Sandbox Reserved 1805: Difference between revisions
From Proteopedia
Jump to navigationJump to search
No edit summary |
No edit summary |
||
| (5 intermediate revisions by the same user not shown) | |||
| Line 16: | Line 16: | ||
== Structural highlights == | == Structural highlights == | ||
In terms of secondary structure, MqnA has both alpha helices and beta sheets present. In this <scene name='95/954102/Secondary_structure/1'>image</scene>, alpha helices are shown in red and beta sheets are shown in yellow. In our enzyme, there are two distinct lobes. These lobes are connected by linkers. Connected to the linkers on either lobe are beta sheets, followed by alpha helices. In terms of <scene name='95/954102/Tertiary1/1'>tertiary structure</scene> and quaternary structure, we see two distinct lobes present in MqnA. In the image, it is clear just how much space is occupied by the atoms, making our catalytic triad tucked away and hidden. Alpha helices are represented in pink, beta sheets are represented in yellow, and coils are represented in white. This demonstrates the importance of the venus flytrap fold that exposes our ligand for binding. Its change in conformation is absolutely vital for its function. The tertiary structure (folded protein structure) is held together by side chain interactions, such as that between SER108 and ARG111 on MqnA. The <scene name='95/954102/Tertiary_structure/1'>quaternary structure</scene> shows how closely packed the amino acids are, leaving little to no access when the ligand is bound. In addition, it is important to note the hydrophobic and polar aspects of the MqnA enzyme shown <scene name='95/954102/Hydrophobicpolar/1'>here.</scene> The color purple represents the polar portions of the enzyme, while grey areas represent hydrophobicity within the enzyme. Furthermore, the grey areas have hydrophobic interactions occurring while purple areas have polar interactions occurring, leading to the tightly folded enzyme. | In terms of secondary structure, MqnA has both alpha helices and beta sheets present. In this <scene name='95/954102/Secondary_structure/1'>image</scene>, alpha helices are shown in red and beta sheets are shown in yellow. In our enzyme, there are two distinct lobes. These lobes are connected by linkers. Connected to the linkers on either lobe are beta sheets, followed by alpha helices. In terms of <scene name='95/954102/Tertiary1/1'>tertiary structure</scene> and quaternary structure, we see two distinct lobes present in MqnA. In the image, it is clear just how much space is occupied by the atoms, making our catalytic triad tucked away and hidden. Alpha helices are represented in pink, beta sheets are represented in yellow, and coils are represented in white. This demonstrates the importance of the venus flytrap fold that exposes our ligand for binding. Its change in conformation is absolutely vital for its function. The tertiary structure (folded protein structure) is held together by side chain interactions, such as that between SER108 and ARG111 on MqnA. The <scene name='95/954102/Tertiary_structure/1'>quaternary structure</scene> shows how closely packed the amino acids are, leaving little to no access when the ligand is bound. In addition, it is important to note the hydrophobic and polar aspects of the MqnA enzyme shown <scene name='95/954102/Hydrophobicpolar/1'>here.</scene> The color purple represents the polar portions of the enzyme, while grey areas represent hydrophobicity within the enzyme. Furthermore, the grey areas have hydrophobic interactions occurring while purple areas have polar interactions occurring, leading to the tightly folded enzyme. | ||
== Other Important Features == | |||
MqnA is a homodimer composed of two molecules connected by linkers that lead to beta sheets which then lead to alpha helices. This structure drives function by allowing it to maintain its specific venus flytrap fold conformation when bound to the ligand. Finally, when considering the main product of the reaction, 3-EPB it is important to know that the substrate's binding site is only partially occupied in the less ordered orthorhombic chain A, suggesting that 3-EPB binding draws residues of lobe 2 toward the active site." Orthorhombic chain A also had less electron density, meaning it could take more than one conformation. | |||
</StructureSection> | </StructureSection> | ||
== References == | == References == | ||
< | <ref>9672406</ref> | ||
