1W8Y
Crystal structure of the nitrocefin acyl-DD-peptidase from Actinomadura R39.
Summary for 1W8Y
| Entry DOI | 10.2210/pdb1w8y/pdb |
| Related | 1W79 1W8Q |
| Descriptor | D-alanyl-D-alanine carboxypeptidase, SULFATE ION, MAGNESIUM ION, ... (5 entities in total) |
| Functional Keywords | hydrolase, penicillin-binding, actinomadura, peptidoglycan, nitrocefin |
| Biological source | Actinomadura sp. |
| Cellular location | Secreted: P39045 |
| Total number of polymer chains | 4 |
| Total formula weight | 203339.04 |
| Authors | Sauvage, E.,Herman, R.,Petrella, S.,Duez, C.,Frere, J.M.,Charlier, P. (deposition date: 2004-10-01, release date: 2005-06-28, Last modification date: 2023-12-13) |
| 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-, 2005 Cited by 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: 15987687DOI: 10.1074/JBC.M503271200 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.4 Å) |
Structure validation
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