Sandbox 38

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= '''Papain''' =

==Introduction==

[[Image:Papain_cartoon.png|200px|left|thumb|Cartoon Peak at Pepsin]]

DID YOU KNOW?

<scene name='Sandbox_35/Papain/1'>Papain</scene>. Meat tenderizer. Old time home remedy for insect, jellyfish, and stingray stings<ref>[http://www.ameriden.com/products/advanced-digestive-enzyme/] Ameridan International</ref>. Who would have thought that a sulfhydryl protease from the latex of the papaya fruit, ''Carica papaya'' and ''Vasconcellea cundinamarcensis'' would have such a practical application beyond proteopedia?

This protease belongs to an extended family of aminopeptidases, dipeptidyl peptidases, endopeptidases, and other enzymes having both exo- and endo-peptidase activity. The inactivated zymogen with N-terminal propeptide regions - helping to stabilize against alkalinity and enabling proper folding - is activated through removal of the propeptide regions <ref>PMID: 7845226</ref><ref>PMID: 12188906</ref>.

<StructureSection load='9pap' size='500' side='right' caption='Structure of Papain (PDB entry [[9PAP]])' scene=''>

==Structure==

Its polypeptide chain consists of 212 amino acid residues folded to form a groove between its two domains containing the active site.

<scene name='Sandbox_35/Secondary_structure_papain/2'>secondary structure</scene>

<scene name='Sandbox_35/2nd_struc_papain_beta/2'>beta sheets</scene>

<scene name='Sandbox_35/2nd_struc_papain_helix/2'>alpha helix</scene> <ref name="9PAP PDB">[http://www.pdb.org/pdb/explore/explore.do?structureId=9PAP]9PAP PDB</ref>

<scene name='Sandbox_35/Active_site_papain/3'>active site</scene> <ref>PMID: 8140097</ref>

<scene name='Sandbox_35/Active_site_asp_158_papain/1'>TextToBeDisplayed</scene>

===Distribution of Residues===

<scene name='Sandbox_35/Papain_acid_and_basic_residues/1'>acidic and basic residues</scene>

<scene name='Sandbox_35/Hydrophobicity_papain/3'>polar and non-polar residue</scene>

<scene name='Sandbox_35/Papain_polar/1'>polar residues</scene>

<scene name='Sandbox_35/Nonpolar_papain/2'>non-polar residues</scene>

===Ligands interactions===

<scene name='Sandbox_35/Cathepsin_l_specific_inhibitor/2'>Cathepsin L specific inhibitor</scene>

Primarily hydrogen bonds with non-water and hydrophobic interactions

<scene name='Sandbox_35/Cathepsin_interaction/3'>interaction</scene>

</StructureSection>

==Catalytic Mechanism==

[[Image:Papainmech6.jpg|200px|left|thumb| General mechanism of papain catalysis<ref>[http://chemistry.umeche.maine.edu/CHY431/Peptidase10.html] University of Maine</ref>.]]

==References==

<references />

<ref group="xtra">PMID:8140097</ref>

http://www.pdb.org/pdb/explore/explore.do?structureId=2PAD

• Show the secondary structures.

• Compare the distribution of polar residues to that of nonpolar residues.

• Highlight the active site.

• If you can find a PDB file of the enzyme that contains a pseudo-substrate (may be inhibitor), highlight it.

• Show the contacts or attractions that are present between the pseudo-substrate and the protein, and if the enzyme has multiple subunits, show the contacts between the subunits.

• Identify any other ligands that are present in the structure and the types of contacts that are present between them and the protein

http://proteopedia.org/wiki/index.php/Sandbox_55#cite_note-18

Table of contents

Pictures

References (cross links)