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<StructureSection load='' size='450' side='right' scene='User:Amy_Kerzmann/Sandbox_5/New_chymotrypsin-triad/2' caption='α-chymoptrypsin (PDB code [[2cha]])'> == '''Chem2052: Example 3 - Serine Proteases''' == '''Serine proteases''' account for over one-third of all known proteolytic enzymes <ref>PMID:17991683</ref>,<ref name="DiCera">PMID:19180666</ref>. 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) <ref name ="DiCera"/>, 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'''''! *<scene name='User:Amy_Kerzmann/Sandbox_5/New_chymotrypsin-triad/2'>Chymotrypsin</scene> *<scene name='User:Amy_Kerzmann/Sandbox_5/New_trypsin-wt-triad/4'>Trypsin</scene> *<scene name='User:Amy_Kerzmann/Sandbox_5/New_elastase-triad/3'>Elastase</scene> == '''Active Sites''' == Serine proteases perform their catalytic roles using three key residues, which are commonly referred to as the '''catalytic triad''': <scene name='User:Amy_Kerzmann/Sandbox_5/New_chymotrypsin-triad/7'>chymotrypsin catalytic triad</scene>. The elements are color coded as follows: {{Template:ColorKey_Element_C}}, {{Template:ColorKey_Element_O}}, {{Template:ColorKey_Element_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''' <ref>PMID: 7016210</ref>. Now compare the active site residues of chymotrypsin to the <scene name='59/596400/Morph/2'>trypsin catalytic triad and the elastase catalytic triad</scene> (<span style="color:lightblue;background-color:black;font-weight:bold;">trypsin is in light blue</span>, PDB code [[1aq7]] and <span style="color:pink;background-color:black;font-weight:bold;">elastase is in pink</span>, PDB code [[4est]]). {{Template:Button Toggle Animation2}} == '''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: {{Template:ColorKey_Hydrophobic}} or {{Template:ColorKey_Polar}}, with <font color="FF0000">'''Aspartate'''</font> highlighted further ). *The <scene name='User:Amy_Kerzmann/Sandbox_5/New_chymotrypsin-triad/4'>chymotrypsin binding pocket</scene>. This structure shows the binding pocket using <scene name='User:Amy_Kerzmann/Sandbox_5/New_chymotrypsin-triad/6'>p-sulfinotoluene</scene>, a bound inhibitor. *The <scene name='User:Amy_Kerzmann/Sandbox_5/New_trypsin-wt-triad/6'>trypsin binding pocket</scene> contains <font color="FF0000">Asp189</font>. Consider the peptide-based inhibitor called <scene name='User:Amy_Kerzmann/Sandbox_5/New_trypsin-wt-triad/9'>aeruginosin 98-B</scene>, which is now shown in balls and sticks, which residue of this inhibitor is interacting with Asp189? *The <scene name='User:Amy_Kerzmann/Sandbox_5/New_elastase-triad/6'>elastase binding pocket</scene>. == '''Understanding the Mechanism''' == ==== '''Catalytic Mechanism''' ==== Lehninger's Principles of Biochemistry (5th edition)describes the catalytic mechanism of chymotrypsin on pages 208-209. An [http://bcs.whfreeman.com/lehninger5e/pages/bcs-main.asp?v=&s=06000&n=00010&i=06010.01&o=|00610|00580|00590|00510|00540|00600|00550|00570|00630|00010|00020|00030|00040|00070|00080|00090|00100|01000|02000|03000|04000|05000|06000|07000|08000|09000|10000|11000|12000|13000|14000|15000|16000|17000|18000|19000|20000|21000|22000|23000|24000|25000|26000|27000|28000|99000| animated version] of the enzyme-catalyzed hydrolysis reaction is also available on the textbook's website. <scene name='User:Amy_Kerzmann/Sandbox_5/New_chymotrypsin-triad/10'> This representation</scene> was designed to match the perspective given by those resources. To provide better orientation after this rotation, here are the <scene name='User:Amy_Kerzmann/Sandbox_5/New_chymotrypsin-triad/11'>binding pocket residues</scene> that were highlighted above. (Or you can <scene name='User:Amy_Kerzmann/Sandbox_5/New_chymotrypsin-triad/16'>label the catalytic triad and Gly193</scene>.) *<scene name='User:Amy_Kerzmann/Sandbox_5/New_chymotrypsin-triad/12'>show p-sulfinotoluene binding</scene> *<scene name='User:Amy_Kerzmann/Sandbox_5/New_chymotrypsin-triad/13'>show just p-sulfinotoluene</scene> (<scene name='User:Amy_Kerzmann/Sandbox_5/New_chymotrypsin-triad/14'>as sticks</scene>) Note that the <scene name='User:Amy_Kerzmann/Sandbox_5/New_chymotrypsin-triad/15'>sulfino group</scene> would be in approximately the same location as the carbonyl group of the substrate peptide. *<scene name='User:Amy_Kerzmann/Sandbox_5/New_chymotrypsin-triad/10'>hide binding pocket</scene> == '''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. ==3D structures of chymotrypsin== [[Chymotrypsin]] ==3D structures of trypsin== [[Trypsin]] ==3D structures of elastase== [[Elastase]] ---- ==References== <references />

• Template:ColorKey Element C
• Template:ColorKey Element N
• Template:ColorKey Element O
• Template:ColorKey Hydrophobic
• Template:ColorKey Polar

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