Sandbox Reserved 1690
From Proteopedia
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== Function of your protein == | == Function of your protein == | ||
| - | This is a picture of my protein 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- | + | 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 | rhamnose-(1→4)-D-glucuronic acid (Rha–GlcA) present in GA side chains to release Rha through | ||
an anomer-retaining mechanism” (Kondo). | an anomer-retaining mechanism” (Kondo). | ||
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== Important amino acids== | == 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 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 == | ||
| + | <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 == | == Other important features == | ||
<scene name='89/892733/Active_site_of_protein/1'>Asn247 with full structure</scene> | <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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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
