1W5D

Crystal structure of PBP4a from Bacillus subtilis

Summary for 1W5D

• Entry DOI: 10.2210/pdb1w5d/pdb
• Descriptor: PENICILLIN-BINDING PROTEIN, CALCIUM ION (3 entities in total)
• Functional Keywords: penicillin-binding protein, d-ala-d-ala-carboxypeptidase, peptidoglycan, bacillus subtilis, beta-lactam, hydrolase, peptidoglycan synthesis
• Biological source: BACILLUS SUBTILIS
• Cellular location: Secreted (Probable): P39844
• Total number of polymer chains: 1
• Total formula weight: 49883.14

Authors

Sauvage, E.,Herman, R.,Petrella, S.,Duez, C.,Frere, J.M.,Charlier, P. (deposition date: 2004-08-06, release date: 2005-12-07, Last modification date: 2024-05-08)

Primary citation

Sauvage, E.,Duez, C.,Herman, R.,Kerff, F.,Petrella, S.,Anderson, J.W.,Adediran, S.A.,Pratt, R.F.,Frere, J.M.,Charlier, P.
Crystal Structure of the Bacillus Subtilis Penicillin-Binding Protein 4A, and its Complex with a Peptidoglycan Mimetic Peptide.
J.Mol.Biol., 371:528-, 2007

PubMed Abstract: The genome of Bacillus subtilis encodes 16 penicillin-binding proteins (PBPs) involved in the synthesis and/or remodelling of the peptidoglycan during the complex life cycle of this sporulating Gram-positive rod-shaped bacterium. PBP4a (encoded by the dacC gene) is a low-molecular mass PBP clearly exhibiting in vitro DD-carboxypeptidase activity. We have solved the crystal structure of this protein alone and in complex with a peptide (D-alpha-aminopymelyl-epsilon-D-alanyl-D-alanine) that mimics the C-terminal end of the Bacillus peptidoglycan stem peptide. PBP4a is composed of three domains: the penicillin-binding domain with a fold similar to the class A beta-lactamase structure and two domains inserted between the conserved motifs 1 and 2 characteristic of the penicillin-recognizing enzymes. The soaking of PBP4a in a solution of D-alpha-aminopymelyl-epsilon-D-alanyl-D-alanine resulted in an adduct between PBP4a and a D-alpha-aminopimelyl-epsilon-D-alanine dipeptide and an unbound D-alanine, i.e. the products of acylation of PBP4a by D-alpha-aminopymelyl-epsilon-D-alanyl-D-alanine with the release of a D-alanine. The adduct also reveals a binding pocket specific to the diaminopimelic acid, the third residue of the peptidoglycan stem pentapeptide of B. subtilis. This pocket is specific for this class of PBPs.

PubMed: 17582436
DOI: 10.1016/J.JMB.2007.05.071

Experimental method

X-RAY DIFFRACTION (2.1 Å)