Crystal structures of undecaprenyl pyrophosphate synthase in complex with magnesium, isopentenyl pyrophosphate, and farnesyl thiopyrophosphate - Roles of the metal ion and conserved residues in catalysis

Undecaprenyl pyrophosphate synthase ( UPPs) catalyzes the consecutive condensation reactions of a farnesyl pyrophosphate (FPP) with eight isopentenyl pyrophosphates (IPP), in which new cis-double bonds are formed, to generate undecaprenyl pyrophosphate that serves as a lipid carrier for peptidoglycan synthesis of bacterial cell wall. The structures of Escherichia coli UPPs were determined previously in an orthorhombic crystal form as an apoenzyme, in complex with Mg2+/sulfate/ Triton, and with bound FPP. In a further search of its catalytic mechanism, the wild-type UPPs and the D26A mutant are crystallized in a new trigonal unit cell with Mg2+/IPP/farnesyl thiopyrophosphate (an FPP analogue) bound to the active site. In the wild-type enzyme, Mg2+ is coordinated by the pyrophosphate of farnesyl thiopyrophosphate, the carboxylate of Asp26, and three water molecules. In the mutant enzyme, it is bound to the pyrophosphate of IPP. The [Mg2+] dependence of the catalytic rate by UPPs shows that the activity is maximal at [Mg2+] = 1 mM but drops significantly when Mg2+ ions are in excess (50 mm). Without Mg2+, IPP binds to UPPs only at high concentration. Mutation of Asp26 to other charged amino acids results in significant decrease of the UPPs activity. The role of Asp26 is probably to assist the migration of Mg2+ from IPP to FPP and thus initiate the condensation reaction by ionization of the pyrophosphate group from FPP. Other conserved residues, including His(43), Ser(71), Asn(74), and Arg(77), may serve as general acid/base and pyrophosphate carrier. Our results here improve the understanding of the UPPs enzyme reaction significantly.