Sandbox 31

>

Please do NOT make changes to this Sandbox. Sandboxes 30-60 are reserved for use by Biochemistry 410 & 412 at Messiah College taught by Dr. Hannah Tims during Fall 2012 and Spring 2013. Papain (PDB ID #: 9pap) spinqualitylabelsall models Structure of HMG-CoA reductase (PDB entry 9pap) Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Introduction Papain is a cysteine hydrolase (EC 3.4.22.2) that is found naturally occurring in Papaya(Carica papaya). Papain is extracted from the latex, leaves and roots of the papaya tree. Thiol proteases like papain are commonly found in different fruits like pineapples, figs, and kiwis. Proteases are a group of enzymes that cleave peptide bonds of protein molecules. Papain is a protease commonly used for cell isolation, protein structural studies, cleaving antibodies, and various other research techniques. In addition to use in research, it is commonly used in industry to tenderize meats, remove skin from hides, and clean soft contact lenses. History Papain was first explorer back in 1873 by G.C. Roy, who studied papaya juice. Later, papain was extracted and named by Wertz and Bouchut who noticed it had proteolytic properties. Papain was the second enzyme to have it's structure determined by x-ray crystallography. Extensive research has be done on the structure and activity of papain and its Structure Papain is formed from a peptide that is 212 amino acids in length. It consists of 25% Alpha helices and 21% Beta Sheet. The structure also consists of three Disulfide bonds between Cysteine Residues. The disulfide bonds exist between Cys 63 and Cys 22, Cys 200 and Cys 153, and Cys 56 and Cys 95. Another important residue to the structure is Cysteine 25 which has a sulfhydryl group that plays a major role in the active site activity[[1]]. The Hydrophobic Residues in papain are primarily located toward the inside of the enzyme or paired by hydrophobic interactions with other hydrophobic residues to exclude water. The Polar Residues are located facing the exterior, in the active site, or paired with other charged residues. The Negatively charged residues (acidic) and the Positively charged residues (basic) make up the polar residues. The charged and polar residues are hydrophilic therefore do not orient themselves to exclude water or solvent. The charged Termini face outward due to their hydrophilic nature. Inhibitors There are many inhibitors of cysteine proteases like papain including antipain, cystatin, Hg2+, and Leupeptin. Leupeptin (PBD ID #: 1pop) I is a commonly studied inhibitor of proteases. It inhibits by binding and interacting with the active site which allows it to block the enzyme's desired protein substrate. There are many Residues that interact with Leupeptin in the active site. The predominant interaction is from hydrophobic interactions between Leupeptin and active site residues. In addition to hydrophobic interactions, there are also some hydrogen bonding interactions to hold Leupeptin in the active site of papain. Leupeptin works well at blocking papain from its enzymatic duties. Active Site and Mechanism The active site of papain has a "Catalytic Triad"including CYS 25, HIS 159, and ASN 175. (Active Site of Papain) File:Papain2.jpg This triad interacts with the substrate to catalyze the reaction. The sulfhydryl group on CYS 25 plays the key role in the mechanism, which is why papain is considered a thiol protease. The sulfur from CYS 25 attacks the backbone amine on the substrate forming a tetrahedral intermediate. Next, the carbonyl is reformed and the carbon nitrogen bond is broken. A water associated with a nitrogen on HIS 159 then attacks the carbonyl forming a second tetrahedral intermediate. The carbonyl then reforms breaking the carbon-sulfur bond. This leaves a carboxy group on the end of one piece of the substrate and an amino group on the end of the other piece. (Mechanism of the Papain Enzyme with substrate) File:Mech.jpg For a Video Explanation of the Cysteine protease mechanism Click Here. References https://dailyfitnessmagz.com/2011/03/papayas-nutrition-facts/ https://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer/analytical-enzymes/papain.html https://peds.oxfordjournals.org/content/7/1/75.abstract https://www.pdb.org/pdb/explore/remediatedSequence.do?structureId=9PAP https://faculty.csusm.edu/lcohen/index.html