Function of your protein
The protein of interest is the enzyme from Picrophilus torrid, a thermoacidophilic archaeon. The MBD enzyme is an essential intermediate of the mevalonate (MVA) pathway, specifically as a catalytic enzyme in the MBD reaction. The function of MBD is to catalyze the removal of the phosphate group from the 3rd carbon of mevalonate 3,5-bisphosphate (MVA3,5BP). The enzyme also accompanies the decarboxylation of the substrate. MBD acts upon MVA3,5BP to produce isopentenyl phosphate (IP), PO4, and CO2 in the MBD reaction.
Biological relevance and broader implications
The MVA pathway is an essential metabolic pathway and a significant source of intermediates for the biosynthesis of isoprenoids in archaeal organisms. Isoprenoids are the most prominent family of natural compounds, with over 80,000 chemicals. By understanding the effects of the MBD enzyme and the corresponding homologous enzymes in the MVA pathway, scientists can better understanding the evolutionary route the metabolic pathway took and its regulatory functions. Through mutagenesis of MBD, scientists were able to evaluate the catalytic importance of essential amino acids amongst homologous enzymes in other MVA pathways that emerged from divergent evolution. More research will only provide more insight into how the pathway has evolved.
Important amino acids
The in the MBD enzyme is called and is located within subunit A. OLA is hydrogen bonded to . In addition to the hydrogen bonding between OLA and Arg128, OLA is also hydrogen bonded to a water molecule which is hydrogen bonded to Arg128. Amino acids residue aspartate is essential for catalytic activity and protein stability. When is replaced, the enzyme experiences a complete loss of MBD activity. The internal surface of the ligand binding cavity consists of mostly non-polar amino acids. The cavity opening is primarily polar amino acids, such as .
Structural highlights
The MBD protein is composed of alpha helix, parallel and anti-parrallel beta sheet, and random coils. The protein consists of two major subunits with a 60% alpha helixes and 40% beta sheets when viewing the tertiary . The alpha helixes and beta sheets within each individual subunit loop and fold to form a . The two subunits of the protein are homodimers, containing essentially identical alpha helixes and beta sheets between the two subunits, with intermolecular forces such as hydrogen bonds connecting them. The proteins contains both polar and non-polar amino acid, making the protein . The MBD enzymes is noted to have evolved from the ATP-depedent PMD enzyme where it lost its ability to bind to kinase and became ATP-indepedent. This belief is supported by the discovery that the MBD enzyme's ligand binding site overlaps with the ATP binding site observed in its homologous enzyme, DMD.
