Structural diversity and plasticity associated with nucleotides targeting orotidine monophosphate decarboxylase.
Orotidine monophosphate decarboxylase (ODCase) generally accepts pyrimidine-based mononucleotides as ligands, but other nucleotides are also known to bind to this enzyme. We investigated the kinetic properties of eight common and endogenous nucleotides with ODCases from three species: Methanobacterium thermoautotrophicum, Plasmodium falciparum, and Homo sapiens. UMP and XMP exhibited higher affinities as compared to the other nucleotides tested. The product of ODCase catalyzed decarboxylation, UMP, displayed inhibition constants (K(i)) of 330 microM against the Mt enzyme and of 210 and 220 microM against the Pf and Hs ODCases, respectively. The K(i) values for XMP were 130 microM and 43 microM, respectively, for Mt and Pf ODCases. Interestingly, XMP's affinity for human ODCase (K(i) = 0.71 microM) is comparable and even slightly better than that of the substrate OMP. Binding of various nucleotides and their structural features in the context of ODCase inhibition and inhibitor design are discussed.
Poduch
Ewa
E
Center for Molecular Design and Preformulations, Toronto General Research Institute, Toronto General Hospital, Toronto, ON, Canada.
Wei
Lianhu
L
Pai
Emil F
EF
Kotra
Lakshmi P
LP
D000818:Animals; D018360:Crystallography, X-Ray; D006801:Humans; D007700:Kinetics; D008024:Ligands; D017014:Methanobacterium / Q000201:enzymology; D008958:Models, Molecular; D009964:Orotidine-5'-Phosphate Decarboxylase / Q000737:chemistry*; D010963:Plasmodium falciparum / Q000201:enzymology; D011485:Protein Binding; D011487:Protein Conformation; D011685:Purine Nucleotides / Q000737:chemistry*; D011742:Pyrimidine Nucleotides / Q000737:chemistry*; D013045:Species Specificity
D008024:Ligands; D011685:Purine Nucleotides; D011742:Pyrimidine Nucleotides; D009964:Orotidine-5'-Phosphate Decarboxylase