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Crystal structures of inhibitor complexes reveal an alternate binding mode in orotidine-5'-monophosphate decarboxylase.

Wu N, Pai EF
J Biol Chem 277 28080-7 (2002)
Related entries: 1loq, 1lor, 1los, 1lp6

Cited: 19 times
EuropePMC logo PMID: 12011084

Abstract

The crystal structures of the enzyme orotidine-5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with its product UMP and the inhibitors 6-hydroxyuridine 5'-phosphate (BMP), XMP, and CMP are reported. A mutant version of the protein, in which four residues of the flexible phosphate-binding loop (180)Gly-Gly(190) were removed and Arg(203) was replaced by alanine, was also analyzed. The XMP and CMP complexes reveal a ligand-binding mode that is distinct from the one identified previously with the aromatic rings located outside the binding pocket. A potential pathway for ligand binding is discussed.

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Reviews citing this publication (3)

  1. Mechanisms and free energies of enzymatic reactions. Gao J, Ma S, Major DT, Nam K, Pu J, Truhlar DG. Chem Rev 106 3188-3209 (2006)
  2. Specificity in transition state binding: the Pauling model revisited. Amyes TL, Richard JP. Biochemistry 52 2021-2035 (2013)
  3. Design of inhibitors of ODCase. Mundra S, Kotra LP. Future Med Chem 6 165-177 (2014)

Articles citing this publication (13)

  1. Structures of the human orotidine-5'-monophosphate decarboxylase support a covalent mechanism and provide a framework for drug design. Wittmann JG, Heinrich D, Gasow K, Frey A, Diederichsen U, Rudolph MG. Structure 16 82-92 (2008)
  2. Catalysis in Enzymatic Decarboxylations: Comparison of Selected Cofactor-dependent and Cofactor-independent Examples. Jordan F, Patel H. ACS Catal 3 1601-1617 (2013)
  3. Interaction of the family-B DNA polymerase from the archaeon Pyrococcus furiosus with deaminated bases. Gill S, O'Neill R, Lewis RJ, Connolly BA. J Mol Biol 372 855-863 (2007)
  4. Substrate distortion contributes to the catalysis of orotidine 5'-monophosphate decarboxylase. Fujihashi M, Ishida T, Kuroda S, Kotra LP, Pai EF, Miki K. J Am Chem Soc 135 17432-17443 (2013)
  5. Structural characterization of the molecular events during a slow substrate-product transition in orotidine 5'-monophosphate decarboxylase. Fujihashi M, Wei L, Kotra LP, Pai EF. J Mol Biol 387 1199-1210 (2009)
  6. Atomic resolution structure of the orotidine 5'-monophosphate decarboxylase product complex combined with surface plasmon resonance analysis: implications for the catalytic mechanism. Fujihashi M, Mito K, Pai EF, Miki K. J Biol Chem 288 9011-9016 (2013)
  7. Indiscriminate binding by orotidine 5'-phosphate decarboxylase of uridine 5'-phosphate derivatives with bulky anionic c6 substituents. Lewis CA, Wolfenden R. Biochemistry 46 13331-13343 (2007)
  8. Accelerated hydrolysis of α-halo and α-cyano pyridinium relative to uracil derivatives: a model for ODCase-catalyzed hydrolysis of 6-cyanoUMP. Huang S, Wong FM, Gassner GT, Wu W. Tetrahedron Lett 52 3960-3962 (2011)
  9. Introduction of a fluorine atom at C3 of 3-deazauridine shifts its antimetabolic activity from inhibition of CTP synthetase to inhibition of orotidylate decarboxylase, an early event in the de novo pyrimidine nucleotide biosynthesis pathway. Balzarini J, Gago F, Kulik W, van Kuilenburg AB, Karlsson A, Peterson MA, Robins MJ. J Biol Chem 287 30444-30454 (2012)
  10. Polarization in the structures of uracil and thiouracils: Implication for binding with orotidine 5'-monophosphate decarboxylase. Huang S, Gronert S, Wu W. Bioorg Med Chem Lett 21 6341-6342 (2011)
  11. Hydrolysis of α-chloro-substituted 2- and 4-pyridones: rate enhancement by zwitterionic structure. Tan RC, Vien JQ, Wu W. Bioorg Med Chem Lett 22 1224-1225 (2012)
  12. Stabilities of Uracil and Pyridone-Based Carbanions: A Systematic Study in the Gas Phase and Solution and Implications for the Mechanism of Orotidine-5'-Monophosphate Decarboxylase. Senger NA, Bliss CE, Keeffe JR, Gronert S, Wu W. Tetrahedron 69 5287-5292 (2013)
  13. 3-D clustering: a tool for high throughput docking. Priestle JP. J Mol Model 15 551-560 (2009)


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