Sandbox 36: Difference between revisions

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 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.  The two domains interact with one another via weak Van der Waals forces in this cleft.  For example, <scene name='Sandbox_36/Papain_intermolecular_interxns/1'>Valine-32</scene> from the L Domain interacts with the carbon atoms on residues Lys174, Ala162 and Pro129 of the R Domain. 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>