Crystal structures of Staphylococcus aureus ketol-acid reductoisomerase in complex with two transition state analogues that have biocidal activity

Ketol-acid reductoisomerase (KARI) is an NAD(P)H and Mg2+-dependent enzyme of the branched-chain amino acid (BCAA) biosynthesis pathway. Here we describe the first crystal structures of Staphylococcus aureus (Sa) KARI, these in complex with two transition state analogs, cyclopropane-1,1-dicarboxylate (CPD) and N-isopropyloxalyl hydroxamate (IpOHA). These compounds bind competitively and in multi-dentate manner to KARI with Ki values of 2.73 μM and 7.9 nM, respectively; however, IpOHA binds slowly to the enzyme. Interestingly, intact IpOHA is present in only ~25% of binding sites, while its deoxygenated form is present in the remaining sites. This deoxy form of IpOHA binds rapidly to Sa KARI, but with much weaker affinity (Ki = 21 μM). Thus, our data pinpoint the origin of the slow binding mechanism of IpOHA. Furthermore, we propose that CPD mimics the early stage of the catalytic reaction (preceding the reduction step), while IpOHA mimics the late stage (after the reduction took place). These structural insights will guide strategies to design potent and rapidly binding derivatives of these compound for the development of novel biocides.