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Sandbox Reserved 1693

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Revision as of 05:25, 3 December 2021

This Sandbox is Reserved from 10/01/2021 through 01/01//2022 for use in Biochemistry taught by Bonnie Hall at Grand View University, Des Moines, USA. This reservation includes Sandbox Reserved 1690 through Sandbox Reserved 1699.

To get started:

Click the edit this page tab at the top. Save the page after each step, then edit it again.
show the Scene authoring tools, create a molecular scene, and save it. Copy the green link into the page.
Add a description of your scene. Use the buttons above the wikitext box for bold, italics, links, headlines, etc.

More help: Help:Editing

==L-rhamnose-a-1,4-D-glucuronate lyase

This is a default text for your page Sandbox 1677. Click above on edit this page to modify. Be careful with the < and > signs.

You may include any references to papers as in: the use of JSmol in Proteopedia ^[1] or to the article describing Jmol ^[2] to the rescue.

1 Function of your protein
2 Biological relevance and broader implications
3 Important amino acids
4 Structural highlights
5 Other important features

Function of your protein

The protein, L-rhamnose-a-1,4-D-glucuronate lyase, is an enzyme from the fungus Fusarium oxysporum 12S (FoRham1) that potentially naturally breaks down and degrades Gum Arabic (GA) by releasing the Rha caps found on the non-reducing ends of GA. According to the study, little is known about GA carbohydrate structure, so this study is being used to understand more about how to degrade/function of GA. I chose to specifically look at the mutant H105F Rha-GlcA ligand which has a PDB file: 7ESN. A colored image of this can be seen (For Reference N-5' = Blue, C-3' = Red)

Biological relevance and broader implications

Important amino acids

Amino acids His85, Tyr150, Arg166, Ser170, Arg220, Pro223, Asn275, Arg331 are important in ligand to protein interaction. . ^[3]

His 85 and Tyr 150 are two amino acids that form hydrogen bonds with the Rha sugar, and His 85 proved to be a key amino acid in the catalytic reaction that divides the Rha-GlcA complex in the binding pocket during the reaction. His 105 showed to form a stabilizing hydrogen bond with His 85, reinforcing the catalytic importance of His 85.

Structural highlights

Secondary Structural Highlights - I found that there are lot of long antiparallel beta sheets in the protein (approx. 30 Beta sheets). I also observed that there was one larger alpha helix, with two smaller hydrophobic helices in the protein structure. This could mean that the protein is very stable, as antiparallel sheets provide more structure stabilization compared to parallel beta sheets. This is all due to how Hbonding between backbones occur. I also have observed that many of the beta sheets are formed of polar amino acids, which plays a role in how the protein folds.

Other important features

This is a sample scene created with SAT to by Group, and another to make of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

References

↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644
↑ Kondo T, Kichijo M, Maruta A, Nakaya M, Takenaka S, Arakawa T, Fushinobu S, Sakamoto T. Structural and functional analysis of gum arabic l-rhamnose-alpha-1,4-d-glucuronate lyase establishes a novel polysaccharide lyase family. J Biol Chem. 2021 Jul 22:101001. doi: 10.1016/j.jbc.2021.101001. PMID:34303708 doi:http://dx.doi.org/10.1016/j.jbc.2021.101001

Retrieved from "http://52.214.119.220/wiki/index.php/Sandbox_Reserved_1693"

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 == Important amino acids==
-Amino acids His85, Tyr150, Arg166, Ser170, Arg220, Pro223, Asn275, Arg331 are important in ligand to protein interaction. <scene name='89/892736/Key_amino_acids/1'>Active Site Amino Acids Highlighted Here (Blue highlighted atoms are amino acids listed.)</scene>.
+Amino acids His85, Tyr150, Arg166, Ser170, Arg220, Pro223, Asn275, Arg331 are important in ligand to protein interaction. <scene name='89/892736/Key_amino_acids/1'>Active Site Amino Acids Highlighted Here (Blue highlighted atoms are amino acids listed.)</scene>. <ref>PMID:34303708</ref>
-His 85 and Tyr 150 are two amino acids that form hydrogen bond with the Rha sugar and His 85 proved to be a key amino acid in the catalytic reaction that separates the Rha-GlcA complex in the binding pocket. His 105 showed to form a stabilizing hydrogen bond with His 85, reinforcing the catalytic importance of His 85. <ref>PMID:34303708</ref>
+His 85 and Tyr 150 are two amino acids that form hydrogen bonds with the Rha sugar, and His 85 proved to be a key amino acid in the catalytic reaction that divides the Rha-GlcA complex in the binding pocket during the reaction. His 105 showed to form a stabilizing hydrogen bond with His 85, reinforcing the catalytic importance of His 85.
 == Structural highlights ==
 Secondary Structural Highlights -

Sandbox Reserved 1693

From Proteopedia

Revision as of 05:25, 3 December 2021

Contents

Function of your protein

Biological relevance and broader implications

Important amino acids

Structural highlights

Other important features

References

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