5X0I

Crystal structure of PKM2 R399E mutant complexed with FBP and serine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mutations in the PKM2 exon-10 region are associated with reduced allostery and increased nuclear translocation.

Chen, T.J.Wang, H.J.Liu, J.S.Cheng, H.H.Hsu, S.C.Wu, M.C.Lu, C.H.Wu, Y.F.Wu, J.W.Liu, Y.Y.Kung, H.J.Wang, W.C.

(2019) Commun Biol 2: 105-105

  • DOI: 10.1038/s42003-019-0343-4

  • PubMed Abstract: 
  • PKM2 is a key metabolic enzyme central to glucose metabolism and energy expenditure. Multiple stimuli regulate PKM2's activity through allosteric modulation and post-translational modifications. Furthermore, PKM2 can partner with KDM8, an oncogenic d ...

    PKM2 is a key metabolic enzyme central to glucose metabolism and energy expenditure. Multiple stimuli regulate PKM2's activity through allosteric modulation and post-translational modifications. Furthermore, PKM2 can partner with KDM8, an oncogenic demethylase and enter the nucleus to serve as a HIF1α co-activator. Yet, the mechanistic basis of the exon-10 region in allosteric regulation and nuclear translocation remains unclear. Here, we determined the crystal structures and kinetic coupling constants of exon-10 tumor-related mutants (H391Y and R399E), showing altered structural plasticity and reduced allostery. Immunoprecipitation analysis revealed increased interaction with KDM8 for H391Y, R399E, and G415R. We also found a higher degree of HIF1α-mediated transactivation activity, particularly in the presence of KDM8. Furthermore, overexpression of PKM2 mutants significantly elevated cell growth and migration. Together, PKM2 exon-10 mutations lead to structure-allostery alterations and increased nuclear functions mediated by KDM8 in breast cancer cells. Targeting the PKM2-KDM8 complex may provide a potential therapeutic intervention.


    Organizational Affiliation

    5Department of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, University of California Davis Cancer Centre, Sacramento, CA 95817 USA.,1Institute of Molecular and Cellular Biology and Department of Life Science, National Tsing-Hua University, Hsinchu, 30013 Taiwan.,3Institute of Biotechnology, National Tsing-Hua University, Hsinchu, 30013 Taiwan.,4Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli, 35053 Taiwan.,2Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli, 35053 Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyruvate kinase PKM
A, B, C, D
551Homo sapiensMutation(s): 1 
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 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B, C, D
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
PYR
Query on PYR

Download SDF File 
Download CCD File 
A, B, C, D
PYRUVIC ACID
C3 H4 O3
LCTONWCANYUPML-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
SER
Query on SER

Download SDF File 
Download CCD File 
A, B, C, D
SERINE
C3 H7 N O3
MTCFGRXMJLQNBG-REOHCLBHSA-N
 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 116.601α = 90.00
b = 137.875β = 90.00
c = 149.709γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data scaling
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-01-20 
  • Released Date: 2018-01-31 
  • Deposition Author(s): Wang, W.C., Chen, T.J.

Funding OrganizationLocationGrant Number
NHRITaiwanNHRI-EX105-10517BI

Revision History 

  • Version 1.0: 2018-01-31
    Type: Initial release
  • Version 1.1: 2019-04-03
    Type: Data collection, Database references
  • Version 1.2: 2019-11-20
    Type: Database references