Sandbox 35: Difference between revisions

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Papain's catalytic mechanism is like serine proteases. Its catalytic triad of residues Cys 25- His159- ~~Arg~~-175 appear to work with a fourth residue, Gln-19, suspected to be involved in oxyanion hole formation. When a peptide binds to the active site, His-159 deprotonates Cys-25 which in turn attacks the substrate carbonyl carbon. The oxyanion hole then stabilizes the resulting covalent, tetrahedral intermediate. Subsequently, nitrogen in the peptide bond is protonated by His-159 (acting as an acid). This action frees the C-terminal portion of the peptide so that it is released. The entrance of water into the active site then attacks the carbonyl carbon while it is deprotonated by His-159, resulting in another tetrahedral covalent intermediate once again stabilized through the oxyanion hole. At the end, carbonyl reformation and the Cys-25 sulfur action as the leaving group releases the N-terminal portion of the peptide. The enzyme is regenerated for the cycle to begin again. <ref name="Maine" />

Papain's catalytic mechanism is like serine proteases. Its catalytic triad of residues Cys 25- His159- Asn-175 appear to work with a fourth residue, Gln-19, suspected to be involved in oxyanion hole formation. When a peptide binds to the active site, His-159 deprotonates Cys-25 which in turn attacks the substrate carbonyl carbon. The oxyanion hole then stabilizes the resulting covalent, tetrahedral intermediate. Subsequently, nitrogen in the peptide bond is protonated by His-159 (acting as an acid). This action frees the C-terminal portion of the peptide so that it is released. The entrance of water into the active site then attacks the carbonyl carbon while it is deprotonated by His-159, resulting in another tetrahedral covalent intermediate once again stabilized through the oxyanion hole. At the end, carbonyl reformation and the Cys-25 sulfur action as the leaving group releases the N-terminal portion of the peptide. The enzyme is regenerated for the cycle to begin again. <ref name="Maine" />

Papain prefers to cleave primarily at hydrophobic residues Alanine, Leucine, Isoleucine, Phenylalanine, Tryptophan, or Tyrosine, except for Valine. <ref>[http://www.sigmaaldrich.com/life-science/biochemicals/biochemical-products.html?TablePage=16410606] Papain Sigma Aldrich </ref> [[Image:Papain Simple Cleavage.jpg|200px|right|thumb|Simple Overview of Papain Cleavage. <ref>[http://www.worthington-biochem.com/pap/default.html] Worthington Biochemical Corporation </ref>]]

==Other Interaction with Inhibitors and Effectors==

[[Image:Papain Simple Cleavage.jpg|200px|right|thumb|Simple Overview of Papain Cleavage. <ref>[http://www.worthington-biochem.com/pap/default.html] Worthington Biochemical Corporation </ref>]]

Except for valine, papain prefers to cleave at hydrophobic residues alanine, leucine, isoleucine, phenylalanine, tryptophan, or tyrosine <ref>[http://www.sigmaaldrich.com/life-science/biochemicals/biochemical-products.html?TablePage=16410606] Papain Sigma Aldrich </ref>. In light of the describe catalytic mechanism it makes sense that substances such as cysteine, sulfide/sulfite, heavy metal chelating agents like EDTA, and N-bromosuccinimide act as activators of the enzyme while PMSF, Hg2+ and other heavy metals, cystatin, leupeptin, sulfhydryl binding agents, carbonyl reagents, and alkylating agents serve as inhibitors.

==Fun Trivia==

Sandbox 35: Difference between revisions

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-Papain's catalytic mechanism is like serine proteases. Its catalytic triad of residues Cys 25- His159- Arg-175 appear to work with a fourth residue, Gln-19, suspected to be involved in oxyanion hole formation. When a peptide binds to the active site, His-159 deprotonates  Cys-25 which in turn attacks the substrate carbonyl carbon. The oxyanion hole then stabilizes the resulting covalent, tetrahedral intermediate. Subsequently, nitrogen in the peptide bond is protonated by His-159 (acting as an acid). This action frees the C-terminal portion of the peptide so that it is released. The entrance of water into the active site then attacks the carbonyl carbon while it is deprotonated by His-159, resulting in another tetrahedral covalent intermediate once again stabilized through the oxyanion hole. At the end, carbonyl reformation and the Cys-25 sulfur action as the leaving group releases the N-terminal portion of the peptide. The enzyme is regenerated for the cycle to begin again. <ref name="Maine" />
+Papain's catalytic mechanism is like serine proteases. Its catalytic triad of residues Cys 25- His159- Asn-175 appear to work with a fourth residue, Gln-19, suspected to be involved in oxyanion hole formation. When a peptide binds to the active site, His-159 deprotonates  Cys-25 which in turn attacks the substrate carbonyl carbon. The oxyanion hole then stabilizes the resulting covalent, tetrahedral intermediate. Subsequently, nitrogen in the peptide bond is protonated by His-159 (acting as an acid). This action frees the C-terminal portion of the peptide so that it is released. The entrance of water into the active site then attacks the carbonyl carbon while it is deprotonated by His-159, resulting in another tetrahedral covalent intermediate once again stabilized through the oxyanion hole. At the end, carbonyl reformation and the Cys-25 sulfur action as the leaving group releases the N-terminal portion of the peptide. The enzyme is regenerated for the cycle to begin again. <ref name="Maine" />
-Papain prefers to cleave primarily at hydrophobic residues Alanine, Leucine, Isoleucine, Phenylalanine, Tryptophan, or Tyrosine, except for Valine. <ref>[http://www.sigmaaldrich.com/life-science/biochemicals/biochemical-products.html?TablePage=16410606] Papain Sigma Aldrich </ref> [[Image:Papain Simple Cleavage.jpg|200px|right|thumb|Simple Overview of Papain Cleavage. <ref>[http://www.worthington-biochem.com/pap/default.html] Worthington Biochemical Corporation </ref>]]
 ==Other Interaction with Inhibitors and Effectors==
+[[Image:Papain Simple Cleavage.jpg|200px|right|thumb|Simple Overview of Papain Cleavage. <ref>[http://www.worthington-biochem.com/pap/default.html] Worthington Biochemical Corporation </ref>]]
+Except for valine, papain prefers to cleave at hydrophobic residues alanine, leucine, isoleucine, phenylalanine, tryptophan, or tyrosine <ref>[http://www.sigmaaldrich.com/life-science/biochemicals/biochemical-products.html?TablePage=16410606] Papain Sigma Aldrich </ref>. In light of the describe catalytic mechanism it makes sense that substances such as cysteine, sulfide/sulfite, heavy metal chelating agents like EDTA, and N-bromosuccinimide act as activators of the enzyme while PMSF, Hg2+ and other heavy metals, cystatin, leupeptin, sulfhydryl binding agents, carbonyl reagents, and alkylating agents serve as inhibitors.
 ==Fun Trivia==