3U2Z

Activator-Bound Structure of Human Pyruvate Kinase M2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Pyruvate kinase M2 activators promote tetramer formation and suppress tumorigenesis.

Anastasiou, D.Yu, Y.Israelsen, W.J.Jiang, J.K.Boxer, M.B.Hong, B.S.Tempel, W.Dimov, S.Shen, M.Jha, A.Yang, H.Mattaini, K.R.Metallo, C.M.Fiske, B.P.Courtney, K.D.Malstrom, S.Khan, T.M.Kung, C.Skoumbourdis, A.P.Veith, H.Southall, N.Walsh, M.J.Brimacombe, K.R.Leister, W.Lunt, S.Y.Johnson, Z.R.Yen, K.E.Kunii, K.Davidson, S.M.Christofk, H.R.Austin, C.P.Inglese, J.Harris, M.H.Asara, J.M.Stephanopoulos, G.Salituro, F.G.Jin, S.Dang, L.Auld, D.S.Park, H.W.Cantley, L.C.Thomas, C.J.Vander Heiden, M.G.

(2012) Nat.Chem.Biol. 8: 839-847

  • DOI: 10.1038/nchembio.1060
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cancer cells engage in a metabolic program to enhance biosynthesis and support cell proliferation. The regulatory properties of pyruvate kinase M2 (PKM2) influence altered glucose metabolism in cancer. The interaction of PKM2 with phosphotyrosine-con ...

    Cancer cells engage in a metabolic program to enhance biosynthesis and support cell proliferation. The regulatory properties of pyruvate kinase M2 (PKM2) influence altered glucose metabolism in cancer. The interaction of PKM2 with phosphotyrosine-containing proteins inhibits enzyme activity and increases the availability of glycolytic metabolites to support cell proliferation. This suggests that high pyruvate kinase activity may suppress tumor growth. We show that expression of PKM1, the pyruvate kinase isoform with high constitutive activity, or exposure to published small-molecule PKM2 activators inhibits the growth of xenograft tumors. Structural studies reveal that small-molecule activators bind PKM2 at the subunit interaction interface, a site that is distinct from that of the endogenous activator fructose-1,6-bisphosphate (FBP). However, unlike FBP, binding of activators to PKM2 promotes a constitutively active enzyme state that is resistant to inhibition by tyrosine-phosphorylated proteins. These data support the notion that small-molecule activation of PKM2 can interfere with anabolic metabolism.


    Organizational Affiliation

    Department of Medicine, Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, MA, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyruvate kinase isozymes M1/M2
A, B, C, D
533Homo sapiensMutation(s): 0 
Gene Names: PKM (OIP3, PK2, PK3, PKM2)
EC: 2.7.1.40
Find proteins for P14618 (Homo sapiens)
Go to Gene View: PKM
Go to UniProtKB:  P14618
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UNX
Query on UNX

Download SDF File 
Download CCD File 
A, B, C, D
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
FBP
Query on FBP

Download SDF File 
Download CCD File 
A, B, C, D
BETA-FRUCTOSE-1,6-DIPHOSPHATE
FRUCTOSE-1,6-BISPHOSPHATE
C6 H14 O12 P2
RNBGYGVWRKECFJ-ARQDHWQXSA-N
 Ligand Interaction
07T
Query on 07T

Download SDF File 
Download CCD File 
B, C
6-(3-aminobenzyl)-4-methyl-2-methylsulfinyl-4,6-dihydro-5H-thieno[2',3':4,5]pyrrolo[2,3-d]pyridazin-5-one
C17 H16 N4 O2 S2
ZWKJWVSEDISQIS-RUZDIDTESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 80.762α = 90.00
b = 151.163β = 102.94
c = 93.213γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
HKL-3000data scaling
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2012-09-12
    Type: Initial release
  • Version 1.1: 2013-01-02
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Refinement description