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From Proteopedia

Introduction

Phosphoglycerate kinase is an enzyme found in glycolysis. Glycolysis is used to break down sugar molecules such as glucose and yields pyruvate. Phosphoglycerate kinase plays an important role in this process. Phosphoglycerate kinase's role in glycolysis is to transfer a phosphate from 1,3-bisphosphate to ADP yielding ATP and 3-phosphoglycerate (3PG). Without phosphoglycerate kinase, one would not be able to digest sugars and produce ATP from them. Phosphoglycerate kinase is composed of a monomer subunit made up of 417 amino acids. It's secondary structure contains alpha helices and beta sheets. Phosphoglycerate kinase is important because it aids in producing ATP without the use of oxygen.

Secondary Structure

The of phosphoglycerate kinase is shown with it's containing alpha helices (purple) and beta sheets (green). It has the appearance of two lobes with a section in the middle connecting the two.

Phosphoglycerate kinase's are shown in orange. Majority of the hydrogen bonds are parallel. One can see the parallel hydrogen bonds by observing the alpha helices and beta sheets. The parallel conformation leads to a diagonal bond where as the antiparallel conformation leads to more straight up and down bonds. By observing the structure, one can see the diagonal bonds eluding to parallel hydrogen bonding. Disulfide bonds are not present in phosphoglycerate kinase.

The are showed in grey. Hydrophobic residues are usually found inside the protein since they dislike water interactions. The are shown in red. The hydrophilic residues are usually found on the outside of the protein since they prefer water interactions over hydrophobic residues. In this structure, the are shown in teal. The molecules are found on the outside of the protein and not found inside. This shows that the hydrophilic residues, typically found on the inside of the protein, do not interact with the water molecules, but the hydrophobic residues, typically found on the outside of the protein, do interact with the molecules.

are found in the center of this enzyme. They are represented by red and orange. The ligand are displayed in the center of the enzyme. Cationic side chains are shown in blue, and histidine side chains are displayed in light blue. Both of these types of side chains interact with the non-hydrolysable substrate. This makes sense since the ligand usually displays a negative charge which would interact with the cationic side chains. Histidine's stabilizing features allows it to interact more commonly with the non-hydrolysable substrate and essentially stabilize the ligand. In the catalytic , shown in dark blue, the active site interacts with the non-hydrolysable substrate as well. This makes sense since the active site lies right next to and intertwines with the non-hydrolysable substrate.