3W07

Atomic resolution structure of orotidine 5'-monophosphate decarboxylase from Methanothermobacter thermoautotrophicus bound with UMP.

3W07 の概要

• エントリーDOI: 10.2210/pdb3w07/pdb
• 関連するPDBエントリー: 1LOQ 3G1D
• 分子名称: Orotidine 5'-phosphate decarboxylase, URIDINE-5'-MONOPHOSPHATE, GLYCEROL, ... (4 entities in total)
• 機能のキーワード: orotidine 5'-monophosphate decarboxylase, 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: 27795.68

構造登録者

Fujihashi, M.,Pai, E.F.,Miki, K. (登録日: 2012-10-22, 公開日: 2013-02-20, 最終更新日: 2024-03-20)

主引用文献

Fujihashi, M.,Mito, K.,Pai, E.F.,Miki, K.
Atomic resolution structure of the orotidine 5'-monophosphate decarboxylase product complex combined with surface plasmon resonance analysis: implications for the catalytic mechanism.
J.Biol.Chem., 288:9011-9016, 2013

PubMed Abstract: Orotidine 5'-monophosphate decarboxylase (ODCase) accelerates the decarboxylation of its substrate by 17 orders of magnitude. One argument brought forward against steric/electrostatic repulsion causing substrate distortion at the carboxylate substituent as part of the catalysis has been the weak binding affinity of the decarboxylated product (UMP). The crystal structure of the UMP complex of ODCase at atomic resolution (1.03 Å) shows steric competition between the product UMP and the side chain of a catalytic lysine residue. Surface plasmon resonance analysis indicates that UMP binds 5 orders of magnitude more tightly to a mutant in which the interfering side chain has been removed than to wild-type ODCase. These results explain the low affinity of UMP and counter a seemingly very strong argument against a contribution of substrate distortion to the catalytic reaction mechanism of ODCase.

PubMed: 23395822
DOI: 10.1074/jbc.M112.427252

実験手法

X-RAY DIFFRACTION (1.03 Å)