2GD1

COENZYME-INDUCED CONFORMATIONAL CHANGES IN GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM BACILLUS STEAROTHERMOPHILLUS

2GD1 の概要

• エントリーDOI: 10.2210/pdb2gd1/pdb
• 分子名称: APO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE, SULFATE ION (3 entities in total)
• 機能のキーワード: oxidoreductase(aldehyde(d)-nad(a))
• 由来する生物種: Geobacillus stearothermophilus
• 細胞内の位置: Cytoplasm: P00362
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 144732.69

構造登録者

Skarzynski, T.,Wonacott, A.J. (登録日: 1989-06-29, 公開日: 1989-10-15, 最終更新日: 2024-02-14)

主引用文献

Skarzynski, T.,Wonacott, A.J.
Coenzyme-induced conformational changes in glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus.
J.Mol.Biol., 203:1097-1118, 1988

PubMed Abstract: The structure of apo-glyceraldehyde-3-phosphate dehydrogenase (GAPDHase) from Bacillus stearothermophilus has been refined using a restrained least-squares method. The final crystallographic R-factor is 0.177 for all 53,315 reflections between 7.0 and 2.5 A. The resulting model has been analysed with respect to lattice interactions, molecular symmetry, temperature factors and solvent structure showing that, apart from local deviations due to intermolecular contact, the molecule exhibits a very high degree of local 222 symmetry. Analysis of differences between the structure of apo-GAPDHase and the previously refined holo-GAPDHase at 1.8 A resolution reveals details of conformational change in the enzyme induced by cofactor binding. The change, which was previously described as a rigid-body rotation of the coenzyme-binding domain with respect to the catalytic domain, is of more complex nature and involves relative shifts of several structural elements in the coenzyme-binding domain and some small changes in the catalytic domain. A possible mechanism of this conformational change is proposed based on the comparison of the refined structures and model-building studies. According to this mechanism, the adenosine moiety of NAD can initially bind to the protein in the apo-enzyme conformation. Several attractive interactions resulting from the initial binding of the coenzyme trigger conformational changes in the molecule of GAPDHase that: (1) create the productive nicotinamide-moiety binding site; (2) improve enzyme-coenzyme interactions at the adenosine moiety; (3) modify the active site to optimize the positioning of catalytic residues and ion-binding sites. Implications of the proposed mechanism for existing experimental data on binding of NAD analogues to GAPDHase are discussed.

PubMed: 3210237
DOI: 10.1016/0022-2836(88)90130-1

実験手法

X-RAY DIFFRACTION (2.5 Å)