1DSS

STRUCTURE OF ACTIVE-SITE CARBOXYMETHYLATED D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM PALINURUS VERSICOLOR

1DSS の概要

• エントリーDOI: 10.2210/pdb1dss/pdb
• 分子名称: D-GLYCERALDEHYDE-3-PHOSPHATE-DEHYDROGENASE, SULFATE ION, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, ... (4 entities in total)
• 機能のキーワード: active-site carboxymethylation, d-glyceraldehyde-3-phosphate-dehydrogenase, 'the-half-of-sites' reaction, molecular symmetry
• 由来する生物種: Palinurus versicolor (South China Sea lobster)
• 細胞内の位置: Cytoplasm: P56649
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 73361.18

構造登録者

Song, S.,Lin, Z. (登録日: 1997-06-04, 公開日: 1998-12-09, 最終更新日: 2024-04-03)

主引用文献

Song, S.Y.,Xu, Y.B.,Lin, Z.J.,Tsou, C.L.
Structure of active site carboxymethylated D-glyceraldehyde-3-phosphate dehydrogenase from Palinurus versicolor.
J.Mol.Biol., 287:719-725, 1999

PubMed Abstract: The structure of active site carboxymethylated D-glyceraldehyde-3-phosphate dehydrogenase from Palinurus versicolor was determined in the presence of coenzyme NAD+ at 1.88 A resolution with a final R-factor of 0.175. The structure refinement was carried out on the basis of the structure of holo-GAPDH at 2.0 A resolution using the program XPLOR. The carboxymethyl group connected to Cys149 is stabilized by a hydrogen bond between its OZ1 and Cys149N, and charge interaction between the carboxyl group and the nicotinamide moiety. The modification of Cys149 induced conformational changes in the active site, in particular, the site of sulphate ion 501 (the proposed attacking inorganic phosphate ion in catalysis), and segment 208-218 nearby. Extensive hydrogen-bonding interactions occur in the active site, which contribute to the higher stability of the modified enzyme. The modification of the active site did not affect the conformation of GAPDH elsewhere, including the subunit interfaces. The structures of the green and red subunits in the asymmetric unit are nearly identical, suggesting that the half-site reactivity of this enzyme is from ligand-induced rather than pre-existing asymmetry. It is proposed that the carboxymethyl group takes the place of the acyl group of the reaction intermediate, and the catalytic mechanism of this enzyme is discussed in the light of a comparison of the structures of the native and the carboxymethylated GAPDH.

PubMed: 10191140
DOI: 10.1006/jmbi.1999.2628

実験手法

X-RAY DIFFRACTION (1.88 Å)