Active-site mutants of the VanC2 d-alanyl-d-serine ligase, characteristic of one vancomycin-resistant bacterial phenotype, revert towards wild-type d-alanyl-d-alanine ligases

AbstractBackground: The rising number of vancomycin-resistant enterococci (VREs) is a major concern to modern medicine because vancomycin is currently the ‘last resort’ drug for life-threatening infections. The d-alanyl-d-X ligases (where X is an hydroxy or amino acid) of bacteria catalyze a critical step in bacterial cell-wall peptidoglycan assembly. In bacteria that produce glycopeptide antibiotics and in opportunistic pathogens, including VREs, d, d-ligases serve as switches that confer antibiotic resistance on the bacteria themselves. Peptidoglycans in vancomycin-sensitive bacteria end in d-alanyl-d-alanine, whereas in vancomycin-resistant bacteria they end in d-alanyl-d-lactate or d-alanyl-d-serine.Results: We demonstrate that the selective utilization of D-serine by the Enterococcus casseliflavus VanC2 ligase can be altered by mutagenesis of one of two residues identified by homology to the X-ray structure of the Escherichia coli d-alanyl-d-alanine ligase (DdIB). The Arg322→Met (R322M) and Phe250→Tyr (F250Y) ligase mutants show a 36–44-fold decrease in the use of d-serine, as well as broadened specificity for utilization of other D-amino acids in place of D-serine. The F250Y R322M double mutant is effectively disabled ass a d-alanyl-d-serine ligase and retains 10% of the catalytic activity of wild-type d-alanyl-d-alanine ligases, reflecting a 6,000-fold switch to the d-alanyl-d-alanine peptide. Correspondingly, the Leu282→Arg mutant of the wild-type E. coli DdIB produced a 560-fold switch towards d-alanyl-d-serine formation.Conclusions: Single-residue changes in the active-site regions of d, d-ligases can cause substantial changes in recognition and activation of hydroxy or amino acids that have consequences for glycopeptide antibiotic efficacy. The observations reported here should provide an approach for combatting antibiotic-resistant bacteria