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Elucidation of the mode of substrate binding to hydroxynitrile lyase from Hevea brasiliensis
Author(s) -
Gruber Karl
Publication year - 2001
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.1068
Subject(s) - chemistry , hevea brasiliensis , substrate (aquarium) , docking (animal) , enzyme catalysis , enzyme , stereochemistry , catalysis , selectivity , molecular model , active site , computational chemistry , lyase , combinatorial chemistry , organic chemistry , natural rubber , oceanography , nursing , geology , medicine
The hydroxynitrile lyase from Hevea brasiliensis ( Hb ‐HNL) is used as a catalyst in enantiospecific syntheses of α‐hydroxynitriles from aldehydes and methyl‐ketones. The catalyzed reaction represents one of the few industrially relevant examples of enzyme mediated CC coupling reactions. In this work, we modeled Hb ‐HNL substrate complexes that have as yet proven inaccessible to experimental structure determination and were able to identify two binding modes for the natural substrate acetone cyanohydrin in docking simulations. Discrimination of the two alternatives was achieved by modeling complexes with two different chiral cyanohydrins followed by an analysis of the respective relative binding energies from molecular mechanics and thermodynamic integration. Only for one of the alternative binding modes the experimentally established S ‐selectivity of the enzyme was correctly predicted. Our results yielded further support for an enzymatic mechanism involving the catalytic triad Ser80, His235, and Asp207 as a general acid/base. A pivotal role was ascribed to Lys236, which seems to be crucial for enzymatic activity at low pH values. In addition, the modeling calculations provided possible explanations for the observed substrate and enantioselectivity of the enzyme that rationalize available mutational data and will be the basis for future protein engineering efforts. Proteins 2001;44:26–31. © 2001 Wiley‐Liss, Inc.