1DV7

CRYSTAL STRUCTURE OF OROTIDINE MONOPHOSPHATE DECARBOXYLASE

1DV7 の概要

• エントリーDOI: 10.2210/pdb1dv7/pdb
• 関連するPDBエントリー: 1DVJ
• 分子名称: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE (2 entities in total)
• 機能のキーワード: tim barrel, dimer, lyase
• 由来する生物種: Methanothermobacter thermautotrophicus
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 24753.50

構造登録者

Wu, N.,Mo, Y.,Gao, J.,Pai, E.F. (登録日: 2000-01-20, 公開日: 2000-04-05, 最終更新日: 2024-02-07)

主引用文献

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

実験手法

X-RAY DIFFRACTION (1.8 Å)