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From Proteopedia

Phosphofructokinase

is a regulatory enzyme that is involved in glycolysis. The particular reaction that it carries out is the catalysis of fructose-6-phosphate to fructose-1,6- bisphosphate via phosphorylation. The phosphofructokinase that is discussed on this page comes from the microbe Listeria innocua. At the center you can see that the phosphofructokinase is bound to a molecule of ATP. In addition, the three green balls represent the three Mg atoms, and the small grey and red group off to the side is the glycerol.

The secondary structure is comprised of . The alpha helices are in yellow and the beta sheets are in grey.

is a very important part of a proteins structure and stability. The hydrogen bonds of phosphofructokinase are designated by the orange dotted lines throughout the structure. Phosphofructokinase contains both anti-parallel and parallel sheets, which are identified by parallel hydrogen bonds and angled hydrogen bonds respectively.

One of the most important determining factors of protein structure lies in the interactions of the with the surrounding environment. The hydrophobic residues are designated with light green while the hydrophobic residues are shown in blue. As would be expected the majority of the hydrophobic residues are located at the center of the protein where they are shielded from the hydrophobic environment.

As previously mentioned, the hydrophobic interactions are critical in determining the protein structure. Here, the show that the water molecules predominantly gather around the outside of the protein, which is where most of the hydrophilic residues lie.

Looking at this phosphofructokinase you can see that the are located around both the ATP and the glycerol. The residues around the glycerol, represented in yellow, are lysine, arginine, histidine, and aspartic acid. These particular residues would be expected because they are all charged and polar, which would be ideal for interacting with glycerol (green) which is a polar molecule. The residues around ATP, in teal, are serine, lysine, and glutamic acid. These residues would also be expected because they are polar and would interact well with the polar ATP (which is in pink). In addition, the catalytic residues are represented in orange.

Taking a further look into the active site of the protein, one can see that phosphofructokinase contains (represented in pink), two glycines, one aspartic acid, and one alanine. The rest of the ligand binding residues are represented in yellow. This particular placement of catalytic residues is to be expected because it allows the catalytic residues to have direct contact with the ligand (the green ATP), thus enabling the reaction to proceed at a faster rate via a catalytic mechanism.