Chymotrypsin
From Proteopedia
Chymotrypsin (Chy or α-Chy) is a digestive enzyme containing an active serine residue. It cleaves peptide bonds of proteins where the amide side of the bond is an aromatic amino acid like tyrosine, phenylalanine or tryptophane. The Chy precursor is the inactive chymotrypsinogen (Chygen) which gets cleaved 4 times by trypsine losing a 6 amino
acid long peptide to become the active Chy. γ-Chy is a covalent acyl adduct of α-Chy. δ-Chy results when Chygen is cleaved only twice by trypsin. The images at the left and at the right correspond to one representative Chymotrypsin, i.e. the crystal structure of Cellulomonas Bogoriensis Chymotrypsin (2ea3). Some additional details in
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Overview
Please click on the as you read through the text and watch how the 3D picture on the right changes. Chymotrypsin is a protease, an enzyme catalyzing the hydrolysis of peptide bonds of proteins. Chymotrypsin helps to digest proteins in our food. Other proteases are crucial for blood clotting (thrombin and other proteases), for the AIDS virus metabolism (HIV protease) and for many other processes relevant to human health and agriculture.
While chymotrypsin occurs in many organisms, the most-studied chymotrypsin is that from cows (bovine chymotrypsin). In its mature form, bovine chymotrypsin is a protein consisting of 245 amino acids. This string of amino acids folds into a . (Can you guess where the substrate might bind? Try spinning around the molecule by dragging it with the mouse cursor. There should be a pocket somewhere on the surface of the enzyme. The active site is colored in this ). The path of the backbone is easier to see in this , which shows that chymotrypsin folds into two large beta sheets.
Active site residues
The active site of an enzyme is the location where the substrate binds and where the chemical reaction occurs. Active site residues are those amino acid residues demonstrated to have importance for catalysis or substrate binding. Chymotrypsin contains three residues, Ser 195, His 57 and Asp 102, which are known as its . Similar three-dimensional arrangements of a serine, a histidine and an aspartate are observed in many other proteases, and the role of these three residues in catalysis has been studied extensively. Serine acts as a nucleophile (contributing the electron pair for a new bond) attacking the carbonyl carbon of the peptide bond to be hydrolyzed. Histidine and aspartate turn serine into a better nucleophile by assisting in removing a hydrogen ion from serine.
Substrate binding and catalysis
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Features of the substrate binding site can be seen in the structure of bovine chymotrypsin bound to the inhibitor N-acetyl-L-leucyl-L-phenylalanyl trifuoromethyl ketone (Ac-Leu-Phe-CF3), which resembles a peptide substrate (see structure in left figure). The colored backgrounds in the figure indicate the four components of structure and shows the bond (yellow on black background) that is position to be cleaved. The default scene shows the three peptide chains of chymotrypsin in spacefill and colored tuquoise, beige, and violet. The inhibitor, which is shown in CPK ball & stick, is sitting in the active site. In this , the residues of catalytic triad are shown in CPK ball & stick and labelled, and the inhibitor is in light gray ball & stick with its phenyl group in orchid. By moving the structure back and forth with your mouse, it is easy to see that the phenyl group is located in the hydrophobic binding pocket of the enzyme. The binding pocket determines the enzyme's preference for cleavage of peptides on the C-terminal side of aromatic residues.
This view shows the carbonyl group of the inhibitor in CPK colors. The triflouromethyl group is bound to the carbonyl carbon via the yellow bond. In a peptide substrate, the triflouromethyl group would be replaced by the first amino acid residue of the rest of the peptide chain, and the yellow bond would be the bond that is cleaved. The carbonyl carbon of the inhibitor is 1.95 Å away from the side chain oxygen of serine 195, and this indicates they are covalently bound (bond indicated by dotted line). Thus, this structure is similar to the tetrahedral intermediate that is formed during the cleavage reaction. The negative charge that develops on the carbonyl oxygen of the substrate is stabilized by hydrogen bonds to the backbone nitrogens of Ser 195 and Gly 193, shown in blue spacefill. The hydrogen atoms involved in these hydrogen bonds are not shown.
3D Structures of Chymotrypsin
Updated on 21-December-2013
Native Chymotrypsin
1yph – bChyA chain A - bovine
4cha, 5cha – BtChy
1kdq – rChyB, chain B (mutant) - rat
2ea3 – Chy – Cellulomonas bogoriensis
1ab9, 8gch, 1gct, 2gct, 3gct, 2gch - gamma BtChy
Native Chymotrypsinogen
2cga, 1chg – bChygen A
2jet – rChygen B chain A,B
Chymotrypsin + polypeptide inhibitors
1cbw, 1mtn - bChy+BPTI
1t7c, 1t8l, 1t8m, 1t8n, 1t8o – bChyA+P1 BPTI variants
1oxg – bChyA+autolysis peptide
1p2m, 1p2n, 1p2o, 1p2q – bChyA+ 4 amino acids in S1 pocket
1n8o – bChyA+ecotin
1ca0 – bChy+APPI
1acb, 4h4f – bChy+Elgin C
2cho – bChy+turkey ovomucoid third domain
Chymotrypsin + inhibitors
3bg4 – ChyA chain A+guamerin
2p8o - bChyA chain A+benzohydroxamic acid/vanadate
1eq9 – Chy+PMSF – fire ant
2cha – bChy+p-sulfinotoluene
γ-Chymotrypsin + inhibitors
1gg6 – γ-bChy+N-acetyl-phenylalanine trifluoromethyl ketone
1ggd – γ-bChy+N-acetyl-phenylalanine trifluoromethyl aldehyde
1afq - γ-bChy+synthetic inhibitor
3gch, 4gch, 5gch - γ-bChy+cinnamate
6gch, 7gch - γ-bChy+trifluoromethy ketone
6cha – γ-bChy+phenylethane boronic acid – transition state inhibitor
1gmc, 1gmd – γ-bChy+hexane – transition state inhibitor
2gmt - γ-bChy+N-acetyl-alanyl-phenylalanyl-chloroethyl ketone
1gmh, 1gcd - γ-bChy+organophosphoryl
1gha, 1ghb - γ-bChy+ N-acetyl-tryptophan
γ-Chymotrypsin + reaction transition state inhibitors
6cha – γ-bChy+phenylethane boronic acid
1gmc, 1gmd – γ-bChy+hexane
δ-Chymotrypsin + inhibitors
1dlk – δ-bChy+peptidyl chloromethyl ketone
Chymotrypsinogen + inhibitors
1gl0, 1gli – ChygenA+PMP_D2v – Locusta migratoria
1k2i - bChygen+7-hydroxycoumarin
2y6t – bChygenA + ecotin
3t62 - bChygenA + Kunitz-type proteinase inhibitor SHPI-1
Further reading
You can learn more about chymotrypsin structure, function and regulation in this publicly available chapter of the Biochemistry textbook by Berg, Tymoczka and Stryer.
Proteopedia Page Contributors and Editors (what is this?)
Michal Harel, Karsten Theis, Alice Harmon, Alexander Berchansky
