Glycogen phosphorylase

Glycogen phosphorylase is one of the phosphorylase enzymes (EC 2.4.1.1). Glycogen phosphorylase catalyzes the rate-limiting step in glycogenolysis in animals by releasing glucose-1-phosphate from the terminal alpha-1,4-glycosidic bond. Glycogen phosphorylase is also studied as a model protein regulated by both reversible phosphorylation and allosteric effects.

Phosphorylase
The crystal structure of the rabbit muscle glycogen phosphorylase-AMP complex. AMP allosteric site (yellow), phosphorylated Ser14 (orange), glycogen binding site (blue), catalytic site (red).^[1]
Identifiers
EC no.	2.4.1.1
CAS no.	9035-74-9
Databases
IntEnz	IntEnz view
BRENDA	BRENDA entry
ExPASy	NiceZyme view
KEGG	KEGG entry
MetaCyc	metabolic pathway
PRIAM	profile
PDB structures	RCSB PDB PDBe PDBsum
Gene Ontology	AmiGO / QuickGO
Search PMC articles PubMed articles NCBI proteins

Mechanism

Glycogen phosphorylase breaks up glycogen into glucose subunits (see also figure below):

(α-1,4 glycogen chain)_n + Pi ⇌ (α-1,4 glycogen chain)_n-1 + α-D-glucose-1-phosphate.^[2]

Glycogen is left with one fewer glucose molecule, and the free glucose molecule is in the form of glucose-1-phosphate. In order to be used for metabolism, it must be converted to glucose-6-phosphate by the enzyme phosphoglucomutase.

Although the reaction is reversible in vitro, within the cell the enzyme only works in the forward direction as shown below because the concentration of inorganic phosphate is much higher than that of glucose-1-phosphate.^[2]

 

Glycogen phosphorylase can act only on linear chains of glycogen (α1-4 glycosidic linkage). Its work will immediately come to a halt four residues away from α1-6 branch (which are exceedingly common in glycogen). In these situations, the debranching enzyme is necessary, which will straighten out the chain in that area. In addition, the enzyme transferase shifts a block of 3 glucosyl residues from the outer branch to the other end, and then a α1-6 glucosidase enzyme is required to break the remaining (single glucose) α1-6 residue that remains in the new linear chain. After all this is done, glycogen phosphorylase can continue. The enzyme is specific to α1-4 chains, as the molecule contains a 30-angstrom-long crevice with the same radius as the helix formed by the glycogen chain; this accommodates 4-5 glucosyl residues, but is too narrow for branches. This crevice connects the glycogen storage site to the active, catalytic site.

Glycogen phosphorylase has a pyridoxal phosphate (PLP, derived from Vitamin B₆) at each catalytic site. Pyridoxal phosphate links with basic residues (in this case Lys680) and covalently forms a Schiff base. Once the Schiff base linkage is formed, holding the PLP molecule in the active site, the phosphate group on the PLP readily donates a proton to an inorganic phosphate molecule, allowing the inorganic phosphate to in turn be deprotonated by the oxygen forming the α-1,4 glycosidic linkage. PLP is readily deprotonated because its negative charge is not only stabilized within the phosphate group, but also in the pyridine ring, thus the conjugate base resulting from the deprotonation of PLP is quite stable. The protonated oxygen now represents a good leaving group, and the glycogen chain is separated from the terminal glycogen in an S_N1 fashion, resulting in the formation of a glucose molecule with a secondary carbocation at the 1 position. Finally, the deprotonated inorganic phosphate acts as a nucleophile and bonds with the carbocation, resulting in the formation of glucose-1-phosphate and a glycogen chain shortened by one glucose molecule.

There is also an alternative proposed mechanism involving a positively charged oxygen in a half-chair conformation.^[3]

 

Structure

The glycogen phosphorylase monomer is a large protein, composed of 842 amino acids with a mass of 97.434 kDa in muscle cells. While the enzyme can exist as an inactive monomer or tetramer, it is biologically active as a dimer of two identical subunits.^[4]

 

R and T States of Glycogen Phosphorylase b Tower Helices, on the left and right respectively. Note the relative positioning of the central tower helices, as well as the increased interactions between subunits in the R state. PDB3CEH, PDB3E3O

In mammals, the major isozymes of glycogen phosphorylase are found in muscle, liver, and brain. The brain type is predominant in adult brain and embryonic tissues, whereas the liver and muscle types are predominant in adult liver and skeletal muscle, respectively.^[5]

The glycogen phosphorylase dimer has many regions of biological significance, including catalytic sites, glycogen binding sites, allosteric sites, and a reversibly phosphorylated serine residue. First, the catalytic sites are relatively buried, 15Å from the surface of the protein and from the subunit interface.^[6] This lack of easy access of the catalytic site to the surface is significant in that it makes the protein activity highly susceptible to regulation, as small allosteric effects could greatly increase the relative access of glycogen to the site.

Perhaps the most important regulatory site is Ser14, the site of reversible phosphorylation very close to the subunit interface. The structural change associated with phosphorylation, and with the conversion of phosphorylase b to phosphorylase a, is the arrangement of the originally disordered residues 10 to 22 into α helices. This change increases phosphorylase activity up to 25% even in the absence of AMP, and enhances AMP activation further.^[7]

The allosteric site of AMP binding on muscle isoforms of glycogen phosphorylase are close to the subunit interface just like Ser14. Binding of AMP at this site, corresponding in a change from the T state of the enzyme to the R state, results in small changes in tertiary structure at the subunit interface leading to large changes in quaternary structure.^[8] AMP binding rotates the tower helices (residues 262-278) of the two subunits 50˚ relative to one another through greater organization and intersubunit interactions. This rotation of the tower helices leads to a rotation of the two subunits by 10˚ relative to one another, and more importantly disorders residues 282-286 (the 280s loop) that block access to the catalytic site in the T state but do not in the R state.^[6]

The final, perhaps most curious site on the glycogen phosphorylase protein is the so-called glycogen storage site. Residues 397-437 form this structure, which allows the protein to covalently bind to the glycogen chain a full 30 Å from the catalytic site . This site is most likely the site at which the enzyme binds to glycogen granules before initiating cleavage of terminal glucose molecules. In fact, 70% of dimeric phosphorylase in the cell exists as bound to glycogen granules rather than free floating.^[9]

Clinical significance

phosphorylase, glycogen; muscle (McArdle syndrome, glycogen storage disease type V)
Identifiers
Symbol	PYGM
NCBI gene	5837
HGNC	9726
OMIM	608455
RefSeq	NM_005609
UniProt	P11217
Other data
EC number	2.4.1.1
Locus	Chr. 11 q12-q13.2
Search for Structures Swiss-model Domains InterPro

phosphorylase, glycogen; liver (Hers disease, glycogen storage disease type VI)
Identifiers
Symbol	PYGL
NCBI gene	5836
HGNC	9725
OMIM	232700
RefSeq	NM_002863
UniProt	P06737
Other data
EC number	2.4.1.1
Locus	Chr. 14 q11.2-24.3
Search for Structures Swiss-model Domains InterPro

phosphorylase, glycogen; brain
Identifiers
Symbol	PYGB
NCBI gene	5834
HGNC	9723
OMIM	138550
RefSeq	NM_002862
UniProt	P11216
Other data
EC number	2.4.1.1
Locus	Chr. 20 p11.2-p11.1
Search for Structures Swiss-model Domains InterPro

The inhibition of glycogen phosphorylase has been proposed as one method for treating type 2 diabetes.^[10] Since glucose production in the liver has been shown to increase in type 2 diabetes patients,^[11] inhibiting the release of glucose from the liver's glycogen's supplies appears to be a valid approach. The cloning of the human liver glycogen phosphorylase (HLGP) revealed a new allosteric binding site near the subunit interface that is not present in the rabbit muscle glycogen phosphorylase (RMGP) normally used in studies. This site was not sensitive to the same inhibitors as those at the AMP allosteric site,^[12] and most success has been had synthesizing new inhibitors that mimic the structure of glucose, since glucose-6-phosphate is a known inhibitor of HLGP and stabilizes the less active T-state.^[13] These glucose derivatives have had some success in inhibiting HLGP, with predicted Ki values as low as 0.016 mM.^[14]

Mutations in the muscle isoform of glycogen phosphorylase (PYGM) are associated with glycogen storage disease type V (GSD V, McArdle's Disease). More than 65 mutations in the PYGM gene that lead to McArdle disease have been identified to date.^[15][16] Symptoms of McArdle disease include muscle weakness, myalgia, and lack of endurance, all stemming from low glucose levels in muscle tissue.^[17]

Mutations in the liver isoform of glycogen phosphorylase (PYGL) are associated with Hers' Disease (glycogen storage disease type VI).^[18][19] Hers' disease is often associated with mild symptoms normally limited to hypoglycemia, and is sometimes difficult to diagnose due to residual enzyme activity.^[20]

The brain isoform of glycogen phosphorylase (PYGB) has been proposed as a biomarker for gastric cancer.^[21]

Regulation

Glycogen phosphorylase is regulated through allosteric control and through phosphorylation. Phosphorylase a and phosphorylase b each exist in two forms a T (tense) inactive state and R (relaxed) state. Phosphorylase b is normally in the T state, inactive due to the physiological presence of ATP and Glucose 6 phosphate, and Phosphorylase a is normally in the R state (active). An isoenzyme of glycogen phosphorylase exists in the liver sensitive to glucose concentration, as the liver acts as a glucose exporter. In essence, liver phosphorylase is responsive to glucose, which causes a very responsive transition from the R to T form, inactivating it; furthermore, liver phosphorylase is insensitive to AMP.

Hormones such as epinephrine, insulin and glucagon regulate glycogen phosphorylase using second messenger amplification systems linked to G proteins. Glucagon activates adenylate cyclase through a G protein-coupled receptor (GPCR) coupled to G_s which in turn activates adenylate cyclase to increase intracellular concentrations of cAMP. cAMP binds to and activates protein kinase A (PKA). PKA phosphorylates phosphorylase kinase, which in turn phosphorylates glycogen phosphorylase b at Ser14, converting it into the active glycogen phosphorylase a.

In the liver, glucagon also activates another GPCR that triggers a different cascade, resulting in the activation of phospholipase C (PLC). PLC indirectly causes the release of calcium from the hepatocytes' endoplasmic reticulum into the cytosol. The increased calcium availability binds to the calmodulin subunit and activates glycogen phosphorylase kinase. Glycogen phosphorylase kinase activates glycogen phosphorylase in the same manner mentioned previously.

Glycogen phosphorylase b is not always inactive in muscle, as it can be activated allosterically by AMP.^[6][9] An increase in AMP concentration, which occurs during strenuous exercise, signals energy demand. AMP activates glycogen phosphorylase b by changing its conformation from a tense to a relaxed form. This relaxed form has similar enzymatic properties as the phosphorylated enzyme. An increase in ATP concentration opposes this activation by displacing AMP from the nucleotide binding site, indicating sufficient energy stores.

Upon eating a meal, there is a release of insulin, signaling glucose availability in the blood. Insulin indirectly activates protein phosphatase 1 (PP1) and phosphodiesterase via a signal transduction cascade. PP1 dephosphorylates glycogen phosphorylase a, reforming the inactive glycogen phosphorylase b. The phosphodiesterase converts cAMP to AMP. Together, they decrease the concentration of cAMP and inhibit PKA. As a result, PKA can no longer initiate the phosphorylation cascade that ends with formation of (active) glycogen phosphorylase a. Overall, insulin signaling decreases glycogenolysis to preserve glycogen stores in the cell and triggers glycogenesis.^[22]

Historical significance

Glycogen phosphorylase was the first allosteric enzyme to be discovered.^[8] It was isolated and its activity characterized in detail by Carl F. Cori, Gerhard Schmidt and Gerty T. Cory.^[23][24]Arda Green and Gerty Cori crystallized it for the first time in 1943 ^[25] and illustrated that glycogen phosphorylase existed in either the a or b forms depending on its phosphorylation state, as well as in the R or T states based on the presence of AMP.^[26]

See also

• AMP deaminase deficiency (MADD)
• Glycogenolysis
• McArdle Disease (GSD-V)
• Metabolic myopathies
• Purine Nucleotide Cycle § Pathology

References

1. PDB: 3E3N​
2. Livanova NB, Chebotareva NA, Eronina TB, Kurganov BI (October 2002). "Pyridoxal 5'-phosphate as a catalytic and conformational cofactor of muscle glycogen phosphorylase B". Biochemistry. Biokhimiia. 67 (10): 1089–98. doi:10.1023/A:1020978825802. PMID 12460107. S2CID 12036788.
3. Palm D, Klein HW, Schinzel R, Buehner M, Helmreich EJ (February 1990). "The role of pyridoxal 5'-phosphate in glycogen phosphorylase catalysis". Biochemistry. 29 (5): 1099–107. doi:10.1021/bi00457a001. PMID 2182117.
4. Browner MF, Fletterick RJ (February 1992). "Phosphorylase: a biological transducer". Trends in Biochemical Sciences. 17 (2): 66–71. doi:10.1016/0968-0004(92)90504-3. PMID 1566331.
5. David ES, Crerar MM (January 1986). "Quantitation of muscle glycogen phosphorylase mRNA and enzyme amounts in adult rat tissues". Biochimica et Biophysica Acta (BBA) - General Subjects. 880 (1): 78–90. doi:10.1016/0304-4165(86)90122-4. PMID 3510670.
6. Johnson LN (March 1992). "Glycogen phosphorylase: control by phosphorylation and allosteric effectors". FASEB Journal. 6 (6): 2274–82. doi:10.1096/fasebj.6.6.1544539. PMID 1544539. S2CID 25954545.
7. Newgard CB, Hwang PK, Fletterick RJ (1989). "The family of glycogen phosphorylases: structure and function". Critical Reviews in Biochemistry and Molecular Biology. 24 (1): 69–99. doi:10.3109/10409238909082552. PMID 2667896.
8. Johnson LN, Barford D (February 1990). "Glycogen phosphorylase. The structural basis of the allosteric response and comparison with other allosteric proteins". The Journal of Biological Chemistry. 265 (5): 2409–12. doi:10.1016/S0021-9258(19)39810-2. PMID 2137445.
9. Meyer F, Heilmeyer LM, Haschke RH, Fischer EH (December 1970). "Control of phosphorylase activity in a muscle glycogen particle. I. Isolation and characterization of the protein-glycogen complex". The Journal of Biological Chemistry. 245 (24): 6642–8. doi:10.1016/S0021-9258(18)62582-7. PMID 4320610.
10. Somsák L, Nagya V, Hadady Z, Docsa T, Gergely P (2003). "Glucose analog inhibitors of glycogen phosphorylases as potential antidiabetic agents: recent developments". Current Pharmaceutical Design. 9 (15): 1177–89. doi:10.2174/1381612033454919. PMID 12769745.
11. Moller DE (December 2001). "New drug targets for type 2 diabetes and the metabolic syndrome". Nature. 414 (6865): 821–7. Bibcode:2001Natur.414..821M. doi:10.1038/414821a. PMID 11742415. S2CID 4426975.
12. Coats WS, Browner MF, Fletterick RJ, Newgard CB (August 1991). "An engineered liver glycogen phosphorylase with AMP allosteric activation". The Journal of Biological Chemistry. 266 (24): 16113–9. doi:10.1016/S0021-9258(18)98523-6. PMID 1874749.
13. Oikonomakos NG, Kontou M, Zographos SE, Tsitoura HS, Johnson LN, Watson KA, et al. (Jul 1994). "The design of potential antidiabetic drugs: experimental investigation of a number of beta-D-glucose analogue inhibitors of glycogen phosphorylase". European Journal of Drug Metabolism and Pharmacokinetics. 19 (3): 185–92. doi:10.1007/BF03188920. PMID 7867660. S2CID 11168623.
14. Hopfinger AJ, Reaka A, Venkatarangan P, Duca JS, Wang S (Sep 1999). "Prediction of Ligand−Receptor Binding Free Energy by 4D-QSAR Analysis: Application to a Set of Glucose Analogue Inhibitors of Glycogen Phosphorylase". Journal of Chemical Information and Computer Sciences. 39 (6): 1141–1150. doi:10.1021/ci9900332.
15. Nogales-Gadea G, Arenas J, Andreu AL (January 2007). "Molecular genetics of McArdle's disease". Current Neurology and Neuroscience Reports. 7 (1): 84–92. doi:10.1007/s11910-007-0026-2. PMID 17217859. S2CID 39626196.
16. Andreu AL, Nogales-Gadea G, Cassandrini D, Arenas J, Bruno C (July 2007). "McArdle disease: molecular genetic update". Acta Myologica. 26 (1): 53–7. PMC 2949323. PMID 17915571.
17. Grünfeld JP, Ganeval D, Chanard J, Fardeau M, Dreyfus JC (June 1972). "Acute renal failure in McArdle's disease. Report of two cases". The New England Journal of Medicine. 286 (23): 1237–41. doi:10.1056/NEJM197206082862304. PMID 4502558.
18. Burwinkel B, Bakker HD, Herschkovitz E, Moses SW, Shin YS, Kilimann MW (April 1998). "Mutations in the liver glycogen phosphorylase gene (PYGL) underlying glycogenosis type VI". American Journal of Human Genetics. 62 (4): 785–91. doi:10.1086/301790. PMC 1377030. PMID 9529348.
19. Chang S, Rosenberg MJ, Morton H, Francomano CA, Biesecker LG (May 1998). "Identification of a mutation in liver glycogen phosphorylase in glycogen storage disease type VI". Human Molecular Genetics. 7 (5): 865–70. doi:10.1093/hmg/7.5.865. PMID 9536091.
20. Tang NL, Hui J, Young E, Worthington V, To KF, Cheung KL, et al. (June 2003). "A novel mutation (G233D) in the glycogen phosphorylase gene in a patient with hepatic glycogen storage disease and residual enzyme activity". Molecular Genetics and Metabolism. 79 (2): 142–5. doi:10.1016/S1096-7192(03)00068-4. PMID 12809646.
21. Shimada S, Matsuzaki H, Marutsuka T, Shiomori K, Ogawa M (July 2001). "Gastric and intestinal phenotypes of gastric carcinoma with reference to expression of brain (fetal)-type glycogen phosphorylase". Journal of Gastroenterology. 36 (7): 457–64. doi:10.1007/s005350170068. PMID 11480789. S2CID 25602637.
22. Alemany S, Pelech S, Brierley CH, Cohen P (April 1986). "The protein phosphatases involved in cellular regulation. Evidence that dephosphorylation of glycogen phosphorylase and glycogen synthase in the glycogen and microsomal fractions of rat liver are catalysed by the same enzyme: protein phosphatase-1". European Journal of Biochemistry. 156 (1): 101–10. doi:10.1111/j.1432-1033.1986.tb09554.x. PMID 3007140.
23. Cori CF, Schmidt G, Cori GT (May 1939). "The Synthesis of a Polysaccharide From Glucose-1-Phosphate in Muscle Extract". Science. 89 (2316): 464–5. Bibcode:1939Sci....89..464C. doi:10.1126/science.89.2316.464. PMID 17731092.
24. Cori GT, Cori CF (July 1940). "The kinetics of the enzymatic synthesis of glycogen from glucose-1-phosphate". Journal of Biological Chemistry. 135 (2): 733–756. doi:10.1016/S0021-9258(18)73136-0.
25. Green AA, Cori GT (July 7, 1943). "Crystalline Muscle Phosphorylase I. Preparation, Properties, and Molecular Weight". Journal of Biological Chemistry. 151: 21–29. doi:10.1016/S0021-9258(18)72110-8.
26. Cori GT, Green AA (July 1943). . Journal of Biological Chemistry. 151 (1): 21–29. doi:10.1016/S0021-9258(18)72113-3. Archived from the original on 2017-04-27. Retrieved 2010-05-18.

Further reading

• Voet JG, Voet D (1995). "Chapter 17: Glycogen Metabolism". Biochemistry (2nd ed.). New York: J. Wiley & Sons. ISBN 978-0-471-58651-7.
• Voet JG, Voet D (2004). "Chapter 18: Glycogen Metabolism". Biochemistry (3rd ed.). New York: J. Wiley & Sons. ISBN 978-0-471-19350-0.
• Goodsell DS (2001-12-01). . Molecule of the Month. RCSB Protein Data Bank. Archived from the original on 2010-07-21. Retrieved 2009-01-10.
• Diwan JJ. . Molecular Biochemistry I. Rensselaer Polytechnic Institute. Archived from the original on 2009-01-25. Retrieved 2009-01-10.

External links

 

Wikimedia Commons has media related to Glycogen phosphorylase.

• GeneReviews/NCBI/NIH/UW entry on Glycogen Storage Disease Type VI - Hers disease
• Glycogen+phosphorylase at the US National Library of Medicine Medical Subject Headings (MeSH)
• Overview of all the structural information available in the PDB for UniProt: P11217 (Human muscle Glycogen phosphorylase) at the PDBe-KB.
• Overview of all the structural information available in the PDB for UniProt: P06737 (Human liver Glycogen phosphorylase) at the PDBe-KB.
• Overview of all the structural information available in the PDB for UniProt: P11216 (Human brain Glycogen phosphorylase) at the PDBe-KB.