CHEM2052 Tutorial

Chem2052: Example 3 - Serine Proteases

Serine proteases account for over one-third of all known proteolytic enzymes ^[1],^[2]. Within the diverse collection of serine proteases, the most famous members are trypsin, chymotrypsin and elastase. Aside from their key roles in digestion (and other physiological processes) ^[2], the unique specificities of these enzymes make them useful tools in biochemistry and molecular biology to ascertain protein sequences.

Looking at the structures below, it is apparent that these three enzymes have similar folds. This conservation of tertiary structure is due to extensive similarities at the level of primary amino acid sequence. However, there are small differences in amino acid sequence among the proteins, which are reflected in their different specificities. Each protein cleaves the peptide backbone after (or on the carbonyl side) of a specific type of sidechain. After examining the molecular basis for these functional similarities and differences, you will hopefully see why serine proteases are a classic example of how structure dictates function!

Active Sites

Serine proteases perform their catalytic roles using three key residues, which are commonly referred to as the catalytic triad: . The elements are color coded as follows: C, O, N.

• Mouse over or click on the structure to determine the residue numbers for the catalytic residues. (The residue code will appear near the mouse pointer or in the lower left-hand corner of the browser window.)
• You can adjust the zoom in each image by holding down the shift key while you click and drag on the structure. Alternatively, you can click on the Jmol symbol in the lower right-hand corner of each image and select a different zoom percentage from the main menu.

This arrangement of amino acids is also called a charge relay system ^[3].

Now compare the active site residues of chymotrypsin to the and the .

Substrate Binding Pockets

The next links examine the binding pockets of each protein. The spacefilled residues have been color coded according to hydrophobicity (residues are indicated as: Hydrophobic or Polar, with Aspartate highlighted further ).

• The . This structure shows the binding pocket using , a bound inhibitor.

• The contains Asp189. Consider the peptide-based inhibitor called , which is now shown in balls and sticks, which residue of this inhibitor is interacting with Asp189?

• The .

Understanding the Mechanism

Catalytic Mechanism

Lehninger's Principles of Biochemistry (5th edition) describes the catalytic mechanism of chymotrypsin on pages 208-209. An animated version of the enzyme-catalyzed hydrolysis reaction is also available on the textbook's website. was designed to match the perspective given by those resources. To provide better orientation after this rotation, here are the that were highlighted above. (Or you can .)

• () Note that the would be in approximately the same location as the carbonyl group of the substrate peptide.

Additional PDB Structures

In order to easily compare the proteins shown on this page, some portions of the crystal structures have been masked. Although each of these serine proteases functions as a monomer, they are often observed as dimers or even tetramers in crystal structures. These higher-order multimers are not the physiological state of the serine protease, but rather a consequence of the experimental method, which requires high protein concentrations. However, some proteins are only functional in the tetrameric state, such as hemoglobin. Therefore, it is important to recognize that one cannot necessarily determine the physiological state from a crystal structure alone.

To view the full, unmodified structures in the RSCB Protein Data Bank, here are links to each of the crystal structures shown above: chymotrypsin (2cha), trypsin (1aq7) and elastase (4est). Keep in mind that these are only representative structures of each serine protease. Other structures can be found at the following links:

• chymotrypsin (7gch) This structure is shown in Figure 6-18 (page 206) of Lehninger's Principles of Biochemistry (5th edition).
• chymotrypsin (1acb) This structure includes a bound protein, showing how the peptide fits into the active site of the enzyme.
• trypsin (2cmy)
• elastase (3est)

3D structures of chymotrypsin

Chymotrypsin

3D structures of trypsin

Trypsin

3D structures of elastase

Elastase

References

1. ↑ Rawlings ND, Morton FR, Kok CY, Kong J, Barrett AJ. MEROPS: the peptidase database. Nucleic Acids Res. 2008 Jan;36(Database issue):D320-5. Epub 2007 Nov 8. PMID:17991683 doi:10.1093/nar/gkm954
2. ↑ ^{2.0 2.1} Di Cera E. Serine proteases. IUBMB Life. 2009 May;61(5):510-5. PMID:19180666 doi:10.1002/iub.186
3. ↑ Banacky P, Linder B. Model of serine proteases charge relay system -- PCILO study. Biophys Chem. 1981 Jun;13(3):223-31. PMID:7016210