Sandbox 30: Difference between revisions

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===Ligands===
===Ligands===
The crystallization procedure used to obtain the 9PAP structure was carried out using a 62% (w/w) methanol and water crystallization medium.  Thus, the papain in this crystal structure is coordinated by <scene name='Sandbox_30/Papain_methanol/1'>methanol molecules</scene>, 29 of which are shown, and <scene name='Sandbox_30/Papain_water/1'>water molecules</scene>, 21 of which occur between adjacent papain molecules and are probably important in maintaining their structural integrity<ref name="9PAP PDB" />.  Both  
The crystallization procedure used to obtain the 9PAP structure was carried out using a 62% (w/w) methanol and water crystallization medium.  Thus, the papain in this crystal structure is coordinated by <scene name='Sandbox_30/Papain_methanol/1'>methanol molecules</scene>, 29 of which are shown, and <scene name='Sandbox_30/Papain_water/1'>water molecules</scene>, 21 of which occur between adjacent papain molecules and are probably important in maintaining their structural integrity<ref name="9PAP PDB" />.  Both  
<scene name='Sandbox_30/Papain_methanol_h-bondint/1'>methanol</scene> (red and grey) and <scene name='Sandbox_30/Papain_water_h-bonds/3'>water</scene> (purple) molecules form a hydrogen bonds with many different residues, which are shown as ball and stick structures in the diagrams. Some of the ethanol molecules also have <scene name='Sandbox_30/Papain_methanol_hydrophobicint/3'>hydrophobic interactions</scene> with the enzyme.
<scene name='Sandbox_30/Papain_methanol_h-bondint/1'>methanol</scene> (red and grey) and <scene name='Sandbox_30/Papain_water_h-bonds/3'>water</scene> (purple) molecules form hydrogen bonds with many different residues, which are shown as ball and stick structures in the diagrams. Some of the ethanol molecules also have <scene name='Sandbox_30/Papain_methanol_hydrophobicint/3'>hydrophobic interactions</scene> with the enzyme.




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[[Image:Papainmech6.jpg|200px|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.]]
[[Image:Papainmech6.jpg|200px|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.]]
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 carbonyl reforms and 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>.
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 carbonyl reforms and 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>.




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