Sandbox 30: Difference between revisions

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==Structure==

The secondary structure of papain consists of 7 <scene name='Sandbox_30/Papain_secondary_helices/3'>α helices</scene>, 17 <scene name='Sandbox_30/Papain_secondary_sheets/3'>β strands</scene>, all of which are antiparallel, and a large amount (about 50% of total residues) of <scene name='Sandbox_30/Papain_secondary_orf/4'>ordered non-repetitive structures</scene>. The <scene name='Sandbox_30/Papain_rainbow/3'>rainbow coloration view</scene>, which goes from blue (amino terminus) to red (carboxyl terminus) is useful for tracing the order of these structures through the chain. Papain also contains three <scene name='Sandbox_30/Papain_disulfides/3'>disulfide bonds</scene>, which connect <scene name='Sandbox_30/Papain_disulfides_22-63/1'>~~C22~~ to ~~C63~~</scene>,

The secondary structure of papain consists of 7 <scene name='Sandbox_30/Papain_secondary_helices/3'>α helices</scene>, 17 <scene name='Sandbox_30/Papain_secondary_sheets/3'>β strands</scene>, all of which are antiparallel, and a large amount (about 50% of total residues) of <scene name='Sandbox_30/Papain_secondary_orf/4'>ordered non-repetitive structures</scene>. The <scene name='Sandbox_30/Papain_rainbow/3'>rainbow coloration view</scene>, which goes from blue (amino terminus) to red (carboxyl terminus) is useful for tracing the order of these structures through the chain. Papain also contains three <scene name='Sandbox_30/Papain_disulfides/3'>disulfide bonds</scene>, which connect <scene name='Sandbox_30/Papain_disulfides_22-63/1'>Cys-22 to Cys63</scene>,

<scene name='Sandbox_30/Papain_disulfides_56-95/1'>~~C56~~ to ~~C95~~</scene>, and <scene name='Sandbox_30/Papain_disulfides_153-200/1'>~~C153~~ to ~~C200~~</scene><ref name="9PAP PDB" />. These disulfide bonds are likely important in conserving the structural integrity of the enzyme as it operates in extracellular environments at high temperatures.

<scene name='Sandbox_30/Papain_disulfides_56-95/1'>Cys-56 to Cys-95</scene>, and <scene name='Sandbox_30/Papain_disulfides_153-200/1'>Cys-153 to Cys-200</scene><ref name="9PAP PDB" />. These disulfide bonds are likely important in conserving the structural integrity of the enzyme as it operates in extracellular environments at high temperatures.

===Residue Distribution===

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==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>.

Like serine proteases, cysteine proteases contain a <scene name='Sandbox_30/Papain_ligand_active-site/2'>catalytic triad</scene> of residues. In the case of papain, these residues are Cys-25, His-159, and Arg-175. Papain also contains a fourth residue, <scene name='Sandbox_30/Papain_ligand_active-sitegln19/4'>Gln-19</scene> that has been shown to play an important role in catalysis and is likely involved in the formation of the oxyanion hole. The mechanism begins when a peptide binds to the active site. Cys-25 is then deprotonated by His-159 and attacks the substrate carbonyl carbon. This forms a covalent, tetrahedral intermediate that is stabilized by the oxyanion hole. Next, His-159 acts as a general acid, protonating the nitrogen in the peptide bond, which acts as a leaving group as the carbonyl reforms. This now free C-terminal portion of the peptide is released. Water then enters the active site and attacks the carbonyl carbon while it is deprotonated by His-159, again forming an oxyanion hole-stabilized tetradral covalent intermediate. Finally, the Cys-25 sulfur acts as a leaving group, releasing the N-terminal portion of the peptide and regenerating the enzyme<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>.

[[Image:Papainmech6.jpg|300px|left|thumb| General mechanism of papain catalysis<ref>[http://chemistry.umeche.maine.edu/CHY431/Peptidase10.html] University of Maine</ref>. Arg-175, which orients His 159, and Gln-19, which contributes to the formation of the oxyanion hole, are not shown.]]

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@@ Line 12: / Line 12: @@
 ==Structure==
-The secondary structure of papain consists of 7 <scene name='Sandbox_30/Papain_secondary_helices/3'>α helices</scene>, 17 <scene name='Sandbox_30/Papain_secondary_sheets/3'>β strands</scene>, all of which are antiparallel, and a large amount (about 50% of total residues) of <scene name='Sandbox_30/Papain_secondary_orf/4'>ordered non-repetitive structures</scene>.  The <scene name='Sandbox_30/Papain_rainbow/3'>rainbow coloration view</scene>, which goes from blue (amino terminus) to red (carboxyl terminus) is useful for tracing the order of these structures through the chain.  Papain also contains three <scene name='Sandbox_30/Papain_disulfides/3'>disulfide bonds</scene>, which connect <scene name='Sandbox_30/Papain_disulfides_22-63/1'>C22 to C63</scene>,
+The secondary structure of papain consists of 7 <scene name='Sandbox_30/Papain_secondary_helices/3'>α helices</scene>, 17 <scene name='Sandbox_30/Papain_secondary_sheets/3'>β strands</scene>, all of which are antiparallel, and a large amount (about 50% of total residues) of <scene name='Sandbox_30/Papain_secondary_orf/4'>ordered non-repetitive structures</scene>.  The <scene name='Sandbox_30/Papain_rainbow/3'>rainbow coloration view</scene>, which goes from blue (amino terminus) to red (carboxyl terminus) is useful for tracing the order of these structures through the chain.  Papain also contains three <scene name='Sandbox_30/Papain_disulfides/3'>disulfide bonds</scene>, which connect <scene name='Sandbox_30/Papain_disulfides_22-63/1'>Cys-22 to Cys63</scene>,
-<scene name='Sandbox_30/Papain_disulfides_56-95/1'>C56 to C95</scene>, and <scene name='Sandbox_30/Papain_disulfides_153-200/1'>C153 to C200</scene><ref name="9PAP PDB" />.  These disulfide bonds are likely important in conserving the structural integrity of the enzyme as it operates in extracellular environments at high temperatures.
+<scene name='Sandbox_30/Papain_disulfides_56-95/1'>Cys-56 to Cys-95</scene>, and <scene name='Sandbox_30/Papain_disulfides_153-200/1'>Cys-153 to Cys-200</scene><ref name="9PAP PDB" />.  These disulfide bonds are likely important in conserving the structural integrity of the enzyme as it operates in extracellular environments at high temperatures.
 ===Residue Distribution===
@@ Line 24: / Line 24: @@
 ==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.'  />
+<applet load='1pop' size='450' frame='true' align='right' scene='Sandbox_30/Papain_ligand_default/3' caption='Papain crystallized with substrate analog leupeptin (green) covalently bound to the catalytic Cys-25.  The PBD code for this structure is 1POP'  />
-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>.
+Like serine proteases, cysteine proteases contain a <scene name='Sandbox_30/Papain_ligand_active-site/2'>catalytic triad</scene> of residues.  In the case of papain, these residues are Cys-25, His-159, and Arg-175.  Papain also contains a fourth residue, <scene name='Sandbox_30/Papain_ligand_active-sitegln19/4'>Gln-19</scene> that has been shown to play an important role in catalysis and is likely involved in the formation of the oxyanion hole.  The mechanism begins when a peptide binds to the active site.  Cys-25 is then deprotonated by His-159 and attacks the substrate carbonyl carbon.  This forms a covalent, tetrahedral intermediate that is stabilized by the oxyanion hole.  Next, His-159 acts as a general acid, protonating the nitrogen in the peptide bond, which acts as a leaving group as the carbonyl reforms.  This now free C-terminal portion of the peptide is released.  Water then enters the active site and attacks the carbonyl carbon while it is deprotonated by His-159, again forming an oxyanion hole-stabilized tetradral covalent intermediate.  Finally, the Cys-25 sulfur acts as a leaving group, releasing the N-terminal portion of the peptide and regenerating the enzyme<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>.
+[[Image:Papainmech6.jpg|300px|left|thumb| General mechanism of papain catalysis<ref>[http://chemistry.umeche.maine.edu/CHY431/Peptidase10.html] University of Maine</ref>.  Arg-175, which orients His 159, and Gln-19, which contributes to the formation of the oxyanion hole, are not shown.]]