1. Catalytic Mechanism of Chymotrypsin slide 1 Chymotrypsin –Protease: catalyze hydrolysis of proteins in small intestine –Specificity: Peptide bond on carboxyl side of aromatic side chains (Y, W, F) & Large hydrophobic residues (Met,…) –Three polypeptide chains cross-linked to each other –Three catalytic residues: Ser195, His57, & Asp102

2. Catalytic Mechanism of Chymotrypsin slide 2

4. Catalytic Mechanism of Chymotrypsin slide 3

5. Catalytic Mechanism of Chymotrypsin slide 4

6. Summary for the Catalytic Mechanism of Chymotrypsin Mechanism –General acid-base catalysis & Covalent catalysis –Two steps: Acylation & Deacylation (rate limiting; reverse of acylation with water substituting the amine component) –Key features Active Ser195 & roles of the three catalytic residues Tetrahedral transition state Oxyanion and Oxyanion hole Acyl-enzyme intermediate

7. Serine Protease Family Chymotrypsin & elastase main chain conformation (superimposed) Serine Proteases –Chymotrypsin –Trypsin –Elastase Similarity –Similar 3D structure –Catalytic triad –Oxyanion hole –Covalent acyl-enzyme intermediate –Secreted by pancrease as inactive precursors

8. Specificity Difference of Chymotrypsin, Trypsin, and Elastase nonpolar pocket Asp (negatively charged) vs. Ser in Chymotrypsin no pocket present as two Gly in chymotrypsin are replaced by Val and Thr Substrate specificity –Chymotrypsin: aromatic or bulky nonpolar side chain –Trypsin: Lys or Arg –Elastase: smaller & uncharged side chains Small structural difference in the binding site explains the substrate specificity

9. Carboxypeptidase A A tightly bound Zn 2+ Essential for catalysis Coordinated to 1 H 2 O, 2 His, 1 Glu Digestive enzyme Hydrolyzes carboxyl terminal peptide bond –Prefer bulky and aliphatic residues 3D structure –Single polypeptide (307 amino acids) –  helices (38%) and  (17%) (compact, ellipsoid)

10. Substrate Binding Induces Large Structural Changes at the Active Site

11. 3D Structure of peptidase A/glycyltyrosine complex –Substrate-induced structural change at active site 12 Å movement of Tyr248-OH & rotation (Moves from surface to substrate terminal COO - ) –New interaction: Tyr 248  O  H  – O  C=O –Closes active-site cavity –Extrude water from cavity Arg145 moves 2 Å –New interaction: Arg 145 & – O  C=O (substrate) Terminal side chain of substrate –Now sits in a hydrophobic pocket –Induced-fit model (Daniel Koshland, Jr.) Substrate Binding Induces Large Structural Changes at the Active Site

12. Substrate Binding at the Active Site

13. Catalytic Mechanism of Carboxypeptidase A The H 2 O molecule is activated by –Bound Zn 2+ and COO – of Glu270 Activated H 2 O attacks the C=O group of the scissile peptide bond Glu270 simultaneously accepts a H + from H 2 O A negatively charged tetrahedral intermediate is formed Intermediate is stabilized by Zn 2+ and Arg127 H + transfer from COOH of Glu270 to the peptide NH Peptide bond is concomitantly cleaved The reaction products diffuse away Summary: –Activation of H 2 O by Zn 2+ and Glu270 –Proton abstraction and donation by Glu270 –Electrostatic stabilization of tetrahedral intermediate by Arg127 and Zn 2+

14. Catalytic Mechanism of Carboxypeptidase A