Phosphoglycerate Kinase
From Proteopedia
Mechanism of Phosphoglycerate Kinase(PGK) Catalysis
Phosphogylcerate kinase is a crucial enzyme of the glycolysis cycle. This cycle is a series of ten reactions which ultimately breaks down glucose into pyruvate while generating 2 NADH and 2 ATP molecules. Phosphogylcerate kinase is the seventh enzyme in the cycle which catalyzes the reaction of 1,3-Biphosphoglycerate and ADP to produce and . This method for ATP production is known as substrate level phosphorylation because it produces energy storing ATP molecules with out the use of oxygen, NADH, or an ATPase. The reaction is highly exergonic allowing it to be coupled with the less thermodynamically favored GADPH reaction of the cycle so both reactions occur spontaneously.
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| 3cin, resolution 1.70Å () | |||||||||
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| Ligands: | , , | ||||||||
| Gene: | TM1419, TM_1419 (Thermotoga maritima MSB8) | ||||||||
| Activity: | Inositol-3-phosphate synthase, with EC number 5.5.1.4 | ||||||||
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| Resources: | FirstGlance, OCA, RCSB, PDBsum, TOPSAN | ||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||
The overall structure of phosphoglycerate kinase is very distinctive. It is a monomeric protein consisting of XXXXX amino acids. The structure is distinctly bilobed with a depressed region between the two lobes or domains. The lobes/domains are clearly connected at only two locations:. The SCOP clssification of PGK is alpha and beta, indicating that its secondary strucutre is composed of roughly equal numbers alpha and beta sheets.
The bilobed structure of PGK is very crucial in its catalytic function. The active site is broken into two pieces, one on the interior of each lobe or domain. On one site the ADP-Mg2+ substrate binds and on the other lobe the 1,3-Biphosphoglycerate substrate binds. Upon binding of both substrate molecules at the active sites, the proteins conformation changes such that the two lobes of the protein swing together [1] When the two domains swing shut, a hydrophobic chamber free from water is established where the reaction can take place. The hinge for this conformational change is beta sheet L and the new conformation is formed via a salt bridge between [2]
Given that phosphoglycerate kinase is a monomeric protein standard Michealis-Menton kinetics would be expected; however, this is not the case. Multiple experiments have shown that the data, when transformed into either double-reciprocal or Eadie-Hofstee plots is non-linear; Eadie-hofstee plots curve upward. One possible explanation for the non-linearity, negative co-opertivity, is ruled out because PGK does not have multiple subunits. In one study that conducted kinetic tests with a 1000 fold range of substrates, at the highest concentrations of substrate the rate was still increasing; this puts the Km value in the 2-5mM range [3] The negatively charged oxygen of the last phosphate group on ADP nucelophillically attacks a phosphate of 1,3-phosphoglycerate. The product, ATP, is favored because it's negatively charged oxygens of the 3 phosphates form hydrogen bonds with the enzyme. The 3 hydrogen bonds of ATP is favored over the 2 hydrogen bonds of ADP.
- ↑ Voet, Donald et al. 2008. Fundamentals of Biochemistry. 3rd ed. 499
- ↑ Blake and Rice. 1981. Phosphoglycerate kinase. Philosophical Transactions of the Royal Society of London. 293:93-104.
- ↑ Scopes, Robert. 1977. The Steady State Kinetics of Yeast Phosphoglycerate Kinase. European Journal of Biochemistry. 85, 503-516. <ref> The mechanism of catalysis has not been established but must be similar to that of hexokinase. Hexokinase catalyzes the removal of a phosphate group from ATP to glucose and has a very similar structure and conformational change via a hinge. PGK has a similar function except it catalyzes the transfer of a phosphate to form ATP instead of using ATP. The reaction of PGK removes a phosphate group from the intermediate molecule, 1,3-biphosphoglycerate and transfers it to ADP to form ATP. Once the substrates bind to the active sites, the protein domains swing shut forcing the substrates into correct position for the reaction to proceed. <ref>Harnan, G. et al. 1992. Domain Motions in Phosphoglycerate Kinase: Determination of Interdomain Distance Distribution by Site Specific Labeling and Time Resolved Flourescense Energy Transfer. PNAS. 89:11764-11768.</li></ol></ref>
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