Comparison of bovine alpha
chymotrypsin and subtilisin from B. Subtilis 

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I. Introduction

Bovine chymotrypsin and bacterial subtilisin are both endoproteases that have little amino acid sequence identity. The 3D structures of these proteins are so different that their backbones can not be superimposed. Each, however, have a catalytic triad (His 57, Asp 102, and Ser 195 for chymotrypsin, adn HIs 64, Asp 32, and Ser 221 for subtilisin). Notice that their order in the two different chains are not comparable, suggesting that they did not evolve from a common gene. Rather through a process of convergent evolution, two different genes evolved to produce two different proteins with the relative position of the three amino acids in the catalytic triad in almost identical positions. The stuctures below show the two proteins aligned at their respective catalytic triad.

For more information see Biochemistry Online: Chapter 7B - Mechanisms of Enzyme Catalysis

II. General Structure

The green backbone is chymotrypsin and the red is subtilisin. Note that the overall protein structures show no homology.
Active Sites: Catalytic Triad

Identify the active site His, Asp and Ser by clicking on the appropriate side chains. Again, the green amino acids are from chymotrypsin and the red are from subtilisin. Notice the close alignment of the catalytic triad even though the overall structures do not align.