Crystal structure of the Actinomadura R39 DD-peptidase reveals new domains in penicillin-binding proteins. (original) (raw)

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Crystal structure of the Actinomadura R39 DD-peptidase reveals new domains in penicillin-binding proteins.

; Herman, Raphaël; Petrella, Stephanie et al.

2005 • In Journal of Biological Chemistry, 280 (35), p. 31249-56

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Keywords :

Actinomycetales/chemistry; Bacterial Proteins/chemistry/metabolism; Cephalosporins/chemistry/metabolism; Cobalt/chemistry; Crystallography, X-Ray; Indicators and Reagents/chemistry/metabolism; Models, Molecular; Penicillins/chemistry/metabolism; Protein Structure, Tertiary; Serine-Type D-Ala-D-Ala Carboxypeptidase/chemistry/metabolism

Abstract :

[en] 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.

Research Center/Unit :

CIP - Centre d'Ingénierie des Protéines - ULiège

Disciplines :

Biochemistry, biophysics & molecular biology

Author, co-author :

Sauvage, Eric ; Université de Liège - ULiège > Centre d'ingénierie des protéines

Herman, Raphaël ; Université de Liège - ULiège > Centre d'ingénierie des protéines

Petrella, Stephanie; Université Pierre et Marie Curie, Paris France > LRMA, INSERM U655

Duez, Colette ; Université de Liège - ULiège > Centre d'ingénierie des protéines

Bouillenne, Fabrice ; Université de Liège - ULiège > Centre d'ingénierie des protéines

Frère, Jean-Marie ; Université de Liège - ULiège > Centre d'ingénierie des protéines

Charlier, Paulette ; Université de Liège - ULiège > Département des sciences de la vie > Cristallographie des macromolécules biologiques

Title :

Crystal structure of the Actinomadura R39 DD-peptidase reveals new domains in penicillin-binding proteins.

Journal title :

Journal of Biological Chemistry

Publisher :

American Society for Biochemistry and Molecular Biology, Baltimore, United States - Maryland

Peer reviewed :

Peer Reviewed verified by ORBi

Available on ORBi :

since 30 November 2010

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