Sandbox Reserved 1458

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Here is a <scene name='79/799586/4x2zhydrophobicity/1'>hydrophobicity-focused view</scene> of PLpro, the importance of hydrophobic and hydrophilic regions are that they determine how the proteins fold and that is the case in PLpro as well. PLpro has a mix of hydrophobic and hydrophilic regions.
Here is a <scene name='79/799586/4x2zhydrophobicity/1'>hydrophobicity-focused view</scene> of PLpro, the importance of hydrophobic and hydrophilic regions are that they determine how the proteins fold and that is the case in PLpro as well. PLpro has a mix of hydrophobic and hydrophilic regions.
Here is a view of the <scene name='79/799586/4x2zligand/3'>ligand</scene>. The important chemical features of the ligand is that they form H bonds with each other and have metal interactions with Zinc. The amino acids that interact with the ligand are Cystine, Threonine and Arginine. Cystine interacts with Zn through metal interactions as well as forms H bonds with other Cystines and Threonine.
Here is a view of the <scene name='79/799586/4x2zligand/3'>ligand</scene>. The important chemical features of the ligand is that they form H bonds with each other and have metal interactions with Zinc. The amino acids that interact with the ligand are Cystine, Threonine and Arginine. Cystine interacts with Zn through metal interactions as well as forms H bonds with other Cystines and Threonine.
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This is the<scene name='79/799586/4x2zcat/1'> catalytic triad</scene> and it helps the protein achieve its function by helping the protein reveal key differences in substrate binding sites of PLpros. Specifically the P3 and P4 sub sites and the residues that interact with the-barrel of ubiquitin are different. This suggest a difference in catalytic activity. It helps the protein function more efficiently by revealing and opening up different binding sites. The catalytic triad include D275, H264, C101.
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This is the <scene name='79/799586/4x2zcat/3'>catalytic triad</scene> and it helps the protein achieve its function by helping the protein reveal key differences in substrate binding sites of PLpros. Specifically the P3 and P4 sub sites and the residues that interact with the-barrel of ubiquitin are different. This suggest a difference in catalytic activity. It helps the protein function more efficiently by revealing and opening up different binding sites. The catalytic triad include D275, H264, C101.
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The <scene name='79/799586/Activesite/1'>active site</scene> is pictured here and has the key amino acids highlighted. Those key amino acids are W156, D223, N155 and IIe. W156 is involved in shaping the S2 subsite for a glycine, D223 and N155 help form the pocket and shape active site. IIe replaces T302 which obstructs the placement of the side chain of lysine residue causing BL1 to be moved creating a larger pocket.
The <scene name='79/799586/Activesite/1'>active site</scene> is pictured here and has the key amino acids highlighted. Those key amino acids are W156, D223, N155 and IIe. W156 is involved in shaping the S2 subsite for a glycine, D223 and N155 help form the pocket and shape active site. IIe replaces T302 which obstructs the placement of the side chain of lysine residue causing BL1 to be moved creating a larger pocket.

Revision as of 04:36, 3 December 2018

This Sandbox is Reserved from October 22, 2018 through April 30, 2019 for use in the course Biochemistry taught by Bonnie Hall at the Grand View University, Des Moines, IA USA. This reservation includes Sandbox Reserved 1456 through Sandbox Reserved 1470.
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Structure of PLpro

PLpro

Drag the structure with the mouse to rotate

References

[1]

  1. Kong L, Shaw N, Yan L, Lou Z, Rao Z. Structural View and Substrate Specificity of Papain-like Protease from Avian Infectious Bronchitis Virus. J Biol Chem. 2015 Mar 13;290(11):7160-8. doi: 10.1074/jbc.M114.628636. Epub 2015 , Jan 21. PMID:25609249 doi:http://dx.doi.org/10.1074/jbc.M114.628636
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