (E2 (a), E2* (b), E3* (c), E4* (d), and E5* (e)) showing the interactions between active-site functional groups and the inhibitors (broken lines). Distances (in Å) for the interactions are denoted adjacent to the broken lines. Covalent cross-links between Lys65, His108, and Tyr159 (see Materials and Methods) are shown in (a).

Figure 4.
Figure 4. Stereo view showing a superposition of the active sites of the E2 complex (a), and E2* complex (b), onto the ES complex. Carbon atoms of the active-site residues in the ES complex are colored grey, while those in the tetrapeptide substrate are colored black. The E2, E2*, and model tetrahedral intermediate complexes are shown with yellow carbon atoms in the protein residues and orange in compound 2. Notice the similarity between the conformations of the substrate and inhibitor, especially the region near the catalytic Ser62. The rmsd between E2 and ES is 0.22 Å, while that of the E2* and ES structures is 0.31 Å, for all atoms in the 16 active-site residues. In (c) the E2 structure is overlaid on an energy-minimized model of the tetrahedral intermediate with peptide substrate. The Figure was produced using MOLSCRIPT.39

The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 345, 521-533) copyright 2005.

Figures were selected by an automated process.