1R2S

CRYSTAL STRUCTURE OF RABBIT MUSCLE TRIOSEPHOSPHATE ISOMERASE

1R2S の概要

• エントリーDOI: 10.2210/pdb1r2s/pdb
• 関連するPDBエントリー: 1R2R 1R2T
• 分子名称: Triosephosphate isomerase (2 entities in total)
• 機能のキーワード: tim; closed loop conformation in the ligand-free state; conformational heterogeneity; tim-barrel, isomerase
• 由来する生物種: Oryctolagus cuniculus (rabbit)
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 106633.59

構造登録者

Aparicio, R.,Ferreira, S.T.,Polikarpov, I. (登録日: 2003-09-29, 公開日: 2003-12-23, 最終更新日: 2023-08-23)

主引用文献

Aparicio, R.,Ferreira, S.T.,Polikarpov, I.
Closed conformation of the active site loop of rabbit muscle triosephosphate isomerase in the absence of substrate: evidence of conformational heterogeneity.
J.Mol.Biol., 334:1023-1041, 2003

PubMed Abstract: The active site loop of triosephosphate isomerase (TIM) exhibits a hinged-lid motion, alternating between the two well defined "open" and "closed" conformations. Until now the closed conformation had only been observed in protein complexes with substrate analogues. Here, we present the first rabbit muscle apo TIM structure, refined to 1.5A resolution, in which the active site loop is either in the open or in the closed conformation in different subunits of the enzyme. In the closed conformation described here, the lid loop residues participate in stabilizing hydrogen bonds characteristic of holo TIM structures, whereas chemical interactions observed in the open loop conformation are similar to those found in the apo structures of TIM. In the closed conformation, a number of water molecules are observed at the projected ligand atom positions that are hydrogen bonded to the active site residues. Additives used during crystallization (DMSO and Tris molecules and magnesium atoms) were modeled in the electron density maps. However, no specific binding of these molecules is observed at, or close to, the active site and the lid loop. To further investigate this unusual closed conformation of the apo enzyme, two more rabbit muscle TIM structures, one in the same and another in a different crystal form, were determined. These structures present the open lid conformation only, indicating that the closed conformation cannot be explained by crystal contact effects. To rationalize why the active site loop is closed in the absence of ligand in one of the subunits, extensive comparison with previously solved TIM structures was carried out, supported by the bulk of available experimental information about enzyme kinetics and reaction mechanism of TIM. The observation of both open and closed lid conformations in TIM crystals might be related to a persistent conformational heterogeneity of this protein in solution.

PubMed: 14643664
DOI: 10.1016/j.jmb.2003.10.022

実験手法

X-RAY DIFFRACTION (2.85 Å)