3B9X

Crystal structure of the E. coli pyrimidine nucleoside hydrolase YeiK in complex with inosine

3B9X の概要

• エントリーDOI: 10.2210/pdb3b9x/pdb
• 関連するPDBエントリー: 1Q8F 2MAS
• 分子名称: Pyrimidine-specific ribonucleoside hydrolase rihB, CALCIUM ION, INOSINE, ... (5 entities in total)
• 機能のキーワード: open (alpha, beta) structure, nh-fold, enzyme-substrate complex, protein-nucleoside complex, glycosidase, hydrolase, metal-binding
• 由来する生物種: Escherichia coli
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 145129.24

構造登録者

Iovane, E.,Degano, M. (登録日: 2007-11-07, 公開日: 2008-04-01, 最終更新日: 2023-11-01)

主引用文献

Iovane, E.,Giabbai, B.,Muzzolini, L.,Matafora, V.,Fornili, A.,Minici, C.,Giannese, F.,Degano, M.
Structural basis for substrate specificity in group I nucleoside hydrolases
Biochemistry, 47:4418-4426, 2008

PubMed Abstract: Enzymes with nucleoside hydrolase activity (NHs) belonging to homology group I either are markedly specific for pyrimidine nucleoside substrates or hydrolyze with comparable efficiencies the N-glycosidic bond in all common nucleosides. The biochemical and structural basis for these differences in substrate specificity is still unknown. Here we characterize the binding interactions between the slowly hydrolyzed substrate inosine and the Escherichia coli pyrimidine-specific NH YeiK using cryotrapping and X-ray crystallography. Guided by the structural features of the Michaelis complex, we show the synergic effect of two specific point mutations in YeiK that increase the catalytic efficiency toward purine nucleosides to values comparable to those of natural nonspecific NHs. We demonstrate that the integrity of an active-site catalytic triad comprised of two hydroxylated amino acids and one histidine residue is a requirement for the highly efficient hydrolysis of inosine by group I NHs. Instead, cleavage of the YeiK-preferred substrate uridine is not affected by mutations at the same locations, suggesting a different fine chemical mechanism for the hydrolysis of the two nucleoside substrates. Our study provides for the first time direct evidence that distinct subsets of amino acid residues are involved in the hydrolysis of purine or pyrimidine nucleosides in group I NHs.

PubMed: 18361502
DOI: 10.1021/bi702448s

実験手法

X-RAY DIFFRACTION (2.3 Å)