Structural insights into stereochemical inversion by diaminopimelate epimerase: An antibacterial drug target

d -amino acids are much less common than theirl -isomers but are widely distributed in most organisms. Manyd -amino acids, including those necessary for bacterial cell wall formation, are synthesized from the correspondingl -isomers by α-amino acid racemases. The important class of pyridoxal phosphate-independent racemases function by an unusual mechanism whose details have been poorly understood. It has been proposed that the stereoinversion involves two active-site cysteine residues acting in concert as a base (thiolate) and an acid (thiol). Although crystallographic structures of several such enzymes are available, with the exception of the recent structures of glutamate racemase fromBacillus subtilis and of proline racemase fromTrypanosoma cruzi , the structures either are of inactive forms (e.g., disulfide) or do not allow unambiguous modeling of the substrates in the active sites. Here, we present the crystal structures of diaminopimelate (DAP) epimerase fromHaemophilus influenzae with two different isomers of the irreversible inhibitor and substrate mimic aziridino-DAP at 1.35- and 1.70-Å resolution. These structures permit a detailed description of this pyridoxal 5′-phosphate-independent amino acid racemase active site and delineate the electrostatic interactions that control the exquisite substrate selectivity of DAP epimerase. Moreover, the active site shows how deprotonation of the substrates’ nonacidic hydrogen at the α-carbon (pKa ≈ 29) by a seemingly weakly basic cysteine residue (pKa ≈ 8–10) is facilitated by interactions with two buried α-helices. Bacterial racemases, including glutamate racemase and DAP epimerase, are potential targets for the development of new agents effective against organisms resistant to conventional antibiotics.