6NU1

Crystal Structure of Human PKM2 in Complex with L-cysteine

Summary for 6NU1

• Entry DOI: 10.2210/pdb6nu1/pdb
• Descriptor: Pyruvate kinase PKM, CYSTEINE, 1,6-di-O-phosphono-beta-D-fructofuranose, ... (7 entities in total)
• Functional Keywords: pyruvate kinase m2, cysteine, inhibition, glycolysis, transferase
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 4
• Total formula weight: 243125.59

Authors

Srivastava, D.,Nandi, S.,Dey, M. (deposition date: 2019-01-30, release date: 2019-08-21, Last modification date: 2023-10-11)

Primary citation

Srivastava, D.,Nandi, S.,Dey, M.
Mechanistic and Structural Insights into Cysteine-Mediated Inhibition of Pyruvate Kinase Muscle Isoform 2.
Biochemistry, 58:3669-3682, 2019

PubMed Abstract: Cancer cells regulate key enzymes in the glycolytic pathway to control the glycolytic flux, which is necessary for their growth and proliferation. One of the enzymes is pyruvate kinase muscle isoform 2 (PKM2), which is allosterically regulated by various small molecules. Using detailed biochemical and kinetic studies, we demonstrate that cysteine inhibits wild-type (wt) PKM2 by shifting from an active tetramer to a mixture of a tetramer and a less active dimer/monomer equilibrium and that the inhibition is dependent on cysteine concentration. The cysteine-mediated PKM2 inhibition is reversed by fructose 1,6-bisphosphate, an allosteric activator of PKM2. Furthermore, kinetic studies using two dimeric PKM2 variants, S437Y PKM2 and G415R PKM2, show that the reversal is caused by the tetramerization of wtPKM2. The crystal structure of the wtPKM2-Cys complex was determined at 2.25 Å, which showed that cysteine is held to the amino acid binding site via its main chain groups, similar to that observed for phenylalanine, alanine, serine, and tryptophan. Notably, ligand binding studies using fluorescence and isothermal titration calorimetry show that the presence of phosphoenolpyruvate alters the binding affinities of amino acids for wtPKM2 and vice versa, thereby unravelling the existence of a functionally bidirectional coupling between the amino acid binding site and the active site of wtPKM2.

PubMed: 31386812
DOI: 10.1021/acs.biochem.9b00349

Experimental method

X-RAY DIFFRACTION (2.25 Å)