Virtuelle (Nano) Welten: PDB Molecule of the Month 50: Glycolysis

Glyceraldehyde-3-Phosphate Dehydrogenase

Halfway through glycolysis, the cell is finally ready to start extracting some energy. In the sixth and seventh steps, the cell will add a new phosphate to each of the molecules, and then use it to make two new ATP molecules. Glyceraldehyde-3-phosphate dehydrogenase takes a phosphate ion and connects it to the molecule. In the process, it also extracts two hydrogen atoms using the hydrogen-carrier molecule NAD, colored magenta here. As mentioned on the first page, these hydrogen atoms may be used to create even more energy using aerobic pathways, or recycled in several ways back onto the broken sugar molecule.

Glyceraldehyde-3-phosphate dehydrogenase is composed of four identical subunits. Many of the structures of this enzyme in the PDB, such as the human form shown here on the left from PDB entry 3gpd, have NAD bound in all four active sites, as well as two phosphate or sulfate ions. One ion is bound in the site occupied by the phosphate group in the sugar molecule, and the other is thought to correspond to the site that positions the incoming phosphate ion for the reaction. PDB entry 1nqo captures the first step in the reaction, when the substrate molecule binds. A nearby cysteine amino acid will then attack the molecule, forming a bond with one carbon atom. The bond is then broken when the phosphate is attached. In this structure, the cysteine is changed to a less active serine to allow study. A nearby histidine also assists in the reaction.

When you are looking at the 1nqo structure, be sure to download the proper biological unit. The primary PDB file contains four chains, but they are not the proper biological tetramer.

The Glycolytic Enzymes

Glyceraldehyde-3-Phosphate Dehydrogenase