Crystal Structure of Hydroxynitrile Lyase from Sorghum bicolor in Complex with the Inhibitor Benzoic Acid: A Novel Cyanogenic Enzyme,

Citations Over TimeTop 17% of 2002 papers

Abstract

The crystal structure of the hydroxynitrile lyase from Sorghum bicolor (SbHNL) in complex with the inhibitor benzoic acid has been determined at 2.3 A resolution and refined to a crystallographic R-factor of 16.5%. The SbHNL sequence places the enzyme in the alpha/beta hydrolase family where the active site nucleophile is predicted to be organized in a characteristic pentapeptide motif which is part of the active site strand-turn-helix motif. In SbHNL, however, a unique two-amino acid deletion is next to the putative active site Ser158, removing thereby the putative oxyanion hole-forming Tyr residue. The presented X-ray structure shows that the overall folding pattern of SbHNL is similar to that of the closely related wheat serine carboxypeptidase (CPD-WII); however, the deletion in SbHNL is forcing the putative active site residues away from the expected hydrolase binding site toward a small hydrophobic cleft, which also contains the inhibitor benzoic acid, defining thereby a completely different SbHNL active site architecture where the traditional view of a classic triad is not given any more. Rather, we propose a mechanism involving general base catalysis by the carboxy-terminal Trp270 carboxyl group and proton transfer toward the leaving nitrile group by an active site water molecule. The unexpected interactions of the inhibitor with the new SbHNL active site also reveal the structural basis for the enzyme's limited substrate specificity. The implications of this structure on the evolution of catalysis in the hydroxynitrile lyase superfamily are discussed.

Related Papers

• → The crystal structure of a triacylglycerol lipase from Pseudomonas cepacia reveals a highly open conformation in the absence of a bound inhibitor(1997)331 cited
• → The crystal structure of Bacillus subtili lipase: a minimal α/β hydrolase fold enzyme(2001)270 cited
• → Crystal structure of the catalytic domain of human bile salt activated lipase(2000)59 cited
• → Structure of XC6422 fromXanthomonas campestrisat 1.6 Å resolution: a small serine α/β-hydrolase(2006)3 cited
• A. 脂肪酶的C端之結構對於較長鏈受質的結合之重要性B. 雙磷酸鹽藥物對於四異戊二烯焦磷酸合成酶的抑制效果在結構上的分析(2010)