Structures of the human orotidine-5'-monophosphate decarboxylase support a covalent mechanism and provide a framework for drug design.
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.
Wittmann
Julia G
JG
Department of Molecular Structural Biology, University of Göttingen, Göttingen, Germany.
Heinrich
Daniel
D
Gasow
Kathrin
K
Frey
Alexandra
A
Diederichsen
Ulf
U
Rudolph
Markus G
MG
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
D009097:Multienzyme Complexes; D014500:Uracil Nucleotides; C027157:uridine 5'-monophosphate synthase; D009962:Orotate Phosphoribosyltransferase; D009964:Orotidine-5'-Phosphate Decarboxylase