Sandbox Reserved 1692

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Revision as of 04:47, 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.

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Structure and Function of FoRham1

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

This enzyme, L-rhamnose- α-1,4-D-glucuronate lyase (FoRham1), is derived from the fungus Fusarium oxysporum and is a helpful tool for determining the structure and function of Gum Arabic (GA) to create potential agents to degrade GA more effectively. When the substrate GA is bound to FoRham1, the nonreducing ends of the glycosidic linkages are broken, releasing L-rhamnose (Rha) caps from GA.^[1] Enzymes that can react with glycosidic linkages of certain carbohydrates can be useful in determining the structure, function, and mechanism of the carbohydrates, giving scientists the tools to manipulate their physical properties for further application to understand their breakdown. Determining this mechanism will give researchers more tools to understand how to degrade GA. Specifically, I focused on the mutant H105F, which has a PDB file of 7ESN. Shown here is the enzyme using N->C coloring.

Biological relevance and broader implications

Gum Arabic (GA) is a representative protein of the family of arabinogalactan proteins (AGPs) and is produced in acacia trees in response to stress conditions, such as drought or wounds. GA has a variety of applications within the industrial world, including the food, cosmetic, and pharmaceutical industries, acting specifically as an emulsion stabilizer, emulsifier, and thickener in pharmaceutical settings. However, the the detailed structure of GA has not determined because of the complex branching that occurs in the polysaccharide. Enzymes that can react with and eliminate glycosidic linkages of carbohydrates are useful for determining the structure and function of these carbohydrates, giving researchers the opportunity to modify their physical properties. To date, there are no enzymes that have completely degraded GA. ^[1]

Important amino acids

Amino Acids provide important interactions for binding in the active site. The side chain, providing stabilizing assistance. ^[1].

Amino Acid Residues form a hydrogen bond with the O-1 atom of Rha, suggesting these residues play a catalytic role for the elimination reaction.

The image to the right shows important amino acids in the active site. Hydrogen bonding and pi-stacking interactions are indicated by the blue and black circles, respectively.

Structural highlights

Secondary Structure: In this enzyme, there are around and three small . The anti-parallel beta sheets provide further stabilization, through strong hydrogen bonding in the backbone, of the enzyme compared to parallel beta sheets. The hydrophobic alpha helices provide structure for the formation of the active site. Here, acts as a catalytic residue that aids in the binding of GA into the active site. Provided is the protein structure in space fill. This structure representation depicts the depths of the active site, showing how tightly bound the ligand is to the enzyme. This representation also shows what size molecule fit into the active site, giving scientists an idea of other similar-sized ligands that may also fit into this binding pocket. Tan represents the enzyme, green represents the ligands, and pink represents the solvent.

Other important features

The structure of FoRham1 consists of a , providing a favorable conformation for the substrate binding into the active site, which is located on the anterior of t

References

↑ ^1.0 ^1.1 ^1.2 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

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 The image to the right shows important amino acids in the active site. Hydrogen bonding and pi-stacking interactions are indicated by the blue and black circles, respectively.
 == Structural highlights ==
-Secondary Structure: In this enzyme, there are around <scene name='89/892735/Beta_sheets/3'>30 anti-parallel beta sheets</scene> and three small <scene name='89/892735/Helices/1'>alpha helices</scene>. The anti-parallel beta sheets provide further stabilization, through strong hydrogen bonding in the backbone, of the enzyme compared to parallel beta sheets. The hydrophobic alpha helices provide structure for the formation of the active site. The structure of FoRham1 consists of a seven-bladed, Beta sheet-propellor domain that contributes to the shape and overall interactions with the active site, which is located on the anterior side of the enzyme. Here, <scene name='89/892735/His48/1'>His48</scene> acts as a catalytic residue that aids in the binding of GA into the active site.
+Secondary Structure: In this enzyme, there are around <scene name='89/892735/Beta_sheets/3'>30 anti-parallel beta sheets</scene> and three small <scene name='89/892735/Helices/1'>alpha helices</scene>. The anti-parallel beta sheets provide further stabilization, through strong hydrogen bonding in the backbone, of the enzyme compared to parallel beta sheets. The hydrophobic alpha helices provide structure for the formation of the active site. Here, <scene name='89/892735/His48/1'>His48</scene> acts as a catalytic residue that aids in the binding of GA into the active site.
 Provided <scene name='89/892735/Spacefill/1'>here</scene> is the protein structure in space fill. This structure representation depicts the depths of the active site, showing how tightly bound the ligand is to the enzyme. This representation also shows what size molecule fit into the active site, giving scientists an idea of other similar-sized ligands that may also fit into this binding pocket. Tan represents the enzyme, green represents the ligands, and pink represents the solvent.
 == Other important features ==
-This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.
+The structure of FoRham1 consists of a <scene name='89/892735/Beta_propeller/4'>seven-bladed Beta-propellor domain</scene>, providing a favorable conformation for the substrate binding into the active site, which is located on the anterior of t
 </StructureSection>
 == References ==
 <references/>

Sandbox Reserved 1692

From Proteopedia

Revision as of 04:47, 8 December 2021

Structure and Function of FoRham1

Contents

Function of your protein

Biological relevance and broader implications

Important amino acids

Structural highlights

Other important features

References

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