First-time crystallization and preliminary X-ray crystallographic analysis of a bacterial-archaeal type UMP kinase, a key enzyme in microbial pyrimidine biosynthesis

Abstract

UMP phosphorylation, a key step for pyrimidine nucleotide biosynthesis, is catalyzed in bacteria by UMP kinase (UMPK), an enzyme specific for UMP that is dissimilar to the eukaryotic UMP/CMP kinase or to other nucleoside monophosphate kinases. UMPK is allosterically regulated and participates in pyrimidine-triggered gene repression. As first step towards determining UMPK structure, the putative UMPK-encoding gene of the hyperthermophilic archaeon Pyrococcus furiosus was cloned and overexpressed in Escherichia coli. The protein product was purified and confirmed to be a genuine UMPK. It was crystallized at 294 K in hanging drops by the vapor diffusion technique using 3.5–4 M Na formate. Cubic 0.2-mm crystals diffracted synchrotron X-rays to 2.4-Å resolution. Space group was I23 ( a= b= c=144.95 Å), and the asymmetric unit contained two monomers, with 52% solvent content. The self-rotation function suggests that the enzyme is hexameric, which agrees with biochemical studies on bacterial UMPKs.