1W79

Crystal structure of the DD-transpeptidase-carboxypeptidase from Actinomadura R39

Summary for 1W79

• Entry DOI: 10.2210/pdb1w79/pdb
• Related: 1W8Q 1W8Y
• Descriptor: D-alanyl-D-alanine carboxypeptidase, SULFATE ION, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: penicillin-binding, peptidoglycan, actinomadura, transpeptidase, antibiotic resistance, hydrolase
• Biological source: Actinomadura sp. R39
• Total number of polymer chains: 4
• Total formula weight: 201585.22

Authors

Sauvage, E.,Herman, R.,Petrella, S.,Duez, C.,Frere, J.M.,Charlier, P. (deposition date: 2004-08-31, release date: 2005-06-28, Last modification date: 2024-05-08)

Primary citation

Sauvage, E.,Herman, R.,Petrella, S.,Duez, C.,Bouillenne, F.,Frere, J.M.,Charlier, P.
Crystal structure of the Actinomadura R39 DD-peptidase reveals new domains in penicillin-binding proteins.
J. Biol. Chem., 280:31249-31256, 2005

PubMed Abstract: Actinomadura sp. R39 produces an exocellular DD-peptidase/penicillin-binding protein (PBP) whose primary structure is similar to that of Escherichia coli PBP4. It is characterized by a high beta-lactam-binding activity (second order rate constant for the acylation of the active site serine by benzylpenicillin: k2/K = 300 mm(-1) s(-1)). The crystal structure of the DD-peptidase from Actinomadura R39 was solved at a resolution of 1.8 angstroms by single anomalous dispersion at the cobalt resonance wavelength. The structure is composed of three domains: a penicillin-binding domain similar to the penicillin-binding domain of E. coli PBP5 and two domains of unknown function. In most multimodular PBPs, additional domains are generally located at the C or N termini of the penicillin-binding domain. In R39, the other two domains are inserted in the penicillin-binding domain, between the SXXK and SXN motifs, in a manner similar to "Matryoshka dolls." One of these domains is composed of a five-stranded beta-sheet with two helices on one side, and the other domain is a double three-stranded beta-sheet inserted in the previous domain. Additionally, the 2.4-angstroms structure of the acyl-enzyme complex of R39 with nitrocefin reveals the absence of active site conformational change upon binding the beta-lactams.

PubMed: 15987687
DOI: 10.1074/jbc.M503271200

Experimental method

X-RAY DIFFRACTION (1.8 Å)