Sandbox 30: Difference between revisions

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==Overview==

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>.

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===Ligands===

The crystallization procedure used to ~~create~~ the 9PAP structure was carried out using a 62% (w/w) methanol and water crystallization medium. Thus, this crystal structure ~~of papain~~ is coordinated by methanol molecules, 29 of which are shown, and water molecules, 21 of which occur between adjacent papain molecules and probably important in maintaining their structural integrity<ref name="9PAP PDB" />. ~~The both~~ methanol and water molecules form a hydrogen bonds with many different ~~parts~~ of the enzyme, ~~while~~ the ~~methanol molecules~~ also ~~interact hydrophobically~~ with it.

The crystallization procedure used to obtain the 9PAP structure was carried out using a 62% (w/w) methanol and water crystallization medium. Thus, the papain in this crystal structure is coordinated by <scene name='Sandbox_30/Papain_methanol/1'>methanol molecules</scene>, 29 of which are shown, and <scene name='Sandbox_30/Papain_methanol/1'>water molecules</scene>, 21 of which occur between adjacent papain molecules and probably important in maintaining their structural integrity<ref name="9PAP PDB" />. Both

<scene name='Sandbox_30/Papain_methanol_h-bondint/1'>methanol</scene> (red and grey) and <scene name='Sandbox_30/Papain_water_h-bonds/3'>water</scene> (purple) molecules form a hydrogen bonds with many different residues, which are shown as ball and stick structures in the diagrams. Some of the ethanol molecules also have <scene name='Sandbox_30/Papain_methanol_hydrophobicint/3'>hydrophobic interactions</scene> with the enzyme.

==Catalytic Mechanism==

Like serine proteases, cysteine proteases contain a catalytic triad of residues. In the case of papain, these residues are CYS-25, HIS-159, and ARG-175. Papain also contains a fourth residue, GLN19 that has been shown to play an important role in catalysis and is likely involved in the formation of the oxyanion hole<ref name="Harrison">[http://pubs.acs.org/doi/abs/10.1021/ja9711472]Harrison, M.J., N.A. Burton, and I.H. Hillier. 1997. Catalytic Mechanism of the Enzyme Papain: Predictions with a Hybrid Quantum Mechanical/Molecular Mechanical Potential. J. Am. Chem. Soc. 119: 12285-12291</ref>.

Sandbox 30: Difference between revisions

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@@ Line 6: / Line 6: @@
 ==Overview==
-<applet load='9PAP' size='450' 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'  />
+<applet load='9PAP' size='450' 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>.
@@ Line 19: / Line 19: @@
 ===Ligands===
-The crystallization procedure used to create the 9PAP structure was carried out using a 62% (w/w) methanol and water crystallization medium.  Thus, this crystal structure of papain is coordinated by methanol molecules, 29 of which are shown, and water molecules, 21 of which occur between adjacent papain molecules and probably important in maintaining their structural integrity<ref name="9PAP PDB" />.  The both methanol and water molecules form a hydrogen bonds with many different parts of the enzyme, while the methanol molecules also interact hydrophobically with it.
+The crystallization procedure used to obtain the 9PAP structure was carried out using a 62% (w/w) methanol and water crystallization medium.  Thus, the papain in this crystal structure is coordinated by <scene name='Sandbox_30/Papain_methanol/1'>methanol molecules</scene>, 29 of which are shown, and <scene name='Sandbox_30/Papain_methanol/1'>water molecules</scene>, 21 of which occur between adjacent papain molecules and probably important in maintaining their structural integrity<ref name="9PAP PDB" />.  Both
+<scene name='Sandbox_30/Papain_methanol_h-bondint/1'>methanol</scene> (red and grey) and <scene name='Sandbox_30/Papain_water_h-bonds/3'>water</scene> (purple) molecules form a hydrogen bonds with many different residues, which are shown as ball and stick structures in the diagrams. Some of the ethanol molecules also have <scene name='Sandbox_30/Papain_methanol_hydrophobicint/3'>hydrophobic interactions</scene> with the enzyme.
+==Catalytic Mechanism==
+<applet load='1pop' size='450' frame='true' align='right' scene='Sandbox_30/Papain_ligand_default/3' caption='Papain crystallized with substrate analog leupeptin covalently bound to the catalytic CYS25.'  />
+Like serine proteases, cysteine proteases contain a catalytic triad of residues.  In the case of papain, these residues are CYS-25, HIS-159, and ARG-175.  Papain also contains a fourth residue, GLN19 that has been shown to play an important role in catalysis and is likely involved in the formation of the oxyanion hole<ref name="Harrison">[http://pubs.acs.org/doi/abs/10.1021/ja9711472]Harrison, M.J., N.A. Burton, and I.H. Hillier. 1997. Catalytic Mechanism of the Enzyme Papain: Predictions with a Hybrid Quantum Mechanical/Molecular Mechanical Potential. J. Am. Chem. Soc. 119: 12285-12291</ref>.