3dqz

Structure of the hydroxynitrile lyase from Arabidopsis thaliana

spinqualitylabelsall models 3dqz, resolution 2.50Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3dqz is a 4 chain structure with sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: CL Gene: F18D22_70, At5g10300 (Arabidopsis thaliana) Resources: FirstGlance, OCA, RCSB, PDBsum Function [HNL_ARATH] Involved in cyanogenesis, the release of HCN from injured tissues (By similarity). Displays R-selective hydroxynitrile lyase activity. Also accepts nitromethane (MeNO2) as a donor in a reaction with aromatic aldehydes to yield (R)-beta-nitro alcohols. Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMed Hydroxynitrile lyases (HNLs) catalyze the cleavage of cyanohydrins to yield hydrocyanic acid (HCN) and the respective carbonyl compound and are key enzymes in the process of cyanogenesis in plants. In organic syntheses, HNLs are used as biocatalysts for the formation of enantiopure cyanohydrins. We determined the structure of the recently identified, R-selective HNL from Arabidopsis thaliana (AtHNL) at a crystallographic resolution of 2.5 A. The structure exhibits an alpha/beta-hydrolase fold, very similar to the homologous, but S-selective, HNL from Hevea brasiliensis (HbHNL). The similarities also extend to the active sites of these enzymes, with a Ser-His-Asp catalytic triad present in all three cases. In order to elucidate the mode of substrate binding and to understand the unexpected opposite enantioselectivity of AtHNL, complexes of the enzyme with both (R)- and (S)-mandelonitrile were modeled using molecular docking simulations. Compared to the complex of HbHNL with (S)-mandelonitrile, the calculations produced an approximate mirror image binding mode of the substrate with the phenyl rings located at very similar positions, but with the cyano groups pointing in opposite directions. A catalytic mechanism for AtHNL is proposed, in which His236 from the catalytic triad acts as a general base and the emerging negative charge on the cyano group is stabilized by main-chain amide groups and an alpha-helix dipole very similar to alpha/beta-hydrolases. This mechanistic proposal is additionally supported by mutagenesis studies. Hydroxynitrile lyases with alpha/beta-hydrolase fold: two enzymes with almost identical 3D structures but opposite enantioselectivities and different reaction mechanisms.,Andexer JN, Staunig N, Eggert T, Kratky C, Pohl M, Gruber K Chembiochem. 2012 Sep 3;13(13):1932-9. doi: 10.1002/cbic.201200239. Epub 2012 Jul, 31. PMID:22851196 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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