October 26, 2007

Chemical Biology of Proteases: Induced Structure and Substrate Modulation in a Viral Protease

Dr. Charles Craik
Departments of Pharmaceutical Chemistry,
Cellular & Molecular Pharmacology,
and Biochemistry & Biophysics
UC San Francisco

The herpesvirus proteases are an example inwhich allosteric regulation of an enzyme activity is achieved through the formation
of quaternary structure.Here, we report a 1.7 Å resolution structure of Kaposi's sarcoma-associated herpesvirus protease in complex
with a hexapeptide transition state analogue that stabilizes the dimeric state of the enzyme. Extended substrate binding sites are induced
upon peptide binding. In particular, 104 Å2 of surface are buried in the newly formed S4 pocket when tyrosine binds at this site.
The peptide inhibitor also induces a rearrangement of residues that stabilizes the oxyanion hole and the dimer interface. Concomitant
with the structural changes, an increase in catalytic efficiency of the enzyme results upon extended substrate binding.A nearly 20-fold
increase in kcat/KM results upon extending the peptide substrate from a tetrapeptide to a hexapeptide exclusively due to a KM effect.
This suggests that the mechanism by which herpesvirus proteases achieve their high specificity is by using extended substrates to
modulate both the structure and activity of the enzyme.

© 2007 Elsevier Ltd. All rights res