Sandbox 34: Difference between revisions
From Proteopedia
Jump to navigationJump to search
No edit summary |
No edit summary |
||
| Line 17: | Line 17: | ||
== Structure == | == 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 in purple, and L in gray, that form a cleft in which the <scene name='Sandbox_34/2subuwithactivesite/2'>active site</scene>, consisting of cysteine-25, histidine-159, and asparagine-175, | 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 in purple, and L in gray, that form a cleft 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>. <scene name='Sandbox_34/Salt_bridges/4'>Salt bridges</scene> 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 | |||
<scene name='Sandbox_34/Hydrophobicpolar/2'>hydrophobic and polar residues</scene> 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. | <scene name='Sandbox_34/Hydrophobicpolar/2'>hydrophobic and polar residues</scene> 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. | ||
| Line 32: | Line 30: | ||
Papain binds both <scene name='Sandbox_34/Papainwithwaterandmtoh/1'>methanol and water molecules</scene> via hydrogen bonds. This solvent mixture of 62%, (w/w) <scene name='Sandbox_34/Entire_protein_with_ligands/3'>methanol</scene> in <scene name='Sandbox_34/Papainwithwateronly/1'>water</scene> was used in order to obtain a C-type crystal, which is . In addition to the methanol molecules, papain also has an interesting hydrogen bonding with water molecules. A refined crystal structure of papain, involving a restrained least-squares procedure at 1.65 A, with an estimated accuracy of 0.1 A, revealed that water forms something similar to a hydration shell around individual molecules of papain. The interaction of papain with these water molecules leads to less interaction between papain molecules, and contributes to the stability of the crystal structure of papain.<ref name="Structure" /> | Papain binds both <scene name='Sandbox_34/Papainwithwaterandmtoh/1'>methanol and water molecules</scene> via hydrogen bonds. This solvent mixture of 62%, (w/w) <scene name='Sandbox_34/Entire_protein_with_ligands/3'>methanol</scene> in <scene name='Sandbox_34/Papainwithwateronly/1'>water</scene> was used in order to obtain a C-type crystal, which is . In addition to the methanol molecules, papain also has an interesting hydrogen bonding with water molecules. A refined crystal structure of papain, involving a restrained least-squares procedure at 1.65 A, with an estimated accuracy of 0.1 A, revealed that water forms something similar to a hydration shell around individual molecules of papain. The interaction of papain with these water molecules leads to less interaction between papain molecules, and contributes to the stability of the crystal structure of papain.<ref name="Structure" /> | ||
[[Image:Papainmech6.jpg|350px|right|thumb| A general mechanism of papain catalysis<ref>[http://chemistry.umeche.maine.edu/CHY431/Peptidase10.html] University of Maine</ref>.]] | |||
=== Specificity === | === Specificity === | ||
