1fa9 Citations

Activation of human liver glycogen phosphorylase by alteration of the secondary structure and packing of the catalytic core.

Abstract

Glycogen phosphorylases catalyze the breakdown of glycogen to glucose-1-phosphate, which enters glycolysis to fulfill the energetic requirements of the organism. Maintaining control of blood glucose levels is critical in minimizing the debilitating effects of diabetes, making liver glycogen phosphorylase a potential therapeutic target. To support inhibitor design, we determined the crystal structures of the active and inactive forms of human liver glycogen phosphorylase a. During activation, forty residues of the catalytic site undergo order/disorder transitions, changes in secondary structure, or packing to reorganize the catalytic site for substrate binding and catalysis. Knowing the inactive and active conformations of the liver enzyme and how each differs from its counterpart in muscle phosphorylase provides the basis for designing inhibitors that bind preferentially to the inactive conformation of the liver isozyme.

Reviews - 1fa9 mentioned but not cited (1)

  1. Structural Basis for Allostery in PLP-dependent Enzymes. Tran JU, Brown BL. Front Mol Biosci 9 884281 (2022)

Articles - 1fa9 mentioned but not cited (6)

  1. Intrasteric control of AMPK via the gamma1 subunit AMP allosteric regulatory site. Adams J, Chen ZP, Van Denderen BJ, Morton CJ, Parker MW, Witters LA, Stapleton D, Kemp BE. Protein Sci 13 155-165 (2004)
  2. The structural basis of ATP as an allosteric modulator. Lu S, Huang W, Wang Q, Shen Q, Li S, Nussinov R, Zhang J. PLoS Comput Biol 10 e1003831 (2014)
  3. Insights into Brain Glycogen Metabolism: THE STRUCTURE OF HUMAN BRAIN GLYCOGEN PHOSPHORYLASE. Mathieu C, Li de la Sierra-Gallay I, Duval R, Xu X, Cocaign A, Léger T, Woffendin G, Camadro JM, Etchebest C, Haouz A, Dupret JM, Rodrigues-Lima F. J Biol Chem 291 18072-18083 (2016)
  4. In Silico Insight into Potential Anti-Alzheimer's Disease Mechanisms of Icariin. Cui Z, Sheng Z, Yan X, Cao Z, Tang K. Int J Mol Sci 17 E113 (2016)
  5. Case Reports Identification and Characterization of a Novel Splice Site Mutation Associated with Glycogen Storage Disease Type VI in Two Unrelated Turkish Families. Grünert SC, Hannibal L, Schumann A, Rosenbaum-Fabian S, Beck-Wödl S, Haack TB, Grimmel M, Bertrand M, Spiekerkoetter U. Diagnostics (Basel) 11 500 (2021)
  6. Anti-diabetic Activity of Brucine in Streptozotocin-Induced Rats: In Silico, In Vitro, and In Vivo Studies. Khan NU, Qazi NG, Khan AU, Ali F, Hassan SSU, Bungau S. ACS Omega 7 46358-46370 (2022)


Reviews citing this publication (18)

  1. Glycosyltransferases: structures, functions, and mechanisms. Lairson LL, Henrissat B, Davies GJ, Withers SG. Annu Rev Biochem 77 521-555 (2008)
  2. Mechanisms of Insulin Action and Insulin Resistance. Petersen MC, Shulman GI. Physiol Rev 98 2133-2223 (2018)
  3. Pancreatic regulation of glucose homeostasis. Röder PV, Wu B, Liu Y, Han W. Exp Mol Med 48 e219 (2016)
  4. Glycogen metabolism in humans. Adeva-Andany MM, González-Lucán M, Donapetry-García C, Fernández-Fernández C, Ameneiros-Rodríguez E. BBA Clin 5 85-100 (2016)
  5. Glycogen phosphorylase inhibitors for treatment of type 2 diabetes mellitus. Treadway JL, Mendys P, Hoover DJ. Expert Opin Investig Drugs 10 439-454 (2001)
  6. Glycogen metabolism has a key role in the cancer microenvironment and provides new targets for cancer therapy. Zois CE, Harris AL. J Mol Med (Berl) 94 137-154 (2016)
  7. New hepatic targets for glycaemic control in diabetes. Agius L. Best Pract Res Clin Endocrinol Metab 21 587-605 (2007)
  8. Glycogen metabolism in cancer. Zois CE, Favaro E, Harris AL. Biochem Pharmacol 92 3-11 (2014)
  9. Glycoside phosphorylases: structure, catalytic properties and biotechnological potential. Puchart V. Biotechnol Adv 33 261-276 (2015)
  10. Structural relationships among regulated and unregulated phosphorylases. Buchbinder JL, Rath VL, Fletterick RJ. Annu Rev Biophys Biomol Struct 30 191-209 (2001)
  11. Structural basis for regulation of RNA-binding proteins by phosphorylation. Thapar R. ACS Chem Biol 10 652-666 (2015)
  12. Glycogen phosphorylase inhibitors: a patent review (2008 - 2012). Gaboriaud-Kolar N, Skaltsounis AL. Expert Opin Ther Pat 23 1017-1032 (2013)
  13. Brain Glycogen Structure and Its Associated Proteins: Past, Present and Future. Brewer MK, Gentry MS. Adv Neurobiol 23 17-81 (2019)
  14. Structural and mechanistic insights into the bifunctional enzyme isocitrate dehydrogenase kinase/phosphatase AceK. Zheng J, Yates SP, Jia Z. Philos Trans R Soc Lond B Biol Sci 367 2656-2668 (2012)
  15. The structure of brain glycogen phosphorylase-from allosteric regulation mechanisms to clinical perspectives. Mathieu C, Dupret JM, Rodrigues Lima F. FEBS J 284 546-554 (2017)
  16. Crystal structures of eukaryote glycosyltransferases reveal biologically relevant enzyme homooligomers. Harrus D, Kellokumpu S, Glumoff T. Cell Mol Life Sci 75 833-848 (2018)
  17. Discovery and Biotechnological Exploitation of Glycoside-Phosphorylases. Li A, Benkoulouche M, Ladeveze S, Durand J, Cioci G, Laville E, Potocki-Veronese G. Int J Mol Sci 23 3043 (2022)
  18. Synthetic strategies, SAR studies, and computer modeling of indole 2 and 3-carboxamides as the strong enzyme inhibitors: a review. Chehardoli G, Bahmani A. Mol Divers 25 535-550 (2021)

Articles citing this publication (40)

  1. Crystal structure of glycogen synthase: homologous enzymes catalyze glycogen synthesis and degradation. Buschiazzo A, Ugalde JE, Guerin ME, Shepard W, Ugalde RA, Alzari PM. EMBO J 23 3196-3205 (2004)
  2. Analysis of the pi-pi stacking interactions between the aminoglycoside antibiotic kinase APH(3')-IIIa and its nucleotide ligands. Boehr DD, Farley AR, Wright GD, Cox JR. Chem Biol 9 1209-1217 (2002)
  3. Diverse effects of two allosteric inhibitors on the phosphorylation state of glycogen phosphorylase in hepatocytes. Latsis T, Andersen B, Agius L. Biochem J 368 309-316 (2002)
  4. Cumulative effect of amino acid replacements results in enhanced thermostability of potato type L alpha-glucan phosphorylase. Yanase M, Takata H, Fujii K, Takaha T, Kuriki T. Appl Environ Microbiol 71 5433-5439 (2005)
  5. Integrated effects of multiple modulators on human liver glycogen phosphorylase a. Ercan-Fang N, Gannon MC, Rath VL, Treadway JL, Taylor MR, Nuttall FQ. Am J Physiol Endocrinol Metab 283 E29-37 (2002)
  6. Functional states of homooligomers: insights from the evolution of glycosyltransferases. Hashimoto K, Madej T, Bryant SH, Panchenko AR. J Mol Biol 399 196-206 (2010)
  7. Structure-activity analysis of the purine binding site of human liver glycogen phosphorylase. Ekstrom JL, Pauly TA, Carty MD, Soeller WC, Culp J, Danley DE, Hoover DJ, Treadway JL, Gibbs EM, Fletterick RJ, Day YS, Myszka DG, Rath VL. Chem Biol 9 915-924 (2002)
  8. Glycogen phosphorylase in glycogen-rich cells is involved in the energy supply for ion regulation in fish gill epithelia. Tseng YC, Huang CJ, Chang JC, Teng WY, Baba O, Fann MJ, Hwang PP. Am J Physiol Regul Integr Comp Physiol 293 R482-91 (2007)
  9. Rac1 protein regulates glycogen phosphorylase activation and controls interleukin (IL)-2-dependent T cell proliferation. Arrizabalaga O, Lacerda HM, Zubiaga AM, Zugaza JL. J Biol Chem 287 11878-11890 (2012)
  10. Treatment of pregnant spiny mice at mid gestation with a synthetic glucocorticoid has sex-dependent effects on placental glycogen stores. O'Connell BA, Moritz KM, Walker DW, Dickinson H. Placenta 34 932-940 (2013)
  11. Biochemical and biological assessment of the inhibitory potency of extracts from vinification byproducts of Vitis vinifera extracts against glycogen phosphorylase. Kantsadi AL, Apostolou A, Theofanous S, Stravodimos GA, Kyriakis E, Gorgogietas VA, Chatzileontiadou DS, Pegiou K, Skamnaki VT, Stagos D, Kouretas D, Psarra AM, Haroutounian SA, Leonidas DD. Food Chem Toxicol 67 35-43 (2014)
  12. High frequency of missense mutations in glycogen storage disease type VI. Beauchamp NJ, Taybert J, Champion MP, Layet V, Heinz-Erian P, Dalton A, Tanner MS, Pronicka E, Sharrard MJ. J Inherit Metab Dis 30 722-734 (2007)
  13. Development of potent, orally active 1-substituted-3,4-dihydro-2-quinolone glycogen phosphorylase inhibitors. Birch AM, Kenny PW, Oikonomakos NG, Otterbein L, Schofield P, Whittamore PR, Whalley DP. Bioorg Med Chem Lett 17 394-399 (2007)
  14. The hepatic PP1 glycogen-targeting subunit interaction with phosphorylase a can be blocked by C-terminal tyrosine deletion or an indole drug. Kelsall IR, Munro S, Hallyburton I, Treadway JL, Cohen PT. FEBS Lett 581 4749-4753 (2007)
  15. The 1.76 A resolution crystal structure of glycogen phosphorylase B complexed with glucose, and CP320626, a potential antidiabetic drug. Oikonomakos NG, Zographos SE, Skamnaki VT, Archontis G. Bioorg Med Chem 10 1313-1319 (2002)
  16. The crystal structure of human muscle glycogen phosphorylase a with bound glucose and AMP: an intermediate conformation with T-state and R-state features. Lukacs CM, Oikonomakos NG, Crowther RL, Hong LN, Kammlott RU, Levin W, Li S, Liu CM, Lucas-McGady D, Pietranico S, Reik L. Proteins 63 1123-1126 (2006)
  17. Sourcing the affinity of flavonoids for the glycogen phosphorylase inhibitor site via crystallography, kinetics and QM/MM-PBSA binding studies: comparison of chrysin and flavopiridol. Tsitsanou KE, Hayes JM, Keramioti M, Mamais M, Oikonomakos NG, Kato A, Leonidas DD, Zographos SE. Food Chem Toxicol 61 14-27 (2013)
  18. Molecular recognition of the protein phosphatase 1 glycogen targeting subunit by glycogen phosphorylase. Pautsch A, Stadler N, Wissdorf O, Langkopf E, Moreth W, Streicher R. J Biol Chem 283 8913-8918 (2008)
  19. Sensitivity of glycogen phosphorylase isoforms to indole site inhibitors is markedly dependent on the activation state of the enzyme. Freeman S, Bartlett JB, Convey G, Hardern I, Teague JL, Loxham SJ, Allen JM, Poucher SM, Charles AD. Br J Pharmacol 149 775-785 (2006)
  20. The glial phosphorylase of glycogen isoform is reduced in the dorsolateral prefrontal cortex in chronic schizophrenia. Pinacho R, Vila E, Prades R, Tarragó T, Castro E, Ferrer I, Ramos B. Schizophr Res 177 37-43 (2016)
  21. Endogenous effectors of human liver glycogen phosphorylase modulate effects of indole-site inhibitors. Ercan-Fang N, Taylor MR, Treadway JL, Levy CB, Genereux PE, Gibbs EM, Rath VL, Kwon Y, Gannon MC, Nuttall FQ. Am J Physiol Endocrinol Metab 289 E366-72 (2005)
  22. Glycogen storage disease type VI: clinical course and molecular background. Aeppli TR, Rymen D, Allegri G, Bode PK, Häberle J. Eur J Pediatr 179 405-413 (2020)
  23. Synthesis of 5-chloro-N-aryl-1H-indole-2-carboxamide derivatives as inhibitors of human liver glycogen phosphorylase a. Onda K, Suzuki T, Shiraki R, Yonetoku Y, Negoro K, Momose K, Katayama N, Orita M, Yamaguchi T, Ohta M, Tsukamoto S. Bioorg Med Chem 16 5452-5464 (2008)
  24. The σ-hole phenomenon of halogen atoms forms the structural basis of the strong inhibitory potency of C5 halogen substituted glucopyranosyl nucleosides towards glycogen phosphorylase b. Kantsadi AL, Hayes JM, Manta S, Skamnaki VT, Kiritsis C, Psarra AM, Koutsogiannis Z, Dimopoulou A, Theofanous S, Nikoleousakos N, Zoumpoulakis P, Kontou M, Papadopoulos G, Zographos SE, Komiotis D, Leonidas DD. ChemMedChem 7 722-732 (2012)
  25. 3'-axial CH2 OH substitution on glucopyranose does not increase glycogen phosphorylase inhibitory potency. QM/MM-PBSA calculations suggest why. Manta S, Xipnitou A, Kiritsis C, Kantsadi AL, Hayes JM, Skamnaki VT, Lamprakis C, Kontou M, Zoumpoulakis P, Zographos SE, Leonidas DD, Komiotis D. Chem Biol Drug Des 79 663-673 (2012)
  26. FR258900, a potential anti-hyperglycemic drug, binds at the allosteric site of glycogen phosphorylase. Tiraidis C, Alexacou KM, Zographos SE, Leonidas DD, Gimisis T, Oikonomakos NG. Protein Sci 16 1773-1782 (2007)
  27. Comment The many metabolic sources of acetyl-CoA to support histone acetylation and influence cancer progression. Feron O. Ann Transl Med 7 S277 (2019)
  28. The Impact of DJOS Surgery, a High Fat Diet and a Control Diet on the Enzymes of Glucose Metabolism in the Liver and Muscles of Sprague-Dawley Rats. Stygar D, Andrare D, Bażanów B, Chełmecka E, Sawczyn T, Skrzep-Poloczek B, Olszańska E, Karcz KW, Jochem J. Front Physiol 10 571 (2019)
  29. Modeling aided design of potent glycogen phosphorylase inhibitors. Deng Q, Lu Z, Bohn J, Ellsworth KP, Myers RW, Geissler WM, Harris G, Willoughby CA, Chapman K, McKeever B, Mosley R. J Mol Graph Model 23 457-464 (2005)
  30. Functional Prediction and Assignment of Methanobrevibacter ruminantium M1 Operome Using a Combined Bioinformatics Approach. Bharathi M, Senthil Kumar N, Chellapandi P. Front Genet 11 593990 (2020)
  31. Novel Liver-targeted conjugates of Glycogen Phosphorylase Inhibitor PSN-357 for the Treatment of Diabetes: Design, Synthesis, Pharmacokinetic and Pharmacological Evaluations. Zhang L, Song C, Miao G, Zhao L, Yan Z, Li J, Wang Y. Sci Rep 7 42251 (2017)
  32. van der Waals interactions govern C-β-d-glucopyranosyl triazoles' nM inhibitory potency in human liver glycogen phosphorylase. Kantsadi AL, Stravodimos GA, Kyriakis E, Chatzileontiadou DSM, Solovou TGA, Kun S, Bokor É, Somsák L, Leonidas DD. J Struct Biol 199 57-67 (2017)
  33. Beta-Sitosterol Facilitates GLUT4 Vesicle Fusion on the Plasma Membrane via the Activation of Rab/IRAP/Munc 18 Signaling Pathways in Diabetic Gastrocnemius Muscle of Adult Male Rats. Pei J, Prasad M, Mohamed Helal G, El-Sherbiny M, Abdelmonem Elsherbini DM, Rajagopal P, Palanisamy CP, Veeraraghavan VP, Jayaraman S, Surapaneni KM. Bioinorg Chem Appl 2022 7772305 (2022)
  34. Lysine Decarboxylase with an Enhanced Affinity for Pyridoxal 5-Phosphate by Disulfide Bond-Mediated Spatial Reconstitution. Sagong HY, Kim KJ. PLoS One 12 e0170163 (2017)
  35. Understanding the Rate-Limiting Step of Glycogenolysis by Using QM/MM Calculations on Human Glycogen Phosphorylase. Brás NF, Fernandes PA, Ramos MJ. ChemMedChem 13 1608-1616 (2018)
  36. Glycogen phosphorylase revisited: extending the resolution of the R- and T-state structures of the free enzyme and in complex with allosteric activators. Leonidas DD, Zographos SE, Tsitsanou KE, Skamnaki VT, Stravodimos G, Kyriakis E. Acta Crystallogr F Struct Biol Commun 77 303-311 (2021)
  37. Allosteric Regulation of Glycogen Phosphorylase by Order/Disorder Transition of the 250' and 280s Loops. Kish M, Subramanian S, Smith V, Lethbridge N, Cole L, Vollmer F, Bond NJ, Phillips JJ. Biochemistry 62 1360-1368 (2023)
  38. Analysis of the expression, function and signaling of glycogen phosphorylase isoforms in hepatocellular carcinoma. Jiang L, Liu S, Deng T, Yang Y, Zhang Y. Oncol Lett 24 244 (2022)
  39. High Consistency of Structure-Based Design and X-Ray Crystallography: Design, Synthesis, Kinetic Evaluation and Crystallographic Binding Mode Determination of Biphenyl-N-acyl-β-d-Glucopyranosylamines as Glycogen Phosphorylase Inhibitors. Fischer T, Koulas SM, Tsagkarakou AS, Kyriakis E, Stravodimos GA, Skamnaki VT, Liggri PGV, Zographos SE, Riedl R, Leonidas DD. Molecules 24 E1322 (2019)
  40. High-resolution structural-omics of human liver enzymes. Su CC, Lyu M, Zhang Z, Miyagi M, Huang W, Taylor DJ, Yu EW. Cell Rep 42 112609 (2023)