Sandbox Reserved 1091: Difference between revisions
From Proteopedia
Jump to navigationJump to search
No edit summary |
No edit summary |
||
| Line 34: | Line 34: | ||
Moreover, we can find three <scene name='82/829344/Calcium_binding_sites/2'>Ca2+ Binding Sites</scene> in the ASP Structure (Ca1, Ca2 and Ca3). <scene name='82/829344/Ca1_et_ca2/4'>Ca1 and Ca2</scene> are situated in the N-terminal domain, and <scene name='82/829344/Ca3/3'>Ca3</scene> is situated in the C-terminal domain. It were assigned to ASP based on electron density, counter charges, and coordination. But in contrary to Kex2 ([[1r64]]), ASP contains no Ca2+ binding sites near its catalytic site. | Moreover, we can find three <scene name='82/829344/Calcium_binding_sites/2'>Ca2+ Binding Sites</scene> in the ASP Structure (Ca1, Ca2 and Ca3). <scene name='82/829344/Ca1_et_ca2/4'>Ca1 and Ca2</scene> are situated in the N-terminal domain, and <scene name='82/829344/Ca3/3'>Ca3</scene> is situated in the C-terminal domain. It were assigned to ASP based on electron density, counter charges, and coordination. But in contrary to Kex2 ([[1r64]]), ASP contains no Ca2+ binding sites near its catalytic site. | ||
| Line 51: | Line 49: | ||
'''The catalytic triad:''' The [http://en.wikipedia.org/wiki/Catalytic_triad catalytic triad] of ASP is composed of '''Asp78''', '''His115''' and '''Ser336'''. These amino acids are the base is the active site of the protein, where the mode of action of the serine protease takes place. A peptide can be inserted in the space of the active site. There, the amino acids of <scene name='82/829344/Catalytic_triad/2'>the catalytic triad</scene> will interact together and the mechanism will lead to a cut in the polypeptide. | '''The catalytic triad:''' The [http://en.wikipedia.org/wiki/Catalytic_triad catalytic triad] of ASP is composed of '''Asp78''', '''His115''' and '''Ser336'''. These amino acids are the base is the active site of the protein, where the mode of action of the serine protease takes place. A peptide can be inserted in the space of the active site. There, the amino acids of <scene name='82/829344/Catalytic_triad/2'>the catalytic triad</scene> will interact together and the mechanism will lead to a cut in the polypeptide. | ||
'''Mechanism:''' The mechanism is the following: The histidine will react with the serine and deprotonate it. The deprotonated hydroxyl group of the serine will act as a nucleophilic species and attack the carbon from the carbonyl function on the peptide. This will lead to the formation of a tetrahedral intermediate. The regeneration of the carbonyl group will be followed by the release of one part of the peptide, with an amine group at its extremity. Then, a second tetrahedral intermediate will be formed, but with the attack of a deprotonated water molecule. In the end, the regeneration of the active site will be done with the release of the part of the peptide with a carboxyl extremity. '''The polypeptide is also cut in two parts and the target protein isn't | '''Mechanism:''' The mechanism is the following: The histidine will react with the serine and deprotonate it. The deprotonated hydroxyl group of the serine will act as a nucleophilic species and attack the carbon from the carbonyl function on the peptide. This will lead to the formation of a tetrahedral intermediate. The regeneration of the carbonyl group will be followed by the release of one part of the peptide, with an amine group at its extremity. Then, a second tetrahedral intermediate will be formed, but with the attack of a deprotonated water molecule. In the end, the regeneration of the active site will be done with the release of the part of the peptide with a carboxyl extremity. '''The polypeptide is also cut in two parts and the target protein isn't functional anymore'''. <ref>http://fr.wikipedia.org/wiki/Fichier:Serine_protease_mechanism_by_snellios.png</ref> | ||
A schematic representation of the mechanism with the involved amino acids can be found under the following link : [http://fr.wikipedia.org/wiki/Fichier:Serine_protease_mechanism_by_snellios.png '''mechanism of the reaction''' ] | A schematic representation of the mechanism with the involved amino acids can be found under the following link : [http://fr.wikipedia.org/wiki/Fichier:Serine_protease_mechanism_by_snellios.png '''mechanism of the reaction''' ] | ||
