Sandbox Reserved 1690
From Proteopedia
(Difference between revisions)
(New page: {{Sandbox_Reserved_BHall_F21}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --> ==Your Heading Here (maybe something like 'Structure')== <StructureSection load='1stp' size='340' side='right' cap...) |
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| - | {{Sandbox_Reserved_BHall_F21}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --> | + | <scene name='89/892733/Active_site_of_protein/1'>Text To Be Displayed</scene><scene name='89/892733/Proposed_ligand/1'>Text To Be Displayed</scene><scene name='89/892733/View_of_our_protein/1'>Text To Be Displayed</scene>{{Sandbox_Reserved_BHall_F21}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --> |
==Your Heading Here (maybe something like 'Structure')== | ==Your Heading Here (maybe something like 'Structure')== | ||
| - | <StructureSection load=' | + | <StructureSection load='7ESN' size='340' side='right' caption='Caption for this structure' scene=''> |
| - | This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the < and > signs. | + | 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 <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue. | You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue. | ||
| - | == Function == | + | == Function of your protein == |
| + | This is a picture of my protein, L-rhamnose-alpha-1,4-D-glucuronate lyase, with The Ligand highlighted as shown. Our protein’s main function is to degrade GA and can be found in Fusarium oxysporum, a phytopathogenic fungus that uses GA as the sole carbon source for growth. It “hydrolyzes the glycosidic linkages of α-L- | ||
| + | rhamnose-(1→4)-D-glucuronic acid (Rha–GlcA) present in GA side chains to release Rha through | ||
| + | an anomer-retaining mechanism” (Kondo). | ||
| + | == Biological relevance and broader implications == | ||
| + | Understanding the function and mechanism of this protein will allow us to create a solid foundation in the future for carbohydrate-related enzymes. This can eventually lead to using this enzyme's mechanism and target for medicinal advancement to help treat Batten's disease, which can cause death from the inability to excrete waste from the body via the form of lipids and proteins. The information obtained by this study associated with it will tell us more about the metabolic activity of the enzyme, which will allow us to use its properties for "elucidating its physiological function in plants" (Kondo) | ||
| - | == | + | == Important amino acids== |
| - | + | I have included a picture of my <scene name='89/892733/Proposed_ligand/2'>Proposed Ligand</scene> here. The catalytic triad of my active site include the amino acids . Additionally, it was concluded that His48 was considered the catalytic residue of the active site. which switches to Q with mutations in the organism that causes death. I have included a list of the important interactions in the active site that are not as major as the active site interactions. | |
| - | + | H- bond to Ser170 | |
| + | H-bond to Arg220 | ||
| + | H-bond to Pro223 | ||
| + | H-bond to Arg166 | ||
| + | H-bond to Tyr15 | ||
| + | However, the article explains that His48 is the catalytic amino acid for the mechanism of this reaction. | ||
== Structural highlights == | == Structural highlights == | ||
| + | <scene name='89/892733/Spacefill_model/1'>Spacefill Model</scene> | ||
| + | <scene name='89/892733/Hydrophobicity_view/1'>Hydrophobicity View</scene>\ | ||
| + | The hydrophobic regions of the protein are extremely important to the mechanism of this protein as the reaction is dependent on the hydrogen bonding taking place at the active site. | ||
| + | <scene name='89/892733/Sheet_structure/1'>Secondary Structures Highlighted</scene> | ||
| + | <scene name='89/892733/His48_shown_in_black/1'>His48 in black in position</scene> | ||
| + | <scene name='89/892733/His85_near_active_site/1'>His85 placement in relation to the protein structure</scene> | ||
| + | == Other important features == | ||
| - | + | <scene name='89/892733/Active_site_of_protein/1'>Asn247 with full structure</scene> | |
| + | This Asn provides hydrogen bonding for the structure. | ||
| + | <scene name='89/892733/Carbohydrate_positioning/1'>Carbohydrate positioning in protein</scene> | ||
</StructureSection> | </StructureSection> | ||
== References == | == References == | ||
<references/> | <references/> | ||
Current revision
| 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. |
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Your Heading Here (maybe something like 'Structure')
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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
