Glycosidase Mechanism

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A recent paper "Snapshots along an Enzymatic Reaction Coordinate: Analysis of a Retaining b-Glycoside Hydrolase" by G. J. Davies et al appeared (Biochem. 37:11707-11712, 1998).  This paper provides valuable insights into what happens during an enzymatic reaction.  The authors were able to determine to high resolution the structure of the free enzyme, the enzyme-substrate complex, a covalent enzyme-substrate intermediate, and the enzyme-product complex. The enzyme is Cel5A from Bacillus agaradhaerens.  In the enzyme the nucleophile is Glu 228 and the Acid/Base is Glu 139.  The reaction proceeds according the mechanism shown below.

 

Figure 1.  Enzyme-substrate complex. Note how the pyranose ring (magenta) is distorted.  This is an excellent example of transition state stabilization and results from the binding energy associated with binding the R group.

 

Figure 2. Covalent intermediate.  Note that the pyranose ring has adopted the more stable chair conformation. The water that is involved in hydrolysis of the covalent intermediate is yellow.

 

Figure 3. Enzyme-product complex.  Note that the pyranose ring has adopted the more stable chair conformation. In the crystal the product gives poorer electron density than the two above structures, suggesting that the product is poorly bound.

 

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Biochemistry 462a
http://www.biochem.arizona.edu/classes/bioc462/462a/462a.html
Department of Biochemistry and Molecular Biophysics
The University of Arizona
mawells@email.arizona.edu 
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