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== Domains ==
== Domains ==
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'''The Subtilisin Domain:''' It contains 10 helices (alpha 1 to 10) and twelve chains (béta 1 to 10 and béta 13 to 14). The N-terminal domain of ASP seems to be like the catalytic domain of ''Kex2'', which is similar to those of subtilisin and other subtilisin-related proteases. This ASP catalytic site contains <scene name='82/829344/Catalytic_triad/1'>the catalytic triad</scene> Asp-78, His-115, and Ser-336 residues characteristic of subtilisins. In addition, 4 loops (L) protrude from the N-terminal subtilisin domain of ASP: Gly-3– Pro-26 (<scene name='82/829344/L1/1'>L1</scene>), Asn-221–Phe-241 (<scene name='82/829344/L2/1'>L2</scene>), Gly-300–Cys-326 (<scene name='82/829344/L3/1'>L3</scene>), and Gln-377–Glu-397 (<scene name='82/829344/L4/1'>L4</scene>). L1, L2, and L3 have random coil structure, whereas L4 forms a hairpin that protrudes toward the P-domain. Moreover, two <scene name='82/829344/Disulfide_bridges/1'>disulfide bridges</scene> are formed between Cys-4 and Cys-24 in L1 and between Cys-301 and Cys-326 in L3, which stabilize those loops.
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'''The Subtilisin Domain:''' It contains 10 helices (alpha 1 to 10) and twelve chains (béta 1 to 10 and béta 13 to 14). The N-terminal domain of ASP seems to be like the catalytic domain of ''Kex2'', which is similar to those of subtilisin and other subtilisin-related proteases. This ASP catalytic site contains <scene name='82/829344/Catalytic_triad/2'>the catalytic triad</scene> Asp-78, His-115, and Ser-336 residues characteristic of subtilisins. In addition, 4 loops (L) protrude from the N-terminal subtilisin domain of ASP: Gly-3– Pro-26 (<scene name='82/829344/L1/1'>L1</scene>), Asn-221–Phe-241 (<scene name='82/829344/L2/1'>L2</scene>), Gly-300–Cys-326 (<scene name='82/829344/L3/1'>L3</scene>), and Gln-377–Glu-397 (<scene name='82/829344/L4/1'>L4</scene>). L1, L2, and L3 have random coil structure, whereas L4 forms a hairpin that protrudes toward the P-domain. Moreover, two <scene name='82/829344/Disulfide_bridges/1'>disulfide bridges</scene> are formed between Cys-4 and Cys-24 in L1 and between Cys-301 and Cys-326 in L3, which stabilize those loops.
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'''The P-domain:''' The core of the P-domain in ASP contains 8 béta-strands (béta 16 18 23 and 26). The <scene name='82/829344/Extra_occluding_region/1'>extra occluding-region</scene> is comprised of two parts, <scene name='82/829344/Pl1/1'>pL1</scene>(Gly 521–Thr 525, béta 5, 6, and 12) and <scene name='82/829344/Pl2/1'>pL2</scene> (Gly-557–Asn-578, béta 25), and it is situated close to <scene name='82/829344/Catalytic_triad/1'>the catalytic triad</scene> Asp-78,His-115,and Ser-336.
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'''The P-domain:''' The core of the P-domain in ASP contains 8 béta-strands (béta 16 18 23 and 26). The <scene name='82/829344/Extra_occluding_region/1'>extra occluding-region</scene> is comprised of two parts, <scene name='82/829344/Pl1/1'>pL1</scene>(Gly 521–Thr 525, béta 5, 6, and 12) and <scene name='82/829344/Pl2/1'>pL2</scene> (Gly-557–Asn-578, béta 25), and it is situated close to <scene name='82/829344/Catalytic_triad/2'>the catalytic triad</scene> Asp-78,His-115,and Ser-336.
https://www.degruyter.com/view/j/bchm.2017.398.issue-10/hsz-2016-0344/graphic/j_hsz-2016-0344_fig_001.jpg
https://www.degruyter.com/view/j/bchm.2017.398.issue-10/hsz-2016-0344/graphic/j_hsz-2016-0344_fig_001.jpg
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== Active site ==
== Active site ==
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'''The catalytic triad:''' The [http://en.wikipedia.org/wiki/Catalytic_triad.com catalytic triad] of ASP is composed of <b>Asp78</b>, <b>His115</b> and <b>Ser336</b>. 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/1'>the catalytic triad</scene> will interact together and the mechanism will lead to a cut in the polypeptide.
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'''The catalytic triad:''' The [http://en.wikipedia.org/wiki/Catalytic_triad.com catalytic triad] of ASP is composed of <b>Asp78</b>, <b>His115</b> and <b>Ser336</b>. 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. Then, a second tetrahedral intermediate will be formed, but with the attack of a deprotonated water molecule. At the end, the regeneration of the active site will be done with the release of the peptide cut in two parts.
'''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. Then, a second tetrahedral intermediate will be formed, but with the attack of a deprotonated water molecule. At the end, the regeneration of the active site will be done with the release of the peptide cut in two parts.

Revision as of 17:54, 15 January 2020

This Sandbox is Reserved from 25/11/2019, through 30/9/2020 for use in the course "Structural Biology" taught by Bruno Kieffer at the University of Strasbourg, ESBS. This reservation includes Sandbox Reserved 1091 through Sandbox Reserved 1115.
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The serine protease from Aeromonas sobria

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References

  1. Fuller RS, Brake A, Thorner J. Yeast prohormone processing enzyme (KEX2 gene product) is a Ca2+-dependent serine protease. Proc Natl Acad Sci U S A. 1989 Mar;86(5):1434-8. PMID:2646633

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