DD-peptidase

The antibiotic activity of certain (3-lactams depends largely on their interaction with two different groups of bacterial enzymes. (3-Lactams, like the penicillins and cephalosporins, inhibit the DD-peptidases/transpeptidases that are responsible for the final step of bacterial cell wall biosynthesis.63 Unfortunately, they are themselves destroyed by the [3-lactamases,64 which thereby provide much of the resistance to these antibiotics. Class A, C, and D [3-lactamases and DD-peptidases all have a conserved serine residue in the active site whose hydroxyl group is the primary nucleophile that attacks the substrate carbonyl. Catalysis in both cases involves a double-displacement reaction with the transient formation of an acyl-enzyme intermediate. The major distinction between [3-lactamases and their evolutionary parents the DD-peptidase residues is the lifetime of the acyl-enzyme it is short in (3-lactamases and long in the DD-peptidases.65-67... 

The functionalized phenaceturates 16 (Fig. 11.10) are substrates of class A and C [3-lactamases, especially the class C enzymes, as observed with the parent unfunctionalized phenaceturates 15. They are also modest inhibitors of these enzymes and the serine DD-peptidase of Streptomyces R61. The inhibition of class C [3-lactamases is turnover dependent, as expected for a mechanism-based inhibitor. Inhibition is not very dependent on the nature of the leaving group, suggesting that the QM is generated in solution after the product phenol has been released from the active site. It therefore... 

Figure B3.5.13 A convincing artifact. In an attempt to study the conformational consequences of adding an acceptor, D-glutamine, to a DD-peptidase, far-UV CD spectra were recorded for the enzyme in the presence of increasing concentrations of glutamine a = 0 mM, b = 3 mM, c = 7 mM, d = 10 mM, e = 20 mM, f = 30 mM, g = 50 mM, and h = 95 mM. The enzyme concentration was 0.1 mg/ml, equivalent to 10 3 M peptide bond, in 10 mM sodium phosphate pH 7.2. A 2-mm cell path length was used.

M Adam, C Damblon, B Plaitin, L Christiaens, JM Frere. Chromogenic depsipep-tide substrates for 3-lactamases and penicillin-sensitive DD-peptidases. Biochem J 270 525-529, 1990. 

The high molecular weight (HMW) DD-peptidases feature two domains one of which is penicillin binding (PB). The subclass A contains bifunctional enzymes (transglycosylases and transpeptidases), and the subclass B, monofunctional enzymes (transpeptidases). Both the classes A and B of HMW DD-peptidases are essential for cell survival <1991ARM37, 1998MI1079>. Proteins of subclass C are involved in /3-lactamase synthesis induction (see Section 2.03.12.2) <1998AAC1>. 

Inactivation of DD-peptidases thus depends on a rapid and nearly quantitative accumulation of E-A intermediate resulting, jointly, from its stability (k2 is very low, of the order of 10 4-10 6s ), and its rapid formation. The factor governing the rate of acyl-enzyme formation is k2IK, where A- = (A j + k2)lki (value of the order of 103-106M-1 s 1). 

Penicillins have been considered for the inhibition of other bacterial serine enzymes than the DD-peptidases and /3-lactamases. For instance, bacterial signal peptidases (SPases) are essential for cell viability and therefore represent nowadays a class of novel antibacterial target <1998NAT186>. SPases are involved in protein translocation through the cytoplasmic membrane in the final step of the bacterial protein secretion pathway <1997PSC1119>. 5(S)-Stereoisomers of penems have been found to inhibit SPases <1995BML443>. The most potent inhibitors are 5/AV-tricyclic penems <2003S1732>. 

Fascinating reports have appeared that seem to support a theory that P-lactamases may have evolved from PBPs, specifically from D-alanyl-D-alanine cleaving peptidase (dd-peptidase). The active-site DD-peptidase of S. R61 has been crystallized and the three-dimensional structure and penicillin-binding site determined by very high (2.8 A)... 

Boyd, D.B. Snoddy, J.D. Lin, H.-S. Molecular simulation of DD-peptidase, a model P-lactam-binding protein synergy between X-ray crystallography and computational chemistry. J. Compu. Chem. 1991,12, 635-644. 

Surface representation of the substrate binding site of DAP. The substrate binding site of DD-peptidase (PDB ID 1IKG) complexed with REX (ball and stick representation) is also superposed to that of DAP. 

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