2VGK

Crystal structure of Actinomadura R39 DD-peptidase complexed with a peptidoglycan-mimetic cephalosporin

Summary for 2VGK

• Entry DOI: 10.2210/pdb2vgk/pdb
• Related: 1W79 1W8Q 1W8Y 2VGJ
• Descriptor: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE, (2R)-2-AMINO-7-{[(1R)-1-CARBOXYETHYL]AMINO}-7-OXOHEPTANOIC ACID, SULFATE ION, ... (5 entities in total)
• Functional Keywords: cell wall biogenesis/degradation, antibiotic resistance, peptidoglycan synthesis, protease, secreted, hydrolase, cell shape, carboxypeptidase, penicillin-binding, actinomadura, peptidoglycan, transpeptidase
• Biological source: ACTINOMADURA SP.
• Cellular location: Secreted: P39045
• Total number of polymer chains: 4
• Total formula weight: 203092.51

Authors

Sauvage, E.,kerff, F.,Herman, R.,Charlier, P. (deposition date: 2007-11-14, release date: 2008-11-25, Last modification date: 2023-12-13)

Primary citation

Sauvage, E.,Powell, A.J.,Heilemann, J.,Josephin, H.R.,Charlier, P.,Davies, C.,Pratt, R.F.
Crystal Structures of Complexes of Bacterial Dd-Peptidases with Peptidoglycan-Mimetic Ligands: The Substrate Specificity Puzzle.
J.Mol.Biol., 381:383-, 2008

PubMed 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.

PubMed: 18602645
DOI: 10.1016/J.JMB.2008.06.012

Experimental method

X-RAY DIFFRACTION (2.25 Å)