Sandbox 30: Difference between revisions

==Overview==

<applet load='9PAP' size='400' frame='true' align='right' scene='Sandbox_30/Papain_default/7' caption='Click on the links to the left to view different structural aspects. PDB code for this 1.65 Å resolution structure is 9PAP.'  />

Papain is a 23.4 kDa, 212 residue cysteine endopeptidase originating from the fruit of ''Carica papaya'', where it is present in significant amounts along with three other cysteine proteases, chymopapain, glycyl endopeptidase, and caricain<ref name="9PAP PDB">[http://www.pdb.org/pdb/explore/explore.do?structureId=9PAP] 9PAP PDB</ref><ref name="sigma">[http://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer/analytical-enzymes/papain.html] Sigma Aldrich</ref><ref name="worthington">[http://www.worthington-biochem.com/pap/default.html] Worthington Biochemical Corporation</ref>.  Its action was first described by G.C. Roy in 1873.  It was studied intensively from the 1950s to the 1960s, during which time it became the second enzyme ever to have its structure determined by x-ray crystallography.  Finally, high resolution structural analysis in the 1980s allowed an accurate description of the enzymes active site<ref name="worthington" />.  As an enzyme, papain displays very wide hydrolase activity, serving as a general amidase and esterase in addition to its protease activity.  As a protease, papain can hydrolyze bonds of basic amino acids, leucine, and glycine.  It shows preference for residues preceded by a large hydrophobic residue, but will not cleave is valine is present on the carboxyl side of a potential cleavage site.  In addition to being a very non-specific enzyme, papain is also unusually heat resistant, with maximal activity occurring at a temperature of 65° C.  These properties have led to use of papain in a large variety areas.  One of these areas is biological research, were papain is utilized in cell isolation.  It is also useful in immunological techniques because of its ability to cleave the connection between the crystallizable fragment domain and the immunoglobulin domain of antibodies<ref name="sigma" />.  Papain has also found use as an inflammation control agent, a digestive aid, and even a meat tenderizer<ref>[http://www.webmd.com/vitamins-supplements/ingredientmono-69-PAPAIN.aspx?activeIngredientId=69&activeIngredientName=PAPAIN] WebMD</ref>.

===Substrate Binding===

Papain interacts with the covalently bound leupeptin in a variety of ways.  Several residues of the enzyme and a few methanol molecules form <scene name='Sandbox_30/Papain_ligand_h-bond_ints/1'>hydrogen bonds</scene> with the ligand (starred).  However, the vast majority of the enzyme-ligand interactions are <scene name='Sandbox_30/Papain_ligand_hydrophobics/1'>hydrophobic</scene>.  Leupeptin is coordinated by a variety of tyrosine, tryptophan, and valine residues<ref name="1POP PDB">[http://www.pdb.org/pdb/explore/explore.do?structureId=1pop] 1POP PDB</ref>.

==References==

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