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Function of your protein

MqnA is a chorismate dehydratase that has been studied in Streptomyces coelicolor. MqnA is important because it catalyzes the initial step in the biosynthesis of menaquinone via the futalosine pathway. MqnA folds like a venus flytrap and binds to Without the venus flytrap folding, the protein would be unable to access the binding site. Products of ScMqnA include 3-EPB and the presumed hydrolysis product, 3,4-dihydroxycyclohexa-1,5-dienoate (3,4-CHD). Menaquinone (MqnA) is of importance to study because it helps make molecules for the electron transport chain.

Biological relevance and broader implications

MqnA is important because it catalyzes the biosynthesis of menaquinone, which is an important player in the electron transport chain. According to Prasad et al. (2022), "Menaquinone serves as an electron carrier in the electron transport chain. Although some prokaryotes utilize ubiquinone solely, mycobacteria and most gram-positive bacteria produce menaquinone exclusively, and many gram-negative bacteria such as Escherichia coli switch from ubiquinone to menaquinone when grown under anaerobic conditions. In humans, menaquinone (vitamin K2) acts as a cosubstrate in the carboxylation of glutamic acids that leads to the activation of proteins" that are considered "essential." Mutations may affect the supply of electron carriers in the electron transport chain, which could negatively affect and possibly kill the organism with the mutation. In humans, blood coagulation, control of cell growth, apoptosis, signal transduction, and calcium metabolism may all be affected by mutations. It is important to study MqnA because the production and availability of menaquinone is important not just for humans, but for bacteria and other prokaryotes as well. We must obtain menaquinone through our diets, so it is important that we understand the science behind our menaquinone sources and how they could possibly be affected by MqnA.

Important amino acids

Amino acids involved in the catalytic triad for MqnA include N17, S86, and Y242. Other amino acids that help bind the main ligand through hydrophobic interactions include I13, N17, V18, P41, E42, V58, V84, S86, C87, S109, R110, T111, S112, I150, G151, F186, and Y242. A view of the catalytic triad is shown with red representing each amino acid within the catalytic triad.

Structural highlights

In terms of secondary structure, MqnA has both alpha helices and beta sheets present. In this , 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 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 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 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.