Structures of the Human Orotidine-5′-Monophosphate Decarboxylase Support a Covalent Mechanism and Provide a Framework for Drug Design

Structure - Tập 16 - Trang 82-92 - 2008
Julia G. Wittmann1, Daniel Heinrich2, Kathrin Gasow1, Alexandra Frey2, Ulf Diederichsen2, Markus G. Rudolph1
1Department of Molecular Structural Biology, University of Göttingen, D-37077 Göttingen, Germany
2Department of Organic and Biomolecular Chemistry, University of Göttingen, D-37077 Göttingen, Germany

Tài liệu tham khảo

Acheson, 1990, Orotidine-5′-monophosphate decarboxylase catalysis: kinetic isotope effects and the state of hybridization of a bound transition-state analogue, Biochemistry, 29, 3198, 10.1021/bi00465a007 Amyes, 2005, Activation of orotidine 5′-monophosphate decarboxylase by phosphite dianion: the whole substrate is the sum of two parts, J. Am. Chem. Soc., 127, 15708, 10.1021/ja055493s Appleby, 2000, The crystal structure and mechanism of orotidine 5′-monophosphate decarboxylase, Proc. Natl. Acad. Sci. USA, 97, 2005, 10.1073/pnas.259441296 Beak, 1976, Mechanism of decarboxylation of 1,3-dimethylorotic acid. A model for orotidine 5′-phosphate decarboxylase, J. Am. Chem. Soc., 98, 3601, 10.1021/ja00428a035 Bello, 2007, A potent, covalent inhibitor of orotidine 5′-monophosphate decarboxylase with antimalarial activity, J. Med. Chem., 50, 915, 10.1021/jm060827p Brünger, 1992, Free R value: a novel statistical quantity for assessing the accuracy of crystal structures, Nature, 355, 472, 10.1038/355472a0 Brünger, 1998, Crystallography & NMR system: a new software suite for macromolecular structure determination, Acta Crystallogr. D Biol. Crystallogr., 54, 905, 10.1107/S0907444998003254 Callahan, 2007, OMP decarboxylase—an enigma persists, Bioorg. Chem., 35, 465, 10.1016/j.bioorg.2007.07.004 Callahan, 2006, A Raman-active competitive inhibitor of OMP decarboxylase, Bioorg. Chem., 34, 59, 10.1016/j.bioorg.2005.12.001 Carreras, 1995, The catalytic mechanism and structure of thymidylate synthase, Annu. Rev. Biochem., 64, 721, 10.1146/annurev.bi.64.070195.003445 1994, The CCP4 suite: programs for protein crystallography, Acta Crystallogr. D Biol. Crystallogr., 50, 760, 10.1107/S0907444994003112 Christopherson, 2002, Inhibitors of de novo nucleotide biosynthesis as drugs, Acc. Chem. Res., 35, 961, 10.1021/ar0000509 Chu, 2003, Thymidylate synthase inhibitors as anticancer agents: from bench to bedside, Cancer Chemother. Pharmacol., 52, S80, 10.1007/s00280-003-0625-9 Cohen, 2006, Imaging the migration pathways for O2, CO, NO, and Xe inside myoglobin, Biophys. J., 91, 1844, 10.1529/biophysj.106.085746 Duff, 2004, Using xenon as a probe for dioxygen-binding sites in copper amine oxidases, J. Mol. Biol., 344, 599, 10.1016/j.jmb.2004.09.075 Ehrlich, 1999, Evidence for a stepwise mechanism of OMP decarboxylase, J. Am. Chem. Soc., 121, 6966, 10.1021/ja990737s Emsley, 2004, Coot: model-building tools for molecular graphics, Acta Crystallogr. D Biol. Crystallogr., 60, 2126, 10.1107/S0907444904019158 Esnouf, 1997, An extensively modified version of MolScript that includes greatly enhanced coloring capabilities, J. Mol. Graph. Model., 15, 132, 10.1016/S1093-3263(97)00021-1 Fersht, 1999 Fujihashi, 2005, An unprecedented twist to ODCase catalytic activity, J. Am. Chem. Soc., 127, 15048, 10.1021/ja054865u Harris, 2000, Structural basis for the catalytic mechanism of a proficient enzyme: orotidine 5′-monophosphate decarboxylase, Biochemistry, 39, 4217, 10.1021/bi992952r Hiromoto, 2006, Crystal structure of 3-hydroxybenzoate hydroxylase from Comamonas testosteroni has a large tunnel for substrate and oxygen access to the active site, J. Mol. Biol., 364, 878, 10.1016/j.jmb.2006.09.031 Ichikawa, 2006, Prediction of clinical outcome of fluoropyrimidine-based chemotherapy for gastric cancer patients, in terms of the 5-fluorouracil metabolic pathway, Gastric Cancer, 9, 145, 10.1007/s10120-006-0373-8 Lee, 2004 Lee, 1997, A proficient enzyme revisited: the predicted mechanism for orotidine monophosphate decarboxylase, Science, 276, 942, 10.1126/science.276.5314.942 Lee, 2001, An alternative explanation for the catalytic proficiency of orotidine 5′-phosphate decarboxylase, J. Am. Chem. Soc., 123, 12837, 10.1021/ja011096f Levine, 1980, Inhibition of orotidine-5′-phosphate decarboxylase by 1-(5′-phospho-beta-d-ribofuranosyl)barbituric acid, 6-azauridine 5′-phosphate, and uridine 5′-phosphate, Biochemistry, 19, 4993, 10.1021/bi00563a010 Merritt, 1994, Raster3D version 2.0. A program for photorealistic molecular graphics, Acta Crystallogr. D Biol. Crystallogr., 50, 869, 10.1107/S0907444994006396 Miller, 2002, Catalytic proficiency: the unusual case of OMP decarboxylase, Annu. Rev. Biochem., 71, 847, 10.1146/annurev.biochem.71.110601.135446 Miller, 2000, Anatomy of a proficient enzyme: the structure of orotidine 5′-monophosphate decarboxylase in the presence and absence of a potential transition state analog, Proc. Natl. Acad. Sci. USA, 97, 2011, 10.1073/pnas.030409797 Miller, 2001, Dissecting a charged network at the active site of orotidine-5′-phosphate decarboxylase, J. Biol. Chem., 276, 15174, 10.1074/jbc.M011429200 Peters, 1986, Sensitivity of human, murine, and rat cells to 5-fluorouracil and 5′-deoxy-5-fluorouridine in relation to drug-metabolizing enzymes, Cancer Res., 46, 20 Poduch, 2006, Design of inhibitors of orotidine monophosphate decarboxylase using bioisosteric replacement and determination of inhibition kinetics, J. Med. Chem., 49, 4937, 10.1021/jm060202r Porter, 2000, Yeast orotidine-5′-phosphate decarboxylase: steady-state and pre-steady-state analysis of the kinetic mechanism of substrate decarboxylation, Biochemistry, 39, 11788, 10.1021/bi001199v Quemeneur, 2004, Restriction of de novo nucleotide biosynthesis interferes with clonal expansion and differentiation into effector and memory CD8 T cells, J. Immunol., 173, 4945, 10.4049/jimmunol.173.8.4945 Radzicka, 1995, A proficient enzyme, Science, 267, 90, 10.1126/science.7809611 Rishavy, 2000, Determination of the mechanism of orotidine 5′-monophosphate decarboxylase by isotope effects, Biochemistry, 39, 4569, 10.1021/bi000376p Roeser, 2007, Probing the oxygen-binding site of the human formylglycine-generating enzyme using halide ions, Acta Crystallogr. D Biol. Crystallog., 63, 621, 10.1107/S0907444907009961 Sievers, 2005, The effective molarity of the substrate phosphoryl group in the transition state for yeast OMP decarboxylase, Bioorg. Chem., 33, 45, 10.1016/j.bioorg.2004.08.005 Silverman, 1982, Model chemistry for a covalent mechanism of action of orotidine 5′-phosphate decarboxylase, J. Am. Chem. Soc., 104, 6434, 10.1021/ja00387a047 Smiley, 1991, Investigation of the enzymatic mechanism of yeast orotidine-5′-monophosphate decarboxylase using 13C kinetic isotope effects, Biochemistry, 30, 6216, 10.1021/bi00239a020 Sterner, 2005, Catalytic versatility, stability, and evolution of the (betaalpha)8-barrel enzyme fold, Chem. Rev., 105, 4038, 10.1021/cr030191z Suchi, 1997, Molecular cloning of the human UMP synthase gene and characterization of point mutations in two hereditary orotic aciduria families, Am. J. Hum. Genet., 60, 525 Vocadlo, 2001, Catalysis by hen egg-white lysozyme proceeds via a covalent intermediate, Nature, 412, 835, 10.1038/35090602 Wade, 2004, A survey of active site access channels in cytochromes P450, J. Inorg. Biochem., 98, 1175, 10.1016/j.jinorgbio.2004.02.007 Wittmann, 2007, Pseudo-merohedral twinning in monoclinic crystals of human orotidine-5′-monophosphate decarboxylase, Acta Crystallogr. D Biol. Crystallogr., 63, 744, 10.1107/S0907444907016605 Wu, 2000, Electrostatic stress in catalysis: structure and mechanism of the enzyme orotidine monophosphate decarboxylase, Proc. Natl. Acad. Sci. USA, 97, 2017, 10.1073/pnas.050417797 Wu, 2002, Crystal structures of inhibitor complexes reveal an alternate binding mode in orotidine-5′-monophosphate decarboxylase, J. Biol. Chem., 277, 28080, 10.1074/jbc.M202362200 Wu, 2002, Mapping the active site-ligand interactions of orotidine 5′-monophosphate decarboxylase by crystallography, Biochemistry, 41, 4002, 10.1021/bi015758p