Structural basis for allosteric regulation of human phosphofructokinase-1
Language English Country England, Great Britain Media electronic
Document type Journal Article
Grant support
P20GM144230
U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)
S10OD023476
U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)
S10 OD023476
NIH HHS - United States
P20 GM144230
NIGMS NIH HHS - United States
R35 GM149542
NIGMS NIH HHS - United States
1R35GM149542
U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)
PubMed
39183237
PubMed Central
PMC11345425
DOI
10.1038/s41467-024-51808-6
PII: 10.1038/s41467-024-51808-6
Knihovny.cz E-resources
- MeSH
- Adenosine Triphosphate * metabolism MeSH
- Allosteric Regulation MeSH
- Cryoelectron Microscopy MeSH
- Phosphofructokinase-1 * metabolism chemistry genetics MeSH
- Glycolysis MeSH
- Liver enzymology metabolism MeSH
- Protein Conformation MeSH
- Humans MeSH
- Models, Molecular MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Names of Substances
- Adenosine Triphosphate * MeSH
- Phosphofructokinase-1 * MeSH
- PFKL protein, human MeSH Browser
- Pfkl protein, mouse MeSH Browser
Phosphofructokinase-1 (PFK1) catalyzes the rate-limiting step of glycolysis, committing glucose to conversion into cellular energy. PFK1 is highly regulated to respond to the changing energy needs of the cell. In bacteria, the structural basis of PFK1 regulation is a textbook example of allostery; molecular signals of low and high cellular energy promote transition between an active R-state and inactive T-state conformation, respectively. Little is known, however, about the structural basis for regulation of eukaryotic PFK1. Here, we determine structures of the human liver isoform of PFK1 (PFKL) in the R- and T-state by cryoEM, providing insight into eukaryotic PFK1 allosteric regulatory mechanisms. The T-state structure reveals conformational differences between the bacterial and eukaryotic enzyme, the mechanisms of allosteric inhibition by ATP binding at multiple sites, and an autoinhibitory role of the C-terminus in stabilizing the T-state. We also determine structures of PFKL filaments that define the mechanism of higher-order assembly and demonstrate that these structures are necessary for higher-order assembly of PFKL in cells.
Department of Biochemistry and Molecular Medicine West Virginia University Morgantown WV USA
Department of Biochemistry University of Washington Seattle WA USA
See more in PubMed
Evans, P. R., Farrants, G. W. & Lawrence, M. C. Crystallographic structure of allosterically inhibited phosphofructokinase at 7 A resolution. J. Mol. Biol.191, 713–720 (1986). 10.1016/0022-2836(86)90455-9 PubMed DOI
Schirmer, T. & Evans, P. R. Structural basis of the allosteric behaviour of phosphofructokinase. Nature343, 140–145 (1990). 10.1038/343140a0 PubMed DOI
Evans, P. R., Farrants, G. W. & Hudson, P. J. Phosphofructokinase: structure and control. Philos. Trans. R. Soc. Lond. B Biol. Sci.293, 53–62 (1981). 10.1098/rstb.1981.0059 PubMed DOI
Poorman, R. A., Randolph, A., Kemp, R. G. & Heinrikson, R. L. Evolution of phosphofructokinase—gene duplication and creation of new effector sites. Nature309, 467–469 (1984). 10.1038/309467a0 PubMed DOI
Kemp, R. G. & Gunasekera, D. Evolution of the allosteric ligand sites of mammalian phosphofructo-1-kinase. Biochemistry41, 9426–9430 (2002). 10.1021/bi020110d PubMed DOI
Banaszak, K. et al. The crystal structures of eukaryotic phosphofructokinases from baker’s yeast and rabbit skeletal muscle. J. Mol. Biol.407, 284–297 (2011). 10.1016/j.jmb.2011.01.019 PubMed DOI
Webb, B. A. et al. Structures of human phosphofructokinase-1 and atomic basis of cancer-associated mutations. Nature523, 111–114 (2015). 10.1038/nature14405 PubMed DOI PMC
Kloos, M., Brüser, A., Kirchberger, J., Schöneberg, T. & Sträter, N. Crystal structure of human platelet phosphofructokinase-1 locked in an activated conformation. Biochem. J.469, 421–432 (2015). 10.1042/BJ20150251 PubMed DOI
Zancan, P., Marinho-Carvalho, M. M., Faber-Barata, J., Dellias, J. M. M. & Sola-Penna, M. ATP and fructose-2,6-bisphosphate regulate skeletal muscle 6-phosphofructo-1-kinase by altering its quaternary structure. IUBMB Life60, 526–533 (2008). 10.1002/iub.58 PubMed DOI
Hesterberg, L. K. & Lee, J. C. Self-association of rabbit muscle phosphofructokinase: effects of ligands. Biochemistry21, 216–222 (1982). 10.1021/bi00531a003 PubMed DOI
Costa Leite, T., Da Silva, D., Guimarães Coelho, R., Zancan, P. & Sola-Penna, M. Lactate favours the dissociation of skeletal muscle 6-phosphofructo-1-kinase tetramers down-regulating the enzyme and muscle glycolysis. Biochem. J.408, 123–130 (2007). 10.1042/BJ20070687 PubMed DOI PMC
Hicks, K. G. et al. Protein-metabolite interactomics of carbohydrate metabolism reveal regulation of lactate dehydrogenase. Science379, 996–1003 (2023). 10.1126/science.abm3452 PubMed DOI PMC
Yi, W. et al. Phosphofructokinase 1 glycosylation regulates cell growth and metabolism. Science337, 975–980 (2012). 10.1126/science.1222278 PubMed DOI PMC
Zhao, S. et al. Regulation of cellular metabolism by protein lysine acetylation. Science327, 1000–1004 (2010). 10.1126/science.1179689 PubMed DOI PMC
Mahrenholz, A. M., Lan, L. & Mansour, T. E. Phosphorylation of heart phosphofructokinase by Ca2+ calmodulin protein kinase. Biochem. Biophys. Res. Commun.174, 1255–1259 (1991). 10.1016/0006-291X(91)91556-R PubMed DOI
Lee, J.-H. et al. Stabilization of phosphofructokinase 1 platelet isoform by AKT promotes tumorigenesis. Nat. Commun.8, 949 (2017). 10.1038/s41467-017-00906-9 PubMed DOI PMC
Fernandes, P. M., Kinkead, J., McNae, I., Michels, P. A. M. & Walkinshaw, M. D. Biochemical and transcript level differences between the three human phosphofructokinases show optimisation of each isoform for specific metabolic niches. Biochem. J.477, 4425–4441 (2020). 10.1042/BCJ20200656 PubMed DOI PMC
Webb, B. A., Dosey, A. M., Wittmann, T., Kollman, J. M. & Barber, D. L. The glycolytic enzyme phosphofructokinase-1 assembles into filaments. J. Cell Biol.216, 2305–2313 (2017). 10.1083/jcb.201701084 PubMed DOI PMC
Amara, N. et al. Selective activation of PFKL suppresses the phagocytic oxidative burst. Cell184, 4480–4494.e15 (2021). 10.1016/j.cell.2021.07.004 PubMed DOI PMC
Rizzo, S. C. & Eckel, R. E. Control of glycolysis in human erythrocytes by inorganic phosphate and sulfate. Am. J. Physiol.211, 429–436 (1966). 10.1152/ajplegacy.1966.211.2.429 PubMed DOI
Mosser, R., Reddy, M. C. M., Bruning, J. B., Sacchettini, J. C. & Reinhart, G. D. Redefining the role of the quaternary shift in Bacillus stearothermophilus phosphofructokinase. Biochemistry52, 5421–5429 (2013). 10.1021/bi4002503 PubMed DOI PMC
Jin, M. et al. Glycolytic enzymes coalesce in G bodies under hypoxic stress. Cell Rep.20, 895–908 (2017). 10.1016/j.celrep.2017.06.082 PubMed DOI PMC
Adams, A. G., Bulusu, R. K. M., Mukhitov, N., Mendoza-Cortes, J. L. & Roper, M. G. Online measurement of glucose consumption from HepG2 cells using an integrated bioreactor and enzymatic assay. Anal. Chem.91, 5184–5190 (2019). 10.1021/acs.analchem.8b05798 PubMed DOI PMC
Santamaria, B., Estevez, A. M., Martinez-Costa, O. H. & Aragon, J. J. Creation of an allosteric phosphofructokinase starting with a nonallosteric enzyme. The case of dictyostelium discoideum phosphofructokinase. J. Biol. Chem.277, 1210–1216 (2002). 10.1074/jbc.M109480200 PubMed DOI
Huang, J. et al. CHARMM36m: an improved force field for folded and intrinsically disordered proteins. Nat. Methods14, 71–73 (2017). 10.1038/nmeth.4067 PubMed DOI PMC
Yao, X.-Q. et al. Dynamic coupling and allosteric networks in the alpha subunit of heterotrimeric G proteins. Biophys. J.110, 427a (2016).10.1016/j.bpj.2015.11.2306 PubMed DOI PMC
Yugi, K. et al. Reconstruction of insulin signal flow from phosphoproteome and metabolome data. Cell Rep.8, 1171–1183 (2014). 10.1016/j.celrep.2014.07.021 PubMed DOI
Lynch, E. M., Kollman, J. M. & Webb, B. A. Filament formation by metabolic enzymes—A new twist on regulation. Curr. Opin. Cell Biol.66, 28–33 (2020). 10.1016/j.ceb.2020.04.006 PubMed DOI PMC
Simonet, J. C., Burrell, A. L., Kollman, J. M. & Peterson, J. R. Freedom of assembly: metabolic enzymes come together. Mol. Biol. Cell31, 1201–1205 (2020). 10.1091/mbc.E18-10-0675 PubMed DOI PMC
Hvorecny, K. L. & Kollman, J. M. Greater than the sum of parts: mechanisms of metabolic regulation by enzyme filaments. Curr. Opin. Struct. Biol.79, 102530 (2023). 10.1016/j.sbi.2023.102530 PubMed DOI PMC
Garcia-Seisdedos, H., Empereur-Mot, C., Elad, N. & Levy, E. D. Proteins evolve on the edge of supramolecular self-assembly. Nature548, 244–247 (2017). 10.1038/nature23320 PubMed DOI
Seisdedos, H. G., Levin, T., Shapira, G., Freud, S. & Levy, E. D. Mutant libraries reveal negative design shielding proteins from supramolecular self-assembly and relocalization in cells. Proc. Natl Acad. Sci. USA 119 10.1073/pnas.2101117119 (2022). PubMed PMC
Lynch, E. M. & Kollman, J. M. Coupled structural transitions enable highly cooperative regulation of human CTPS2 filaments. Nat. Struct. Mol. Biol.27, 42–48 (2020). 10.1038/s41594-019-0352-5 PubMed DOI PMC
Lynch, E. M. et al. Human CTP synthase filament structure reveals the active enzyme conformation. Nat. Struct. Mol. Biol.24, 507–514 (2017). 10.1038/nsmb.3407 PubMed DOI PMC
Barry, R. M. et al. Large-scale filament formation inhibits the activity of CTP synthetase. eLife3, e03638 (2014). 10.7554/eLife.03638 PubMed DOI PMC
Stoddard, P. R. et al. Polymerization in the actin ATPase clan regulates hexokinase activity in yeast. Science367, 1039–1042 (2020). 10.1126/science.aay5359 PubMed DOI PMC
Hunkeler, M. et al. Structural basis for regulation of human acetyl-CoA carboxylase. Nature558, 470–474 (2018). 10.1038/s41586-018-0201-4 PubMed DOI
Pony, P., Rapisarda, C., Terradot, L., Marza, E. & Fronzes, R. Filamentation of the bacterial bi-functional alcohol/aldehyde dehydrogenase AdhE is essential for substrate channeling and enzymatic regulation. Nat. Commun.11, 1426 (2020). 10.1038/s41467-020-15214-y PubMed DOI PMC
Kim, G. et al. Aldehyde-alcohol dehydrogenase undergoes structural transition to form extended spirosomes for substrate channeling. Commun. Biol.3, 298 (2020). 10.1038/s42003-020-1030-1 PubMed DOI PMC
Hu, H.-H. et al. Filamentation modulates allosteric regulation of PRPS. eLife11, e79552 (2022). 10.7554/eLife.79552 PubMed DOI PMC
Burrell, A. L. et al. IMPDH1 retinal variants control filament architecture to tune allosteric regulation. Nat. Struct. Mol. Biol.29, 47–58 (2022). 10.1038/s41594-021-00706-2 PubMed DOI PMC
Johnson, M. C. & Kollman, J. M. Cryo-EM structures demonstrate human IMPDH2 filament assembly tunes allosteric regulation. eLife9, e53243 (2020). 10.7554/eLife.53243 PubMed DOI PMC
Hvorecny, K. L., Hargett, K., Quispe, J. D. & Kollman, J. M. Human PRPS1 filaments stabilize allosteric sites to regulate activity. Nat. Struct. Mol. Biol.30, 391–402 (2023). 10.1038/s41594-023-00921-z PubMed DOI PMC
Jang, S. et al. Glycolytic enzymes localize to synapses under energy stress to support synaptic function. Neuron90, 278–291 (2016). 10.1016/j.neuron.2016.03.011 PubMed DOI PMC
Kohnhorst, C. L. et al. Identification of a multienzyme complex for glucose metabolism in living cells. J. Biol. Chem.292, 9191–9203 (2017). 10.1074/jbc.M117.783050 PubMed DOI PMC
Brüser, A., Kirchberger, J., Kloos, M., Sträter, N. & Schöneberg, T. Functional linkage of adenine nucleotide binding sites in mammalian muscle 6-phosphofructokinase. J. Biol. Chem.287, 17546–17553 (2012). 10.1074/jbc.M112.347153 PubMed DOI PMC
Suloway, C. et al. Automated molecular microscopy: the new Leginon system. J. Struct. Biol.151, 41–60 (2005). 10.1016/j.jsb.2005.03.010 PubMed DOI
Vallat, R. Pingouin: statistics in Python. J. Open Source Softw.3, 1026 (2018).10.21105/joss.01026 DOI
Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods14, 290–296 (2017). 10.1038/nmeth.4169 PubMed DOI
Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D. Biol. Crystallogr.66, 213–221 (2010). 10.1107/S0907444909052925 PubMed DOI PMC
Croll, T. I. ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Acta Crystallogr D. Struct. Biol.74, 519–530 (2018). 10.1107/S2059798318002425 PubMed DOI PMC
Pettersen, E. F. et al. UCSF Chimera-a visualization system for exploratory research and analysis. J. Comput. Chem.25, 1605–1612 (2004). 10.1002/jcc.20084 PubMed DOI
Young, G. et al. Quantitative mass imaging of single biological macromolecules. Science360, 423–427 (2018). 10.1126/science.aar5839 PubMed DOI PMC
Voronkova, M. A. et al. Cancer-associated somatic mutations in human phosphofructokinase-1 reveal a critical electrostatic interaction for allosteric regulation of enzyme activity. Biochem. J.480, 1411–1427 (2023). 10.1042/BCJ20230207 PubMed DOI PMC
The PyMOL molecular graphics system, Version 2.5.4 Schrödinger, LLC. https://www.pymol.org/ (2022).
Abraham, M. J. et al. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX1–2, 19–25 (2015).10.1016/j.softx.2015.06.001 DOI
Jo, S., Kim, T., Iyer, V. G. & Im, W. CHARMM-GUI: a web-based graphical user interface for CHARMM. J. Comput. Chem.29, 1859–1865 (2008). 10.1002/jcc.20945 PubMed DOI
Kim, S. et al. CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules. J. Comput. Chem.38, 1879–1886 (2017). 10.1002/jcc.24829 PubMed DOI PMC
Vanommeslaeghe, K. et al. CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J. Comput. Chem.31, 671–690 (2010). 10.1002/jcc.21367 PubMed DOI PMC
Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W. & Klein, M. L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys.79, 926–935 (1983).
Feenstra, K. A., Hess, B. & Berendsen, H. J. C. Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems. J. Comput. Chem.20, 786–798 (1999). 10.1002/(SICI)1096-987X(199906)20:8<786::AID-JCC5>3.0.CO;2-B PubMed DOI
Darden, T., York, D. & Pedersen, L. Particle mesh Ewald: an N⋅log(N) method for Ewald sums in large systems. J. Chem. Phys.98, 10089–10092 (1993).10.1063/1.464397 DOI
Hockney, R. W., Goel, S. P. & Eastwood, J. W. Quiet high-resolution computer models of a plasma. J. Comput. Phys.14, 148–158 (1974).10.1016/0021-9991(74)90010-2 DOI
Hess, B., Bekker, H., Berendsen, H. J. C. & Fraaije, J. G. E. M. LINCS: a linear constraint solver for molecular simulations. J. Comput. Chem.18, 1463–1472 (1997).10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H DOI
Miyamoto, S. & Kollman, P. A. Settle: an analytical version of the SHAKE and RATTLE algorithm for rigid water models. J. Comput. Chem.13, 952–962 (1992).10.1002/jcc.540130805 DOI
Berendsen, H. J. C., van Postma, J., Van Gunsteren, W. F., DiNola, A. & Haak, J. R. Molecular dynamics with coupling to an external bath. J. Chem. Phys.81, 3684–3690 (1984).10.1063/1.448118 DOI
Bussi, G., Donadio, D. & Parrinello, M. Canonical sampling through velocity rescaling. J. Chem. Phys.126, 014101 (2007). 10.1063/1.2408420 PubMed DOI
Parrinello, M. & Rahman, A. Polymorphic transitions in single crystals: a new molecular dynamics method. J. Appl. Phys.52, 7182–7190 (1981).10.1063/1.328693 DOI
Michaud-Agrawal, N., Denning, E. J., Woolf, T. B. & Beckstein, O. MDAnalysis: a toolkit for the analysis of molecular dynamics simulations. J. Comput. Chem.32, 2319–2327 (2011). 10.1002/jcc.21787 PubMed DOI PMC
Grant, B. J., Skjaerven, L. & Yao, X.-Q. The Bio3D packages for structural bioinformatics. Protein Sci.30, 20–30 (2021). 10.1002/pro.3923 PubMed DOI PMC
Humphrey, W., Dalke, A. & Schulten, K. VMD: visual molecular dynamics. J. Mol. Graph.14, 33–38 (1996). 27–8. 10.1016/0263-7855(96)00018-5 PubMed DOI