title: Structures of the human orotidine-5'-monophosphate decarboxylase support a covalent mechanism and provide a framework for drug design.
abstract: UMP synthase (UMPS) catalyzes the last two steps of de novo pyrimidine nucleotide synthesis and is a potential cancer drug target. The C-terminal domain of UMPS is orotidine-5'-monophosphate decarboxylase (OMPD), a cofactor-less yet extremely efficient enzyme. Studies of OMPDs from micro-organisms led to the proposal of several noncovalent decarboxylation mechanisms via high-energy intermediates. We describe nine crystal structures of human OMPD in complex with substrate, product, and nucleotide inhibitors. Unexpectedly, simple compounds can replace the natural nucleotides and induce a closed conformation of OMPD, defining a tripartite catalytic site. The structures outline the requirements drugs must meet to maximize therapeutic effects and minimize cross-species activity. Chemical mimicry by iodide identified a CO(2) product binding site. Plasticity of catalytic residues and a covalent OMPD-UMP complex prompt a reevaluation of the prevailing decarboxylation mechanism in favor of covalent intermediates. This mechanism can also explain the observed catalytic promiscuity of OMPD.
authors.affiliation: Department of Molecular Structural Biology, University of Göttingen, Göttingen, Germany.
authors.forename: Julia G
authors.initials: JG
authors.lastname: Wittmann
authors.forename: Daniel
authors.initials: D
authors.lastname: Heinrich
authors.forename: Kathrin
authors.initials: K
authors.lastname: Gasow
authors.forename: Alexandra
authors.initials: A
authors.lastname: Frey
authors.forename: Ulf
authors.initials: U
authors.lastname: Diederichsen
authors.forename: Markus G
authors.initials: MG
authors.lastname: Rudolph
mesh_terms: D015195:Drug Design; D006801:Humans; D007700:Kinetics; D008958:Models, Molecular; D009097:Multienzyme Complexes / Q000737:chemistry* / Q000378:metabolism*; D009962:Orotate Phosphoribosyltransferase / Q000737:chemistry* / Q000378:metabolism*; D009964:Orotidine-5'-Phosphate Decarboxylase / Q000737:chemistry* / Q000187:drug effects / Q000378:metabolism*; D011487:Protein Conformation; D014500:Uracil Nucleotides / Q000737:chemistry / Q000378:metabolism
chemical_list: D009097:Multienzyme Complexes; D014500:Uracil Nucleotides; C027157:uridine 5'-monophosphate synthase; D009962:Orotate Phosphoribosyltransferase; D009964:Orotidine-5'-Phosphate Decarboxylase