Sandbox Reserved 1693
From Proteopedia
(Difference between revisions)
| Line 8: | Line 8: | ||
The protein, L-rhamnose-a-1,4-D-glucuronate lyase, is an enzyme from the fungus Fusarium oxysporum 12S that naturally breaks down and degrades Gum Arabic (GA) by releasing the Rha caps found on the non-reducing ends 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 <scene name='89/892736/Protein_with_ligand_view_1/5'> here</scene>(For Reference N-5' = Blue, C-3' = Red) | The protein, L-rhamnose-a-1,4-D-glucuronate lyase, is an enzyme from the fungus Fusarium oxysporum 12S that naturally breaks down and degrades Gum Arabic (GA) by releasing the Rha caps found on the non-reducing ends 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 <scene name='89/892736/Protein_with_ligand_view_1/5'> here</scene>(For Reference N-5' = Blue, C-3' = Red) | ||
| - | The enzyme in this study, FoRham1 is a mutant Rha-releasing enzyme that specifically uses a-L-rhamnose-a-1,4-D-glucuronic acid (Rha-GlcA) as a substrate.<ref>PMID:34303708</ref> The mechanism provided in the literature shows FoRham1 removing the Rha cap from the GlcA, producing Rha sugar and GA as products. By doing this, scientist hope to be able get a better understanding of GA structure and characteristics to then advance its usefulness to society. | + | The enzyme in this study, FoRham1 is a mutant Rha-releasing enzyme that specifically uses a-L-rhamnose-a-1,4-D-glucuronic acid (Rha-GlcA) as a <scene name='89/892736/Highlighted_rha-glca-yellow/1'>substrate</scene>.<ref>PMID:34303708</ref> The mechanism provided in the literature shows FoRham1 removing the Rha cap from the GlcA, producing Rha sugar and GA as products. By doing this, scientist hope to be able get a better understanding of GA structure and characteristics to then advance its usefulness to society. |
== Biological relevance and broader implications == | == Biological relevance and broader implications == | ||
According to scientific literature, little is known about GA carbohydrate structure. This study is being used to understand more about the degradation/function of GA, as there is no known enzyme that can completely degrade GA. Although GA structure has been studied significantly with the use of chemical methods such as NMR and methylation, a detailed structure has not been produced as it is a complex branched polysaccharide. | According to scientific literature, little is known about GA carbohydrate structure. This study is being used to understand more about the degradation/function of GA, as there is no known enzyme that can completely degrade GA. Although GA structure has been studied significantly with the use of chemical methods such as NMR and methylation, a detailed structure has not been produced as it is a complex branched polysaccharide. | ||
| Line 14: | Line 14: | ||
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> | 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 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. | + | 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 == | == Structural highlights == | ||
Secondary Structural Highlights - | Secondary Structural Highlights - | ||
Revision as of 21:56, 8 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:
More help: Help:Editing |
==L-rhamnose-a-1,4-D-glucuronate lyase
| |||||||||||
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
- ↑ 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
