Trypsin: Difference between revisions

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[[Image:Serine_protease_mechanism_by_snellios.png |thumb|right|Serine Protease Mechanism]]

[[Image:Triad_1.jpg|thumb|right|Catalytic Triad]]

The function of Trypsin is to break down peptides using a hydrolysis reaction into amino acid building blocks. This mechanism is a general catalytic mechanism that all Serine proteases use. The active site where this mechanism occurs in Trypsin is composed of three amino acids and called a ~~<scene name='Sandbox_45/Ctriadd102h57s195/4'>~~catalytic triad~~</scene>~~. The three catalytic residues are Serine 195, Histidine 57, and Aspartate 102 <ref>Pratt, C.W., Voet, D., Voet, J.G. Fundamentals of Biochemistry - Life at the Molecular Level - Third Edition. Voet, Voet and Pratt, 2008.</ref>. The structure of the catalytic triad and the mechanism are shown in the figures to the right. In the mechanism, serine is bonded to the imidazole ring of the histidine. When histidine accepts a proton from serine an alkoxide nucleophile is formed. This nucleophile attacks the substrate when the substrate is present. The role of the aspartate residue is hold histidine in the proper position to make it a good proton acceptor. What makes this mechanism works is that a pocket if formed from the three residues and the three residues function to hold each other in proper position for nucleophilic attack.

The function of Trypsin is to break down peptides using a hydrolysis reaction into amino acid building blocks. This mechanism is a general catalytic mechanism that all Serine proteases use. The active site where this mechanism occurs in Trypsin is composed of three amino acids and called a catalytic triad. The three catalytic residues are Serine 195, Histidine 57, and Aspartate 102 <ref>Pratt, C.W., Voet, D., Voet, J.G. Fundamentals of Biochemistry - Life at the Molecular Level - Third Edition. Voet, Voet and Pratt, 2008.</ref>. The structure of the catalytic triad and the mechanism are shown in the figures to the right. In the mechanism, serine is bonded to the imidazole ring of the histidine. When histidine accepts a proton from serine an alkoxide nucleophile is formed. This nucleophile attacks the substrate when the substrate is present. The role of the aspartate residue is hold histidine in the proper position to make it a good proton acceptor. What makes this mechanism works is that a pocket if formed from the three residues and the three residues function to hold each other in proper position for nucleophilic attack.

The steps of the mechanism involve two tetrahedral intermediates and an Acyl-enzyme intermediate <ref>Structural Biochemistry. 10 June 2010. 30 October 2010.<http://en.wikibooks.org/wiki/Structural_Biochemistry/Enzyme/Catalytic_Triad>.</ref>. The mechanism can be followed in more detail in the figure on the right <ref>Image From: http://www.bmolchem.wisc.edu/courses/spring503/503-sec1/DRAWINGS/503-3a-2serineprotease.jpg</ref>.

==Oxyanion Hole==

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   [[Image:Serine_protease_mechanism_by_snellios.png |thumb|right|Serine Protease Mechanism]]
 [[Image:Triad_1.jpg|thumb|right|Catalytic Triad]]
-The function of Trypsin is to break down peptides using a hydrolysis reaction into amino acid building blocks. This mechanism is a general catalytic mechanism that all Serine proteases use.  The active site where this mechanism occurs in Trypsin is composed of three amino acids and called a <scene name='Sandbox_45/Ctriadd102h57s195/4'>catalytic triad</scene>. The three catalytic residues are Serine 195, Histidine 57, and Aspartate 102 <ref>Pratt, C.W., Voet, D., Voet, J.G. Fundamentals of Biochemistry - Life at the Molecular Level - Third Edition. Voet, Voet and Pratt, 2008.</ref>. The structure of the catalytic triad and the mechanism are shown in the figures to the right. In the mechanism, serine is bonded to the imidazole ring of the histidine. When histidine accepts a proton from serine an alkoxide nucleophile is formed. This nucleophile attacks the substrate when the substrate is present. The role of the aspartate residue is hold histidine in the proper position to make it a good proton acceptor. What makes this mechanism works is that a pocket if formed from the three residues and the three residues function to hold each other in proper position for nucleophilic attack.
+The function of Trypsin is to break down peptides using a hydrolysis reaction into amino acid building blocks. This mechanism is a general catalytic mechanism that all Serine proteases use.  The active site where this mechanism occurs in Trypsin is composed of three amino acids and called a catalytic triad. The three catalytic residues are Serine 195, Histidine 57, and Aspartate 102 <ref>Pratt, C.W., Voet, D., Voet, J.G. Fundamentals of Biochemistry - Life at the Molecular Level - Third Edition. Voet, Voet and Pratt, 2008.</ref>. The structure of the catalytic triad and the mechanism are shown in the figures to the right. In the mechanism, serine is bonded to the imidazole ring of the histidine. When histidine accepts a proton from serine an alkoxide nucleophile is formed. This nucleophile attacks the substrate when the substrate is present. The role of the aspartate residue is hold histidine in the proper position to make it a good proton acceptor. What makes this mechanism works is that a pocket if formed from the three residues and the three residues function to hold each other in proper position for nucleophilic attack.
 The steps of the mechanism involve two tetrahedral intermediates and an Acyl-enzyme intermediate <ref>Structural Biochemistry. 10 June 2010. 30 October 2010.<http://en.wikibooks.org/wiki/Structural_Biochemistry/Enzyme/Catalytic_Triad>.</ref>. The mechanism can be followed in more detail in the figure on the right <ref>Image From: http://www.bmolchem.wisc.edu/courses/spring503/503-sec1/DRAWINGS/503-3a-2serineprotease.jpg</ref>.
 ==Oxyanion Hole==