Sandbox Reserved 1805

This Sandbox is Reserved from Mar 1 through Jun 1, 2023 for use in the course CHEM 351 Biochemistry taught by Bonnie_Hall at the Grand View University, Des Moines, USA. This reservation includes Sandbox Reserved 1796 through Sandbox Reserved 1811.

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MqnA Structure

spinqualitylabelsall models Caption for this structure Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D This is a default text for your page '. Click above on edit this page' to modify. Be careful with the < and > signs. You may include any references to papers as in: the use of JSmol in Proteopedia or to the article describing Jmol to the rescue. 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 its substrate (chorismate) via its ligand. 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 (2). In humans, menaquinone (vitamin K2) acts as a cosubstrate in the carboxylation of glutamic acids that leads to the activation of proteins essential for blood coagulation, control of cell growth, apoptosis, signal transduction, and calcium metabolism." Additionally, understanding the venus flytrap folding structure of this enzyme helps us understand the binding sites of similar enzymes. 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 just the ligan is shown Structural highlights In terms of secondary structure, MqnA has both alpha helices and beta sheets present. In this image, 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 tertiary 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. 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 quaternary structure shows how closely packed the amino acids are, leaving little to no access without the venus flytrap fold. This is a sample scene created with SAT to color by Group, and another to make a transparent representation of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.