7VB5

Crystal structure of hydroxynitrile lyase from Linum usitatissimum complexed with acetone cyanohydrin

7VB5 の概要

• エントリーDOI: 10.2210/pdb7vb5/pdb
• 分子名称: Aliphatic (R)-hydroxynitrile lyase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, ZINC ION, ... (10 entities in total)
• 機能のキーワード: hydroxynitrile lyase, nad, zn, cnh, lyase
• 由来する生物種: Linum usitatissimum (flax)
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 198873.22

構造登録者

Zheng, D.,Nakabayashi, M.,Asano, Y. (登録日: 2021-08-30, 公開日: 2022-02-09, 最終更新日: 2024-10-30)

主引用文献

Zheng, D.,Nakabayashi, M.,Asano, Y.
Structural characterization of Linum usitatissimum hydroxynitrile lyase: A new cyanohydrin decomposition mechanism involving a cyano-zinc complex.
J.Biol.Chem., 298:101650-101650, 2022

PubMed Abstract: Hydroxynitrile lyase from Linum usitatissimum (LuHNL) is an enzyme involved in the catabolism of cyanogenic glycosides to release hydrogen cyanide upon tissue damage. This enzyme strictly conserves the substrate- and NAD(H)-binding domains of Zn-containing alcohol dehydrogenase (ADH); however, there is no evidence suggesting that LuHNL possesses ADH activity. Herein, we determined the ligand-free 3D structure of LuHNL and its complex with acetone cyanohydrin and (R)-2-butanone cyanohydrin using X-ray crystallography. These structures reveal that an A-form NAD is tightly but not covalently bound to each subunit of LuHNL. The restricted movement of the NAD+ molecule is due to the "sandwich structure" on the adenine moiety of NAD. Moreover, the structures and mutagenesis analysis reveal a novel reaction mechanism for cyanohydrin decomposition involving the cyano-zinc complex and hydrogen-bonded interaction of the hydroxyl group of cyanohydrin with Glu323/Thr65 and HO/Lys162 of LuHNL. The deprotonated Lys162 and protonated Glu323 residues are presumably stabilized by a partially desolvated microenvironment. In summary, the substrate binding geometry of LuHNL provides insights into the differences in activities of LuHNL and ADH, and identifying this novel reaction mechanism is an important contribution to the study of hydroxynitrile lyases.

PubMed: 35101448
DOI: 10.1016/j.jbc.2022.101650

実験手法

X-RAY DIFFRACTION (1.58 Å)