Sandbox GGC13
Crystal Structure of Lactate Dehydrogenase A
This is a default text for your page Sandbox GGC13. 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 [1] or to the article describing Jmol [2] to the rescue. FunctionLactate Dehydrogenase(LDH) is a large, two domain- protein which catalyzes the conversion of pyruvate to lactate under anaerobic conditions. This conversion is coupled with the reduction of NAD+ to form the electron carrying NADH. Muscular LDH is involved in the Cori Cycle where it transports newly synthesized lactate to the liver. Liver LDH converts the lactate back to pyruvate in order to provide the precursor for gluconeogenesis. DiseaseLactate dehydrogenase is found in its various isoenzyme forms throughout the body, including: brain, red blood cells, lungs, kidney, placenta, pancreas, muscle, and liver. It is kept at relatively low concentrations and is only utilized as a pathway under anaerobic conditions as it produces less ATP/glucose than oxidative phosphorylation. High levels of LDH are generally indicative of poor health. LDH translation is found to be overly expressed in pancreatic cancer and showed correlation with cell growth success rate. Increased LDH levels are also associated with conditions such as Rhabdomyolysis which is characterized by the breakdown of skeletal muscle. This is due in part to LDH in red blood cells being released through hemolysis. RelevanceStructural highlightsLactate dehydrogenase is a tetramer protein which can form five different isoenzymes. Subunits exist primarily in two isoforms: M and H, which differ in a single residue. The M subunit contains an alanine while the H subunit contains a glutamine. The combination of subunits defines which isoenzyme is formed and indicates where the enzyme will be present in the body. Lactate dehydrogenase A is composed of four M subunits. The subunits can adopt two conformations, open and closed, which determine the subunits activity. The active site contains three different binding pockets to accommodate the substrate, Nicotinamide, and adenine. The substrate binding pocket relies on heavily on hydrogen binding and ionic interactions in order to effectively bind the substrate. Upon binding, the substrate binding pocket undergoes a conformational change where interactions between the substrate or inhibitor and a glutamine residue (Q99) essentially pull the active loop closed. Close up interactions between the substrate binding pocket and the inhibitor, oxamate. The substrate active site to which oxamate is bound is in the closed conformation.
The nicotinamide and adenine binding pockets work together to successfully bind NADH. Both binding pockets implement hydrogen bonding and hydrophobic interactions with their ligand fragment. In addition to the interactions within the binding pockets, NADH is also supported by ionic forces between arginine (R99) and the pyrophosphate groups. Close up interactions between the NADH and adenine binding pockets and the cofactor, NADH.
The hydroxyl groups of NADH's ribose fragments interacts with the H-bond network created by the substrate and asparagine (N137). Simplified wireframe model displaying the inhibitor-NADH Hydrogen bond network involving asparagine.
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References
Poli, G., Granchi, C., Aissaoui, M., Minutolo, F., & Tuccinardi, T. (2017). Three-Dimensional Analysis of the Interactions between hLDH5 and Its Inhibitors. Molecules, 22(12), 2217. https://doi.org/10.3390/molecules22122217
