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From Proteopedia
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Serine proteases account for over one-third of all known proteolytic enzymes. 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), the unique specificities of these enzymes make them useful tools in biochemistry and molecular biology to ascertain protein sequences. | Serine proteases account for over one-third of all known proteolytic enzymes. 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), the unique specificities of these enzymes make them useful tools in biochemistry and molecular biology to ascertain protein sequences. | ||
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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 the different specificities. Each protein cleaves the peptide backbone after (or on the carbonyl side) of a specific type of sidechain; chymotrypsin prefers to cut after aromatic residues, trypsin after basic residues and elastase after smaller neutral residues. 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'''''! | 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 the different specificities. Each protein cleaves the peptide backbone after (or on the carbonyl side) of a specific type of sidechain; chymotrypsin prefers to cut after aromatic residues, trypsin after basic residues and elastase after smaller neutral residues. 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'''''! | ||
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== '''Disulfide Bonds''' == | == '''Disulfide Bonds''' == | ||
| - | These proteases each have four to six disulfide bonds. One | + | These proteases each have four to six disulfide bonds. One cystine linkage that is conserved among all the structures is between Cys191 and Cys220. These residues were shown in spacefill representation under the "Substrate Binding Pockets" heading, but are more easily viewed in sticks format as can be seen here for <scene name='User:Amy_Kerzmann/Sandbox_5/New_chymotrypsin-triad/9' target='0'>chymotrypsin</scene>, |
<scene name='User:Amy_Kerzmann/Sandbox_5/New_trypsin-wt-triad/aa' target='1'>trypsin</scene> and <scene name='User:Amy_Kerzmann/Sandbox_5/New_elastase-triad/9' target='2'>elastase</scene>. What role might this covalent bond have in the protein's function? Does its conservation among several proteins with similar function provide any suggestion to its importance? | <scene name='User:Amy_Kerzmann/Sandbox_5/New_trypsin-wt-triad/aa' target='1'>trypsin</scene> and <scene name='User:Amy_Kerzmann/Sandbox_5/New_elastase-triad/9' target='2'>elastase</scene>. What role might this covalent bond have in the protein's function? Does its conservation among several proteins with similar function provide any suggestion to its importance? | ||
Revision as of 23:49, 11 February 2010
Contents |
Serine Proteases
Serine proteases account for over one-third of all known proteolytic enzymes. 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), 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 the different specificities. Each protein cleaves the peptide backbone after (or on the carbonyl side) of a specific type of sidechain; chymotrypsin prefers to cut after aromatic residues, trypsin after basic residues and elastase after smaller neutral residues. 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!
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Active Sites
Serine proteases perform their catalytic roles using three key residues, which are commonly referred to as the catalytic triad: Ser, His, Asp. Highlight the . The elements are color coded as follows: C, O, N.
- Mouse over or click on the structure image to determine the residue numbers for Ser, Asp and His. (The residue code should 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. Considering that the serine sidechain becomes activated for catalysis when it is negatively charged, how would the protons move among the highlighted Ser, Asp and His residues? Are these proton exchanges what you would expect from your knowledge of their pKa values?
Now compare the active site residues of chymotrypsin to the and the .
Substrate Binding Pockets
As we have just seen, these three serine proteases have relatively similar active sites. What then accounts for their varying specificities? To answer this question, 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 is large, deep and relatively hydrophobic. This structure accommodates bulky aromatic and aliphatic sidechains, as indicated by the position of a , a bound inhibitor.
- The contains Asp189 to select for positively charged sidechains, such as . The arginine sidechain is part of a larger peptide-based inhibitor called , which is now shown in balls and sticks.
- The is more constrained, explaining the preference for smaller residues. Which residue provides the key steric hinderance to prevent larger sidechains from entering the binding pocket?
Disulfide Bonds
These proteases each have four to six disulfide bonds. One cystine linkage that is conserved among all the structures is between Cys191 and Cys220. These residues were shown in spacefill representation under the "Substrate Binding Pockets" heading, but are more easily viewed in sticks format as can be seen here for , and . What role might this covalent bond have in the protein's function? Does its conservation among several proteins with similar function provide any suggestion to its importance?
