Sandbox Wabash5
From Proteopedia
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Trypsin is a serine protease that contains serine, histidine<scene name='72/725334/Beidou_test_his/3'>HIS</scene>, and aspartic acid residues. Trypsin catalyzes peptide bond hydrolysis through acid catalysis, base catalysis, and covalent catalysis. In the first step serine acts as a nucleophile to attack the substrate peptide bond, which forms a tetrahedral intermediate via covalent catalysis. Then a acyl-enzyme intermediate is formed and the C-terminal fragment is released. A water molecule attacks the acyl enzyme leading to the creation of a second tetrahedral intermediate. This is followed by the release of the N-terminal fragment, which results in the creation of the active enzyme. | Trypsin is a serine protease that contains serine, histidine<scene name='72/725334/Beidou_test_his/3'>HIS</scene>, and aspartic acid residues. Trypsin catalyzes peptide bond hydrolysis through acid catalysis, base catalysis, and covalent catalysis. In the first step serine acts as a nucleophile to attack the substrate peptide bond, which forms a tetrahedral intermediate via covalent catalysis. Then a acyl-enzyme intermediate is formed and the C-terminal fragment is released. A water molecule attacks the acyl enzyme leading to the creation of a second tetrahedral intermediate. This is followed by the release of the N-terminal fragment, which results in the creation of the active enzyme. | ||
| - | Scene 1:catalytic triad <scene name='72/725334/Catalytic_triad/1'>catalytic triad</scene> | + | Scene 1:catalytic triad <scene name='72/725334/Catalytic_triad/1'>catalytic triad</scene>. |
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Scene 2:acyl intermediate <scene name='72/725334/Acyl_intermediate/1'>acyl intermediate</scene> | Scene 2:acyl intermediate <scene name='72/725334/Acyl_intermediate/1'>acyl intermediate</scene> | ||
| - | Scene 3: oxyanion hole <scene name='72/725334/Oxyanion_hole/1'>oxyanionhole</scene> | + | |
| - | Scene 4: specificity pocket <scene name='Sandbox_45/Specificitypocketasp189gly216/2'>specificity pocket</scene> | + | Scene 3: oxyanion hole <scene name='72/725334/Oxyanion_hole/1'>oxyanionhole</scene>. This scene shows the oxyanion hole between Ser 195 and Gly 193, which is an important part of the stabilization of the tetrahedral intermediate. The oxyanion hole is formed between the hydrogen atoms of the amide groups in these two residues. |
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| + | Scene 4: specificity pocket <scene name='Sandbox_45/Specificitypocketasp189gly216/2'>specificity pocket</scene><ref>http://www.proteopedia.org/wiki/index.php/Trypsin</ref>. The Asp 189 interacts with the Gly 216, which is driven by the specificity of this pocket. | ||
BY: MICHAEL GREEN AND AARON BECKER AND BEIDOU CHENG | BY: MICHAEL GREEN AND AARON BECKER AND BEIDOU CHENG | ||
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This is a sample scene created with SAT to <scene name='72/725334/Stick_substrate/1'>Stick Peptide</scene> by Group. | This is a sample scene created with SAT to <scene name='72/725334/Stick_substrate/1'>Stick Peptide</scene> by Group. | ||
| - | One key features of the mechanism of trypsin hydrolysis is Ser-195 | ||
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| - | Another | ||
</StructureSection> | </StructureSection> | ||
== References == | == References == | ||
Revision as of 01:57, 19 February 2016
The Mechanism of Trypsin
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References
- ↑ http://www.proteopedia.org/wiki/index.php/Trypsin
- ↑ Radisky ES, Lee JM, Lu CJ, Koshland DE Jr. Insights into the serine protease mechanism from atomic resolution structures of trypsin reaction intermediates. Proc Natl Acad Sci U S A. 2006 May 2;103(18):6835-40. Epub 2006 Apr 24. PMID:16636277
