Sandbox 32

From Proteopedia

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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.

Contents 1 Introduction 2 Structure 3 Catalytic Mechanism 4 References

Introduction

spinqualitylabelsall models Click on the links to the left to view different structural aspects. PDB code for this 1.65 Å resolution structure is 9PAP. Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

Papain is a sulfhydryl protease from papaya latex (Carica papaya) and is used in food and pharmaceutical industries (6). It's PDB ID is 9PAP and it has an E.C. # of 3.4.22.2. It is a simple protease containing a single chain of amino acids.

Structure

Papain contains 212 amino acid resiudes and a molecular weight of 23.4 kDa. It's secondary structure contains 7 that make up 25% of the protein, and 17 making up about 17% (4).

In its 3D structure, Papain is stabilized by many . These interactions have been shown to be very important in the overall structure and folding of the protein (6). In fact, papain is made up of , L and R (L=green and R=blue). The L domain contains alpha-helical structural components (residues 10-111, 208-212) while the R domain (residues 1-9, 112-207) is characterized by anti-parallel beta sheet structure (6). In addition to these interactions, the overall structure of papain is stabilized by three . There are 6 cysteine residues that make up these bonds.

Catalytic Mechanism

As a sulfhydryl protease, Papain has a catalytic site with three important residues --Cysteine-25, Histidine-159,and Asparganine176 (3). The catalytic site is located in the between the L and R domains of the protein The centers around Cysteine-25 as it is a sulfhydryl protease. Sulfur on the cysteine will nucelophilicaly attack its substrate. Histidine acts to accept a proton from sulfur, allowing it to be negatively charged. In the oxyanion hole, asparganine stabilizes the rest of the protein, substrate molecule.

The sulfhydryl protease contains many . There are also a few residues and no positively charged residues except for histidine. Along with these hydrophobic/hydrophillic interactions, also are important structural components. There are 6 cysteine residues that form disulfide bonds at.....

As a sulfhydrly protease, Papain has a catalytic site with three important residues--Cysteine

References

1. Kamphuis, I. G., Kalk, K.H., Swarte, M.B., & Drenth, J (1984). Structure of papain refined at 1.65 A resolution. J. Mol. Biol. 179, 233-56.

2. Lowe, G. The structure and mechanism of action of papain (1970). Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 257, 237-248.

3. PDB (2011). Retrieved November 10, 2011 from http://www.pdb.org/pdb/explore/explore.do?structureId=9PAP

4. PDBsum (2011). Retrieve November 12, 2011 from http://www.ebi.ac.uk/pdbsum/9pap

5. Sathish, Hasige A., Kumar, Parigi Ramesh, & Prakash, Vishweshwaraiah (2009). The differential stability of the left and right domains of papain. Process Biochemistry. 44, 710-16.