Sandbox 36: Difference between revisions
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Papain has several methanol <scene name='Sandbox_36/Papain_ligands/1'>ligands</scene> associated with it. Various residues on papain <scene name='Sandbox_36/Papain_ligands_fgj/1'>hydrogen bond</scene> to these methanol molecules (methanol molecules are shown in green and associated residues are shown in blue).<ref> http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl </ref> | Papain has several methanol <scene name='Sandbox_36/Papain_ligands/1'>ligands</scene> associated with it. Various residues on papain <scene name='Sandbox_36/Papain_ligands_fgj/1'>hydrogen bond</scene> to these methanol molecules (methanol molecules are shown in green and associated residues are shown in blue).<ref> http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl </ref> | ||
==Catalytic Diad== | ==Active Site and 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. <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 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. Electrostatic interactions are seen between <scene name='Sandbox_36/Papain_intermolecular_interxns/3'>Glu35 and Lys174</scene> where the carboxyl group of Glu35 forms an ionic bond with the ammonia group of the Lys174 residue. The sum total of interactions within the cleft between the two domains ensure that the lobes do not move with respect to one another. <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 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> | ||
