The role of residue S139 of mandelate racemase: synergistic effect of S139 and E317 on transition state stabilization

Mandelate racemase (MR) from Pseudomonas putida catalyzes the specific carbon-hydrogen bond cleavage of carbon acids with high pK(a) values. To further explore the catalytic mechanism of MR, "hot spots" contributing to transition state (TS) stabilization were identified by molecular dynamics (MD) simulations. MD simulations of MR with mandelic acid interpreted S139 in the active site cavity formed a hydrogen bond (HB) with one carboxyl oxygen of mandelate which also interacts with E317 through HB. Mutation of S139A by site-directed mutagenesis led to a significant reduction of catalytic efficiency (k(cat) K-m(-1)) about 45-fold and 60-fold in R -> S and S -> R directions, indicating the significance of Ser139 in mandelate racemization. MD of mutant S139A with mandelic acid efficiently provided insight for the decreased k(cat) K-m(-1) value and clearly demonstrated the synergistic effect of S139 and E317 on the stabilization of substrate at ground/TS.