Crystal Structure of the Bacillus subtilis Penicillin-binding Protein 4a, and its Complex with a Peptidoglycan Mimetic Peptide

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-α-aminopymelyl-ε-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 β-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-α-aminopymelyl-ε-d-alanyl-d-alanine resulted in an adduct between PBP4a and a d-α-aminopimelyl-ε-d-alanine dipeptide and an unbound d-alanine, i.e. the products of acylation of PBP4a by d-α-aminopymelyl-ε-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.