Cytidine triphosphate synthetases (CTPSs) produce CTP from UTP and glutamine, and regulate intracellular CTP levels through interactions with the four ribonucleotide triphosphates. We solved the 2.3-Å resolution crystal structure of Escherichia coli CTPS using Hg-MAD phasing. The structure reveals a nearly symmetric 222 tetramer, in which each bifunctional monomer contains a dethiobiotin synthetase-like amidoligase N-terminal domain and a Type 1 glutamine amidotransferase C-terminal domain. For each amidoligase active site, essential ATP-and UTPbinding surfaces are contributed by three monomers, suggesting that activity requires tetramer formation, and that a nucleotide-dependent dimer-tetramer equilibrium contributes to the observed positive cooperativity. A gated channel that spans 25 Å between the glutamine hydrolysis and amidoligase active sites provides a path for ammonia diffusion. The channel is accessible to solvent at the base of a cleft adjoining the glutamine hydrolysis active site, providing an entry point for exogenous ammonia. Guanine nucleotide binding sites of structurally related GTPases superimpose on this cleft, providing insights into allosteric regulation by GTP. Mutations that confer nucleoside drug resistance and release CTP inhibition map to a pocket that neighbors the UTP-binding site and can accommodate a pyrimidine ring. Its location suggests that competitive feedback inhibition is affected via a distinct product/drug binding site that overlaps the substrate triphosphate binding site. Overall, the E. coli structure provides a framework for homology modeling of other CTPSs and structure-based design of anti-CTPS therapeutics. † This work was funded by the UC Systemwide Biotechnology Training Program Grant #2002-07, and the National Institutes of Health, General Medical Sciences, #GM63109. ‡ Protein Data Bank accession number 1S1M.
NIH Public Access
Author ManuscriptBiochemistry. Author manuscript; available in PMC 2010 June 24.
NIH-PA Author ManuscriptNIH-PA Author Manuscript
NIH-PA Author ManuscriptCytidine triphosphate synthetases (CTPSs, 1 E. C. 6.4.3.2, uridine triphosphate ammonia lyases, 525-630 amino acid residues) are essential ubiquitous enzymes that catalyze the ratelimiting step of de novo CTP biosynthesis (1,2). Genes pyrG (bacteria), ctrA (some gram positive bacteria), URA7 and URA8 (Saccharomyces cerevisiae), and CTPS1 and CTPS2 (human) encode CTP synthetase enzymes, with most eukaryotes expressing two isoforms.CTPSs not only provide a key precursor for synthesis of DNA, RNA, and phospholipid (3,4), they also control the intracellular CTP concentrations that limit these processes (5-9).CTP is derived from UTP in three reaction steps catalyzed by CTPSs (Figure 1a). In one active site, the UTP O4 oxygen is activated by Mg-ATP-dependent phosphorylation, followed by displacement of the resulting 4-phosphate moiety by ammonia (10,11). In a separate site, ammonia is generated via rate-limiting glutamine hydrolysis (glutaminase) activity (12). CTPS activity was first re...