Structure of M2 pyruvate kinase in complex with phenylalanine

Experimental Data Snapshot

  • Resolution: 2.55 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 

Starting Model: experimental
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M2 pyruvate kinase provides a mechanism for nutrient sensing and regulation of cell proliferation.

Morgan, H.P.O'Reilly, F.J.Wear, M.A.O'Neill, J.R.Fothergill-Gilmore, L.A.Hupp, T.Walkinshaw, M.D.

(2013) Proc Natl Acad Sci U S A 110: 5881-5886

  • DOI: https://doi.org/10.1073/pnas.1217157110
  • Primary Citation of Related Structures:  
    4FXF, 4FXJ

  • PubMed Abstract: 

    We show that the M2 isoform of pyruvate kinase (M2PYK) exists in equilibrium between monomers and tetramers regulated by allosteric binding of naturally occurring small-molecule metabolites. Phenylalanine stabilizes an inactive T-state tetrameric conformer and inhibits M2PYK with an IC50 value of 0.24 mM, whereas thyroid hormone (triiodo-L-thyronine, T3) stabilizes an inactive monomeric form of M2PYK with an IC50 of 78 nM. The allosteric activator fructose-1,6-bisphosphate [F16BP, AC50 (concentration that gives 50% activation) of 7 μM] shifts the equilibrium to the tetrameric active R-state, which has a similar activity to that of the constitutively fully active isoform M1PYK. Proliferation assays using HCT-116 cells showed that addition of inhibitors phenylalanine and T3 both increased cell proliferation, whereas addition of the activator F16BP reduced proliferation. F16BP abrogates the inhibitory effect of both phenylalanine and T3, highlighting a dominant role of M2PYK allosteric activation in the regulation of cancer proliferation. X-ray structures show constitutively fully active M1PYK and F16BP-bound M2PYK in an R-state conformation with a lysine at the dimer-interface acting as a peg in a hole, locking the active tetramer conformation. Binding of phenylalanine in an allosteric pocket induces a 13° rotation of the protomers, destroying the peg-in-hole R-state interface. This distinct T-state tetramer is stabilized by flipped out Trp/Arg side chains that stack across the dimer interface. X-ray structures and biophysical binding data of M2PYK complexes explain how, at a molecular level, fluctuations in concentrations of amino acids, thyroid hormone, and glucose metabolites switch M2PYK on and off to provide the cell with a nutrient sensing and growth signaling mechanism.

  • Organizational Affiliation

    Centre for Translational and Chemical Biology, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyruvate kinase isozymes M1/M2A,
B [auth D],
D [auth B]
551Homo sapiensMutation(s): 0 
Gene Names: OIP3PK2PK3PKMPKM2pyruvate Kinase M2
UniProt & NIH Common Fund Data Resources
Find proteins for P14618 (Homo sapiens)
Explore P14618 
Go to UniProtKB:  P14618
GTEx:  ENSG00000067225 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14618
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ATP

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L [auth D],
V [auth B]
C10 H16 N5 O13 P3
Query on FBP

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H [auth A],
N [auth D],
R [auth C],
X [auth B]
C6 H14 O12 P2
Query on OXL

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E [auth A],
I [auth D],
O [auth C],
S [auth B]
C2 O4
Query on K

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F [auth A],
J [auth D],
P [auth C],
T [auth B]
Query on MG

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G [auth A]
K [auth D]
M [auth D]
Q [auth C]
U [auth B]
G [auth A],
K [auth D],
M [auth D],
Q [auth C],
U [auth B],
W [auth B]
Binding Affinity Annotations 
IDSourceBinding Affinity
FBP PDBBind:  4FXF IC50: 6500 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.55 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.6α = 90
b = 139.35β = 90.52
c = 111.28γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-27
    Type: Initial release
  • Version 1.1: 2013-04-24
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Refinement description, Structure summary