3EX2

human orotidyl-5'-monophosphate decarboxylase in complex with 6-cyano-UMP

Summary for 3EX2

• Entry DOI: 10.2210/pdb3ex2/pdb
• Related: 3EWU 3EWW 3EWX 3EWY 3EWZ 3EX0 3EX1 3EX3 3EX4 3EX5 3EX6
• Descriptor: Orotidine-5'-phosphate decarboxylase, 6-cyanouridine 5'-phosphate, GLYCEROL, ... (4 entities in total)
• Functional Keywords: decarboxylase, tim barrel, unusual catalysis, disease mutation, glycosyltransferase, lyase, multifunctional enzyme, pyrimidine biosynthesis, transferase
• Biological source: Homo sapiens
• Total number of polymer chains: 2
• Total formula weight: 57389.96

Authors

Heinrich, D.,Diederichsen, U.,Rudolph, M. (deposition date: 2008-10-16, release date: 2009-04-07, Last modification date: 2023-12-27)

Primary citation

Heinrich, D.,Diederichsen, U.,Rudolph, M.G.
Lys314 is a nucleophile in non-classical reactions of orotidine-5'-monophosphate decarboxylase
Chemistry, 15:6619-6625, 2009

PubMed Abstract: Orotidine-5'-monophosphate decarboxylase (OMPD) catalyzes the decarboxylation of orotidine-5'-monophosphate (OMP) to uridine-5'-monophosphate (UMP) in an extremely proficient manner. The reaction does not require any cofactors and proceeds by an unknown mechanism. In addition to decarboxylation, OMPD is able to catalyze other reactions. We show that several C6-substituted UMP derivatives undergo hydrolysis or substitution reactions that depend on a lysine residue (Lys314) in the OMPD active site. 6-Cyano-UMP is converted to UMP, and UMP derivatives with good leaving groups inhibit OMPD by a suicide mechanism in which Lys314 covalently binds to the substrate. These non-classical reactivities of human OMPD were characterized by cocrystallization and freeze-trapping experiments with wild-type OMPD and two active-site mutants by using substrate and inhibitor nucleotides. The structures show that the C6-substituents are not coplanar with the pyrimidine ring. The extent of this substrate distortion is a function of the substituent geometry. Structure-based mechanisms for the reaction of 6-substituted UMP derivatives are extracted in accordance with results from mutagenesis, mass spectrometry, and OMPD enzyme activity. The Lys314-based mechanisms explain the chemodiversity of OMPD, and offer a strategy to design mechanism-based inhibitors that could be used for antineoplastic purposes for example.

PubMed: 19472232
DOI: 10.1002/chem.200900397

Experimental method

X-RAY DIFFRACTION (1.55 Å)