Sandbox 34: Difference between revisions

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=== Introduction ===

'''Papain''' is a cysteine protease, also known as '''papaya proteinase I''', from the peptidase C1 family (E.C. 3.4.22.2).<ref name="UniProt">http://www.uniprot.org/uniprot/P00784</ref> It functions as an endopeptidase, amidase, and esterase,<ref name="Worthington">http://www.worthington-biochem.com/pap/default.html</ref> with its optimal activity values for pH lying between 6.0 and 7.0, and its optimal temperature for activity is 65 °C. Its pI values are 8.75 and 9.55, and it is best visualized at a wavelength of 278 nm. <ref>http://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer/analytical-enzymes/papain.html</ref> While only consisting of a single peptide chain, papain has <scene name='Sandbox_34/Subunitsrandl/1'>two domains</scene> that form a cleft in which the <scene name='Sandbox_34/2subuwithactivesite/2'>active site</scene> lies.<ref name="PDBSum">http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=9pap&template=clefts.html&r=speedfill</ref> Naturally found in the latex of the papaya fruit, one of the most common uses of papain is as a meat tenderizer because of its ability to hydrolyze esters and amides.<ref>IUBMB Enzyme Nomenclature: www.chem.qmul.ac.uk/iubmb/enzyme/EC3/4/22/2.html</ref> Another common use is as a digestive aid. Papaya is commonly referenced as a preferred fruit for those suffering from gastroesophageal reflux disease due to its ability to help the the stomach with digestion of complex proteins.

'''Papain''' is a cysteine protease, also known as '''papaya proteinase I''', from the peptidase C1 family (E.C. 3.4.22.2).<ref name="UniProt">http://www.uniprot.org/uniprot/P00784</ref> It functions as an endopeptidase, amidase, and esterase,<ref name="Worthington">http://www.worthington-biochem.com/pap/default.html</ref> with its optimal activity values for pH lying between 6.0 and 7.0, and its optimal temperature for activity is 65 °C. Its pI values are 8.75 and 9.55, and it is best visualized at a wavelength of 278 nm. <ref>http://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer/analytical-enzymes/papain.html</ref> While only consisting of a single peptide chain, papain has <scene name='Sandbox_34/Subunitsrandl/1'>two domains</scene> that form a cleft in which the <scene name='Sandbox_34/2subuwithactivesite/3'>active site</scene> lies.<ref name="PDBSum">http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=9pap&template=clefts.html&r=speedfill</ref> Naturally found in the latex of the papaya fruit, one of the most common uses of papain is as a meat tenderizer because of its ability to hydrolyze esters and amides.<ref>IUBMB Enzyme Nomenclature: www.chem.qmul.ac.uk/iubmb/enzyme/EC3/4/22/2.html</ref> Another common use is as a digestive aid. Papaya is commonly referenced as a preferred fruit for those suffering from gastroesophageal reflux disease due to its ability to help the the stomach with digestion of complex proteins.

=== History ===

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== Structure ==

Papain is a relatively simple enzyme. It consists of only one chain of 212 residues with three disulfide bonds, illustrated in yellow. The single chain is separated into <scene name='Sandbox_34/Subunitsrandl/1'>two domains</scene>: R is shown in purple, and L in gray. A cleft is formed in which the <scene name='Sandbox_34/2subuwithactivesite/2'>active site</scene>, consisting of cysteine-25, histidine-159, and asparagine-175, resides.<ref name="PDBSum" ~~/><Structure load='9pap' size='400' frame='true' align='left' caption='Papain and Structure' scene='Sandbox_34/Entire_protein_with_ligandscy2/2'~~ />Many hydrogen bonds exist throughout the molecule, holding it in its 3D conformation. These stabilizing bonds, represented in white, are present both in the <scene name='Sandbox_34/Pap_with_h-bonding_btwnbckbne/1'>backbone</scene>, and between <scene name='Sandbox_34/Pap_with_h-bonding_btwnsdchns/2'>residues</scene>.

Papain is a relatively simple enzyme. It consists of only one chain of 212 residues with three disulfide bonds, illustrated in yellow. The single chain is separated into <scene name='Sandbox_34/Subunitsrandl/1'>two domains</scene>: R is shown in purple, and L in gray. A cleft is formed in which the <scene name='Sandbox_34/2subuwithactivesite/3'>active site</scene>, consisting of cysteine-25, histidine-159, and asparagine-175, resides.<ref name="PDBSum" />Many hydrogen bonds exist throughout the molecule, holding it in its 3D conformation. These stabilizing bonds, represented in white, are present both in the <scene name='Sandbox_34/Pap_with_h-bonding_btwnbckbne/1'>backbone</scene>, and between <scene name='Sandbox_34/Pap_with_h-bonding_btwnsdchns/2'>residues</scene>.

<scene name='Sandbox_34/Salt_bridges/4'>Salt bridges</scene> also strongly contribute to the stability of the protein structure. In this particular image, clarification of residue coordination is demonstrated by color: paired residues are shown in the same color, oxygen is shown in red, and nitrogen is shown in blue A modified cysteine residue with a sulfhydryl group, <scene name='Sandbox_34/9pap_sulfhydryl_group/1'>cysteine sulfonic acid</scene>, is necessary for the activity of the enzyme.<ref>http://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer/analytical-enzymes/papain.html</ref> In 9PAP, the primary representation of papain used in this article, the sulfhydryl group has been oxidized. Papain contains many <scene name='Sandbox_34/Hydrophobicpolar/1'>hydrophobic and polar regions</scene>. The <scene name='Sandbox_34/Hydrophobic_residues/1'>hydrophobic residues</scene> are illustrated in gray, and the <scene name='Sandbox_34/Polar_residues/1'>polar residues</scene> are illustrated in magenta. It is easy to see that the hydrophobic and polar residues segregate themselves such that hydrophobic residues are buried within turns or the interior of the molecule, and that polar regions are towards the exterior of the molecule.

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@@ Line 7: / Line 7: @@
 === Introduction ===
-<Structure load='9pap' size='350' frame='true' align='right' caption='Papain' scene='Sandbox_34/Entire_protein_with_ligandscys/1' />
+<Structure load='9pap' size='350' frame='true' align='right' caption='Papain' scene='Sandbox_34/Entire_protein_with_ligandscys/2' />
-'''Papain''' is a cysteine protease, also known as '''papaya proteinase I''', from the peptidase C1 family (E.C. 3.4.22.2).<ref name="UniProt">http://www.uniprot.org/uniprot/P00784</ref> It functions as an endopeptidase, amidase, and esterase,<ref name="Worthington">http://www.worthington-biochem.com/pap/default.html</ref> with its optimal activity values for pH lying between 6.0 and 7.0, and its optimal temperature for activity is 65 °C. Its pI values are 8.75 and 9.55, and it is best visualized at a wavelength of 278 nm. <ref>http://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer/analytical-enzymes/papain.html</ref> While only consisting of a single peptide chain, papain has <scene name='Sandbox_34/Subunitsrandl/1'>two domains</scene> that form a cleft in which the <scene name='Sandbox_34/2subuwithactivesite/2'>active site</scene> lies.<ref name="PDBSum">http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=9pap&template=clefts.html&r=speedfill</ref> Naturally found in the latex of the papaya fruit, one of the most common uses of papain is as a meat tenderizer because of its ability to hydrolyze esters and amides.<ref>IUBMB Enzyme Nomenclature: www.chem.qmul.ac.uk/iubmb/enzyme/EC3/4/22/2.html</ref> Another common use is as a digestive aid. Papaya is commonly referenced as a preferred fruit for those suffering from gastroesophageal reflux disease due to its ability to help the the stomach with digestion of complex proteins.
+'''Papain''' is a cysteine protease, also known as '''papaya proteinase I''', from the peptidase C1 family (E.C. 3.4.22.2).<ref name="UniProt">http://www.uniprot.org/uniprot/P00784</ref> It functions as an endopeptidase, amidase, and esterase,<ref name="Worthington">http://www.worthington-biochem.com/pap/default.html</ref> with its optimal activity values for pH lying between 6.0 and 7.0, and its optimal temperature for activity is 65 °C. Its pI values are 8.75 and 9.55, and it is best visualized at a wavelength of 278 nm. <ref>http://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer/analytical-enzymes/papain.html</ref> While only consisting of a single peptide chain, papain has <scene name='Sandbox_34/Subunitsrandl/1'>two domains</scene> that form a cleft in which the <scene name='Sandbox_34/2subuwithactivesite/3'>active site</scene> lies.<ref name="PDBSum">http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=9pap&template=clefts.html&r=speedfill</ref> Naturally found in the latex of the papaya fruit, one of the most common uses of papain is as a meat tenderizer because of its ability to hydrolyze esters and amides.<ref>IUBMB Enzyme Nomenclature: www.chem.qmul.ac.uk/iubmb/enzyme/EC3/4/22/2.html</ref> Another common use is as a digestive aid. Papaya is commonly referenced as a preferred fruit for those suffering from gastroesophageal reflux disease due to its ability to help the the stomach with digestion of complex proteins.
 === History ===
@@ Line 16: / Line 16: @@
+<Structure load='9pap' size='400' frame='true' align='left' caption='Papain and Structure' scene='Sandbox_34/Subunitsrandl/3'/>
 == Structure ==
-Papain is a relatively simple enzyme. It consists of only one chain of 212 residues with three disulfide bonds, illustrated in yellow. The single chain is separated into <scene name='Sandbox_34/Subunitsrandl/1'>two domains</scene>: R is shown in purple, and L in gray. A cleft is formed in which the <scene name='Sandbox_34/2subuwithactivesite/2'>active site</scene>, consisting of cysteine-25, histidine-159, and asparagine-175, resides.<ref name="PDBSum" /><Structure load='9pap' size='400' frame='true' align='left' caption='Papain and Structure' scene='Sandbox_34/Entire_protein_with_ligandscy2/2' />Many hydrogen bonds exist throughout the molecule, holding it in its 3D conformation. These stabilizing bonds, represented in white, are present both in the <scene name='Sandbox_34/Pap_with_h-bonding_btwnbckbne/1'>backbone</scene>, and between <scene name='Sandbox_34/Pap_with_h-bonding_btwnsdchns/2'>residues</scene>.
+Papain is a relatively simple enzyme. It consists of only one chain of 212 residues with three disulfide bonds, illustrated in yellow. The single chain is separated into <scene name='Sandbox_34/Subunitsrandl/1'>two domains</scene>: R is shown in purple, and L in gray. A cleft is formed in which the <scene name='Sandbox_34/2subuwithactivesite/3'>active site</scene>, consisting of cysteine-25, histidine-159, and asparagine-175, resides.<ref name="PDBSum" />Many hydrogen bonds exist throughout the molecule, holding it in its 3D conformation. These stabilizing bonds, represented in white, are present both in the <scene name='Sandbox_34/Pap_with_h-bonding_btwnbckbne/1'>backbone</scene>, and between <scene name='Sandbox_34/Pap_with_h-bonding_btwnsdchns/2'>residues</scene>.
 <scene name='Sandbox_34/Salt_bridges/4'>Salt bridges</scene> also strongly contribute to the stability of the protein structure. In this particular image, clarification of residue coordination is demonstrated by color: paired residues are shown in the same color, oxygen is shown in red, and nitrogen is shown in blue A modified cysteine residue with a sulfhydryl group, <scene name='Sandbox_34/9pap_sulfhydryl_group/1'>cysteine sulfonic acid</scene>, is necessary for the activity of the enzyme.<ref>http://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer/analytical-enzymes/papain.html</ref> In 9PAP, the primary representation of papain used in this article, the sulfhydryl group has been oxidized.  Papain contains many <scene name='Sandbox_34/Hydrophobicpolar/1'>hydrophobic and polar regions</scene>. The <scene name='Sandbox_34/Hydrophobic_residues/1'>hydrophobic residues</scene> are illustrated in gray, and the <scene name='Sandbox_34/Polar_residues/1'>polar residues</scene> are illustrated in magenta. It is easy to see that the hydrophobic and polar residues segregate themselves such that hydrophobic residues are buried within turns or the interior of the molecule, and that polar regions are towards the exterior of the molecule.