7VB5

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

Summary for 7VB5

• Entry DOI: 10.2210/pdb7vb5/pdb
• Descriptor: Aliphatic (R)-hydroxynitrile lyase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, ZINC ION, ... (10 entities in total)
• Functional Keywords: hydroxynitrile lyase, nad, zn, cnh, lyase
• Biological source: Linum usitatissimum (flax)
• Total number of polymer chains: 4
• Total formula weight: 198873.22

Authors

Zheng, D.,Nakabayashi, M.,Asano, Y. (deposition date: 2021-08-30, release date: 2022-02-09, Last modification date: 2024-10-30)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.58 Å)