1DVJ

CRYSTAL STRUCTURE OF OROTIDINE MONOPHOSPHATE DECARBOXYLASE COMPLEXED WITH 6-AZAUMP

Summary for 1DVJ

• Entry DOI: 10.2210/pdb1dvj/pdb
• Related: 1DV7
• Descriptor: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE, 6-AZA URIDINE 5'-MONOPHOSPHATE (3 entities in total)
• Functional Keywords: tim barrel, dimer, lyase
• Biological source: Methanothermobacter thermautotrophicus
• Total number of polymer chains: 4
• Total formula weight: 107959.27

Authors

Wu, N.,Mo, Y.,Gao, J.,Pai, E.F. (deposition date: 2000-03-30, release date: 2000-04-05, Last modification date: 2024-02-07)

Primary citation

Wu, N.,Mo, Y.,Gao, J.,Pai, E.F.
Electrostatic stress in catalysis: structure and mechanism of the enzyme orotidine monophosphate decarboxylase.
Proc.Natl.Acad.Sci.USA, 97:2017-2022, 2000

PubMed Abstract: Orotidine 5'-monophosphate decarboxylase catalyzes the conversion of orotidine 5'-monophosphate to uridine 5'-monophosphate, the last step in biosynthesis of pyrimidine nucleotides. As part of a Structural Genomics Initiative, the crystal structures of the ligand-free and the6-azauridine 5'-monophosphate-complexed forms have been determined at 1.8 and 1.5 A, respectively. The protein assumes a TIM-barrel fold with one side of the barrel closed off and the other side binding the inhibitor. A unique array of alternating charges (Lys-Asp-Lys-Asp) in the active site prompted us to apply quantum mechanical and molecular dynamics calculations to analyze the relative contributions of ground state destabilization and transition state stabilization to catalysis. The remarkable catalytic power of orotidine 5'-monophosphate decarboxylase is almost exclusively achieved via destabilization of the reactive part of the substrate, which is compensated for by strong binding of the phosphate and ribose groups. The computational results are consistent with a catalytic mechanism that is characterized by Jencks's Circe effect.

PubMed: 10681441
DOI: 10.1073/pnas.050417797

Experimental method

X-RAY DIFFRACTION (1.5 Å)