7vb6 | pdb_00007vb6

Crystal structure of hydroxynitrile lyase from Linum usitatissium complexed with (R)-2-hydroxy-2-methylbutanenitrile

spinqualitylabelsall models 7vb6, resolution 1.74Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 7vb6 is a 4 chain structure with sequence from Linum usitatissimum. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.74Å Ligands: 5Z9, BTB, EDO, GOL, MG, NAD, SNC, ZN Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function AHNL_LINUS Involved in the catabolism of cyanogenic glycosides. Naturally occurring substrates are the aliphatic acetone cyanohydrin and butan-2-one cyanohydrin, which are the aglycones of the cyanogenic glycosides linamarin, lotaustralin, linustatin and neolinustatin. Can use various aliphatic ketones and aldehydes as substrates, but not aromatic ketones.[REFERENCE:5] Publication Abstract from PubMed 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 Zn2+-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 H2O/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. Structural characterization of Linum usitatissimum hydroxynitrile lyase: a new cyanohydrin decomposition mechanism involving a cyano-zinc complex.,Zheng D, Nakabayashi M, Asano Y J Biol Chem. 2022 Jan 28:101650. doi: 10.1016/j.jbc.2022.101650. PMID:35101448 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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