Sandbox 36: Difference between revisions
From Proteopedia
Jump to navigationJump to search
No edit summary |
|||
| Line 15: | Line 15: | ||
==Catalytic Diad== | ==Catalytic Diad== | ||
The 212 residues of Papain can be split nearly in half to produce <scene name='Sandbox_36/Papain_domains/2'>two domains</scene> though the enzyme consists only of one polypeptide chain.<ref>http://books.google.com/books?hl=en&lr=&id=fk1hbZdPTEgC&oi=fnd&pg=PA79&dq=aromatic+residues+in+papain&ots=L8SvlkQaZU&sig=xZ2l8kj52PD7DzuiAQ1zah0CU2M#v=onepage&q=aromatic%20residues%20in%20papain&f=false</ref> The <scene name='Sandbox_36/Papain_active_site_use/3'>active site</scene> is located in the cleft between the two domains. The two domains interact with one another via hydrophobic interactions, hydrogen bonds, and electrostatic interactions in this cleft. For example, <scene name='Sandbox_36/Papain_intermolecular_interxns/1'>Valine-32</scene> from the L Domain hydrophobically interacts with the carbon atoms on residues Lys174, Ala162 and Pro129 of the R Domain. | The 212 residues of Papain can be split nearly in half to produce <scene name='Sandbox_36/Papain_domains/2'>two domains</scene> though the enzyme consists only of one polypeptide chain.<ref>http://books.google.com/books?hl=en&lr=&id=fk1hbZdPTEgC&oi=fnd&pg=PA79&dq=aromatic+residues+in+papain&ots=L8SvlkQaZU&sig=xZ2l8kj52PD7DzuiAQ1zah0CU2M#v=onepage&q=aromatic%20residues%20in%20papain&f=false</ref> The <scene name='Sandbox_36/Papain_active_site_use/3'>active site</scene> is located in the cleft between the two domains. The two domains interact with one another via hydrophobic interactions, hydrogen bonds, and electrostatic interactions in this cleft. For example, <scene name='Sandbox_36/Papain_intermolecular_interxns/1'>Valine-32</scene> from the L Domain hydrophobically interacts with the carbon atoms on residues Lys174, Ala162 and Pro129 of the R Domain. <scene name='Sandbox_36/Papain_intermolecular_interxns/2'>Gln 19 </scene> hydrogen bonds multiple times with the oxygen atoms of Ser176 and also with the oxygen atom on Tyr88. | ||
The active site contains a <scene name='Sandbox_36/Papain_catalytic_diad/2'>catalytic diad</scene> made up of Cysteine-25 and Histidine-159. Aspartate-158 also plays a role in catalysis but it is not considered part of the diad. Papain's active site can accommodate seven amino acids of a substrate. When the peptide is cleaved, the first four resides reside on the amino side of the peptide bond while the other three reside on the carboxyl side. <ref>http://pubs.acs.org/doi/abs/10.1021/bi00544a013 </ref> Papain prefers to cleave at: (hydrophobic)-(Arg or Lys)- cleaves here -(not Val). Hydrophobic is Ala, Val, Leu, Ile, Phe, Trp, or Tyr. <ref> http://www.sigmaaldrich.com/life-science/biochemicals/biochemical-products.html?TablePage=16410606 </ref> | The active site contains a <scene name='Sandbox_36/Papain_catalytic_diad/2'>catalytic diad</scene> made up of Cysteine-25 and Histidine-159. Aspartate-158 also plays a role in catalysis but it is not considered part of the diad. Papain's active site can accommodate seven amino acids of a substrate. When the peptide is cleaved, the first four resides reside on the amino side of the peptide bond while the other three reside on the carboxyl side. <ref>http://pubs.acs.org/doi/abs/10.1021/bi00544a013 </ref> Papain prefers to cleave at: (hydrophobic)-(Arg or Lys)- cleaves here -(not Val). Hydrophobic is Ala, Val, Leu, Ile, Phe, Trp, or Tyr. <ref> http://www.sigmaaldrich.com/life-science/biochemicals/biochemical-products.html?TablePage=16410606 </ref> | ||
