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-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.
Sauvage
Eric
E
Centre d'Ingénierie des Protéines, Université de Liège, Institut de Physique B5 et Institut de Chimie B6a, Sart Tilman, B-4000 Liège, Belgium. Eric.Sauvage@ulg.ac.be
Duez
Colette
C
Herman
Raphaël
R
Kerff
Frédéric
F
Petrella
Stephanie
S
Anderson
John W
JW
Adediran
S A
SA
Pratt
R F
RF
Frère
Jean-Marie
JM
Charlier
Paulette
P
D000595:Amino Acid Sequence; D001412:Bacillus subtilis / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D040761:Biomimetic Materials / Q000737:chemistry / Q000378:metabolism*; D018360:Crystallography, X-Ray; D007769:Lactams / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D046915:Penicillin-Binding Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D010455:Peptides / Q000737:chemistry / Q000378:metabolism*; D010457:Peptidoglycan / Q000737:chemistry / Q000378:metabolism*; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D012680:Sensitivity and Specificity; D016415:Sequence Alignment
D007769:Lactams; D046915:Penicillin-Binding Proteins; D010455:Peptides; D010457:Peptidoglycan