Sandbox Reserved 781
From Proteopedia
| This Sandbox is Reserved from Oct 10, 2013, through May 20, 2014 for use in the course "CHEM 410 Biochemistry 1 and 2" taught by Hanna Tims at the Messiah College. This reservation includes Sandbox Reserved 780 through Sandbox Reserved 807. |
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Introduction
Phosphoglycerate kinase or PGK (seen to the right) is a major enzyme in glycolysis, the cycle which breaks down glucose into pyruvate, and generates 2 NADH and 2 ATP molecules. PGK is the 7th enzyme in this cycle, and it catalyzes the reaction of 1,3-bisphosphoglycerate and ADP into 3-phosphoglycerate and ATP. This reaction occurs through a nucleophilic substitution (Sn2) mechanism between ADP and one of the phosphate groups on 1,3-bisphosphoglycerate. A phosphate group is transferred from 1,3-bisphosphoglycerate to ADP making ATP. PGK is one of only two enzymes in glycolysis that generate ATP. PGK is a monomeric enzyme with two distinct domains, containing 417 residues and weighing approximately 45kD.
Structure
The of phosphoglycerate kinase can be seen here, with the bound ligands in the center. The secondary structure of this enzyme consists of (in cyan) and shown in orange.
The that stabilize the proteins backbone are highlighted in purple. The angle of the H-bonds in the beta sheets can indicate whether they are parallel or anti-parallel sheets. Straight H-bonds occur in anti-parallel sheets while H-bonds that are at an angle occur in parallel sheets. This enzyme has mostly parallel sheets with a few anti.
The can be seen here labeled in gray. And the can be seen here in pink. You can see that the hydrophilic residues mostly line the surface of the enzyme, while the hydrophobic residues are stuffed on the inside, to minimize unwanted interactions. The of hydrophobics (red) and hydrophilics (blue) show that the hydrophilic molecules are on the outer layer of the protein.
Water molecules are usually tightly bound to enzymes, you can see where the water molecules (blue) access phosphoglycerate kinase. You can also see the ligand shown in green, which is interacting with many water molecules. The water molecules mostly surround the surface of the protein (stabilizing the hydrophilic residues), while there are few water molecules in the middle of the domains.
The ADP and 3-phosphoglycerate (green) are shown surrounded by certain residues. Residues shown in blue are cationic (+) and red are anionic (-). You can see that the cationic residues surround phosphoglycerate stabilizing it inside the active site.
The residues in the active site can be seen highlighted in gold.
