Crystal structure of the Actinomadura R39 DD-peptidase reveals new domains in penicillin-binding proteins.
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.
Sauvage
Eric
E
Centre d'Ingénierie des Protéines, Université de Liège, Institut de Physique B5, B-4000 Liège, Belgium. eric.sauvage@ulg.ac.be
Herman
Raphaël
R
Petrella
Stephanie
S
Duez
Colette
C
Bouillenne
Fabrice
F
Frère
Jean-Marie
JM
Charlier
Paulette
P
D000192:Actinomycetales / Q000737:chemistry*; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D002511:Cephalosporins / Q000737:chemistry / Q000378:metabolism; D003035:Cobalt / Q000737:chemistry; D018360:Crystallography, X-Ray; D007202:Indicators and Reagents / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D010406:Penicillins / Q000737:chemistry / Q000378:metabolism; D017434:Protein Structure, Tertiary; D046929:Serine-Type D-Ala-D-Ala Carboxypeptidase / Q000737:chemistry* / Q000378:metabolism
D001426:Bacterial Proteins; D002511:Cephalosporins; D007202:Indicators and Reagents; D010406:Penicillins; D003035:Cobalt; D046929:Serine-Type D-Ala-D-Ala Carboxypeptidase; C021720:nitrocefin