From Proteopedia

Glyceraldehyde-3-phosphate dehydrogenase

Introduction and Basic Structure

Glyceraldehyde-3-phosphate dehydrogenase, or more commonly called, , is a tetrahedral protein. The specific enzyme being used is Human Placental Glyceraldehyde-3-Phosphate Dehydrogenase, which is found in humans. G-3-P is an enzyme used in glycolysis to produce NADH through a mechanism with phosphate and NAD+, which binds to the ligand binding site of G-3-P. The G-3-P is converted to 3-phospho-D-glyceroyl-phosphate. The has both alpha helices (purple) and beta sheets (green). The alpha helices are in four separate sections, but are mostly on the external sections of the enzyme. The beta sheets are closer to the center of the enzyme. The shows a more accurate representation of what this enzyme looks like.

Bonding

The are colored in orange. Based on the amount of the thin orange lines, it is clear that there are many hydrogen bonds. However, there are no within the structure, or they would have been highlighted in green. The only special binding in the G-3-P enzyme is the hydrogen bonding. Looking at the structure with the highlights the structure of the beta sheets. When the beta sheets are parallel, the hydrogen bonds are strained at an angle. In the anti-parallel sheets, the bonding is less strained so the hydrogen bonds are perpendicular to beta sheets. The image shows that majority of the beta sheets are parallel in structure, but there are a few anti-parallel sections of the beta sheets.

Residues

The are shown in grey. The are shown in royal blue. The hydrophobic residues are on the internal part of the enzyme while the hydrophilic sections surround the hydrophobic residues. The hydrophilic resides on the outside of the enzyme will increase interaction with the surrounding aqueous solvent.

Solvent

The enzyme is typically surrounded by a solvent, like ,shown here in light purple. The waters attached to chain Q are highlighted. Looking at their interaction with the enzyme, it is obvious that they are restricted to the outside of the enzyme. When looking at how the water interacts with the , the interactions are the same. Since outside contains the hydrophilic residues that interact more readily with water, the water is limited to the surface of the molecule. The interior contains the hydrophobic residues, which are unfavorable to have interacting with water. Therefore, no waters are in the middle where the hydrophobic residues are. The water is evenly distributed over the outside of the enzyme.

Cofactor and Cofactor Contacts

The sections in the entire molecule are highlighted while the rest of the molecule is a light green. The different colors in the cofactor binding sites indicate the charges present. The blue indicates a positive charge and the red indicates a negative charge. There are only three cofactor binding sites in the enzyme. Looking at the P chain, the is shown. Within each cofactor binding site, is present. This is the only molecule that is ever bound in the site. As seen in the P chain, the cofactor site includes more than just NAD. The NAD binds to other . The NAD is colored purple and the residues are in green. It is bound to asparagine, isoleucine, arginine, another arginine, and aspartic acid. Of the five amino acids that NAD is bound to, four are polar, which makes them more favorable to bind to the cofactor site.

Catalytic Residues

G-3-P has two types , shown in purple. They are Cysteine 152 and Histidine 179. Each chain only has one of each catalytic residue. They are near the NAD binding site (shown in green). These residues assist in the binding of NAD to the cofactor site.