Sandbox 38: Difference between revisions

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== Function: ==

[[Image:Papainmech6.jpg|200px|left|thumb| mechanism of papain <ref>[http://chemistry.umeche.maine.edu/CHY431/Peptidase10.html] University of Maine</ref>.]]The <scene name='Sandbox_38/Active_site/3'>active site</scene> of this hydrolytic enzyme is able to break peptide bonds through the help of a catalytic ~~diad~~, consisting of Cys-25 by His-159. The Cys-25 residue is deprotonated by His-159, while Asp-125 is able to stabilize the Histadine ring in order for this deprotonation to take place. The Cys-25 residue is then able to perform a nucleophilic attack on the carbonyl carbon of the peptide backbone, freeing the amino terminal of the peptide, and forming a covalent intermediate. Next, the enzyme is deacylated by water, and the carboxy-terminal portion of the peptide is released. A link for the specific mechanism of this process can be viewed on the left hand side of this page.

[[Image:Papainmech6.jpg|200px|left|thumb| mechanism of papain <ref>[http://chemistry.umeche.maine.edu/CHY431/Peptidase10.html] University of Maine</ref>.]]The <scene name='Sandbox_38/Active_site/3'>active site</scene> of this hydrolytic enzyme is able to break peptide bonds through the help of a catalytic triad, consisting of Cys-25, His-159, and Arg-175. The Cys-25 residue is deprotonated by His-159, while Asp-125 is able to stabilize the Histadine ring in order for this deprotonation to take place. The Cys-25 residue is then able to perform a nucleophilic attack on the carbonyl carbon of the peptide backbone, freeing the amino terminal of the peptide, and forming a covalent intermediate. Next, the enzyme is deacylated by water, and the carboxy-terminal portion of the peptide is released. A link for the specific mechanism of this process can be viewed on the left hand side of this page.

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== Ligands of Papain ==

Papain binds to an abundance of <scene name='Sandbox_38/Ligands/1'>ligands</scene>, as they are the molecules colored green. These ligands interact with Papain through various <scene name='Sandbox_38/Ligand_hydrogen_bonds/1'>hydrogen bonds</scene>, which are distinctly colored blue. A pseudosubstrate that is able to mimic the actual substrate and therefore inhibit Papain is called Leupeptin. The <scene name='Sandbox_38/Leupeptin-papain_complex/1'>leupeptin-papain complex</scene> (PDC ID: 1POP), clearly indicated by the blue Nitrogen of the substrate, indicates that the inhibitors carbonyl carbon is covalently bound to the Cys-25 sulfer atom of papain and is organized in a tetrahedral manner. The carbonyl oxygen atom of the inhibitor is not only able to face the oxyanion hole, it is also able to form hydrogen bond contacts with Gln-19 and Cys-25.

Papain binds to an abundance of <scene name='Sandbox_38/Ligands/1'>ligands</scene>, as they are the molecules colored green. Since methanol was used as a solvent in the crystallization of Papain, many of these molecules surround the protein. These ligands interact with Papain through various <scene name='Sandbox_38/Ligand_hydrogen_bonds/1'>hydrogen bonds</scene>, which are distinctly colored blue. <scene name='Sandbox_38/Water_interactions/1'>Water molecules</scene> are also able to surround the molecule and form hydrogen bonds as well. A pseudosubstrate that is able to mimic the actual substrate and therefore inhibit Papain is called Leupeptin. The <scene name='Sandbox_38/Leupeptin-papain_complex/1'>leupeptin-papain complex</scene> (PDC ID: 1POP), clearly indicated by the blue Nitrogen of the substrate, indicates that the inhibitors carbonyl carbon is covalently bound to the Cys-25 sulfer atom of papain and is organized in a tetrahedral manner. The carbonyl oxygen atom of the inhibitor is not only able to face the oxyanion hole, it is also able to form hydrogen bond contacts with Gln-19 and Cys-25.

References:

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@@ Line 14: / Line 14: @@
 == Function: ==
-[[Image:Papainmech6.jpg|200px|left|thumb| mechanism of papain <ref>[http://chemistry.umeche.maine.edu/CHY431/Peptidase10.html] University of Maine</ref>.]]The <scene name='Sandbox_38/Active_site/3'>active site</scene> of this hydrolytic enzyme is able to break peptide bonds through the help of a catalytic diad, consisting of Cys-25 by His-159.  The Cys-25 residue is deprotonated by His-159, while Asp-125 is able to stabilize the Histadine ring in order for this deprotonation to take place. The Cys-25 residue is then able to perform a nucleophilic attack on the carbonyl carbon of the peptide backbone, freeing the amino terminal of the peptide, and forming a covalent intermediate.  Next, the enzyme is deacylated by water, and the carboxy-terminal portion of the peptide is released. A link for the specific mechanism of this process can be viewed on the left hand side of this page.
+[[Image:Papainmech6.jpg|200px|left|thumb| mechanism of papain <ref>[http://chemistry.umeche.maine.edu/CHY431/Peptidase10.html] University of Maine</ref>.]]The <scene name='Sandbox_38/Active_site/3'>active site</scene> of this hydrolytic enzyme is able to break peptide bonds through the help of a catalytic triad, consisting of Cys-25, His-159, and Arg-175.  The Cys-25 residue is deprotonated by His-159, while Asp-125 is able to stabilize the Histadine ring in order for this deprotonation to take place. The Cys-25 residue is then able to perform a nucleophilic attack on the carbonyl carbon of the peptide backbone, freeing the amino terminal of the peptide, and forming a covalent intermediate.  Next, the enzyme is deacylated by water, and the carboxy-terminal portion of the peptide is released. A link for the specific mechanism of this process can be viewed on the left hand side of this page.
@@ Line 26: / Line 26: @@
 == Ligands of Papain ==
-Papain binds to an abundance of <scene name='Sandbox_38/Ligands/1'>ligands</scene>, as they are the molecules colored green.  These ligands interact with Papain through various <scene name='Sandbox_38/Ligand_hydrogen_bonds/1'>hydrogen bonds</scene>, which are distinctly colored blue.  A pseudosubstrate that is able to mimic the actual substrate and therefore inhibit Papain is called Leupeptin.  The <scene name='Sandbox_38/Leupeptin-papain_complex/1'>leupeptin-papain complex</scene> (PDC ID: 1POP), clearly indicated by the blue Nitrogen of the substrate, indicates that the inhibitors carbonyl carbon is covalently bound to the Cys-25 sulfer atom of papain and is organized in a tetrahedral manner. The carbonyl oxygen atom of the inhibitor is not only able to face the oxyanion hole, it is also able to form hydrogen bond contacts with Gln-19 and Cys-25.
+Papain binds to an abundance of <scene name='Sandbox_38/Ligands/1'>ligands</scene>, as they are the molecules colored green. Since methanol was used as a solvent in the crystallization of Papain, many of these molecules surround the protein.   These ligands interact with Papain through various <scene name='Sandbox_38/Ligand_hydrogen_bonds/1'>hydrogen bonds</scene>, which are distinctly colored blue.  <scene name='Sandbox_38/Water_interactions/1'>Water molecules</scene> are also able to surround the molecule and form hydrogen bonds as well. A pseudosubstrate that is able to mimic the actual substrate and therefore inhibit Papain is called Leupeptin.  The <scene name='Sandbox_38/Leupeptin-papain_complex/1'>leupeptin-papain complex</scene> (PDC ID: 1POP), clearly indicated by the blue Nitrogen of the substrate, indicates that the inhibitors carbonyl carbon is covalently bound to the Cys-25 sulfer atom of papain and is organized in a tetrahedral manner. The carbonyl oxygen atom of the inhibitor is not only able to face the oxyanion hole, it is also able to form hydrogen bond contacts with Gln-19 and Cys-25.
 References: