6WP4

Pyruvate Kinase M2 mutant-S37E


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis for allosteric regulation of pyruvate kinase M2 by phosphorylation and acetylation.

Nandi, S.Razzaghi, M.Srivastava, D.Dey, M.

(2020) J Biol Chem 295: 17425-17440

  • DOI: https://doi.org/10.1074/jbc.RA120.015800
  • Primary Citation of Related Structures:  
    6WP3, 6WP4, 6WP5, 6WP6

  • PubMed Abstract: 

    Pyruvate kinase muscle isoform 2 (PKM2) is a key glycolytic enzyme and transcriptional coactivator and is critical for tumor metabolism. In cancer cells, native tetrameric PKM2 is phosphorylated or acetylated, which initiates a switch to a dimeric/monomeric form that translocates into the nucleus, causing oncogene transcription. However, it is not known how these post-translational modifications (PTMs) disrupt the oligomeric state of PKM2. We explored this question via crystallographic and biophysical analyses of PKM2 mutants containing residues that mimic phosphorylation and acetylation. We find that the PTMs elicit major structural reorganization of the fructose 1,6-bisphosphate (FBP), an allosteric activator, binding site, impacting the interaction with FBP and causing a disruption in oligomerization. To gain insight into how these modifications might cause unique outcomes in cancer cells, we examined the impact of increasing the intracellular pH (pH i ) from ∼7.1 (in normal cells) to ∼7.5 (in cancer cells). Biochemical studies of WT PKM2 (wtPKM2) and the two mimetic variants demonstrated that the activity decreases as the pH is increased from 7.0 to 8.0, and wtPKM2 is optimally active and amenable to FBP-mediated allosteric regulation at pH i 7.5. However, the PTM mimetics exist as a mixture of tetramer and dimer, indicating that physiologically dimeric fraction is important and might be necessary for the modified PKM2 to translocate into the nucleus. Thus, our findings provide insight into how PTMs and pH regulate PKM2 and offer a broader understanding of its intricate allosteric regulation mechanism by phosphorylation or acetylation.


  • Organizational Affiliation

    Department of Chemistry, University of Iowa, Iowa City, Iowa, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyruvate kinase PKM
A, B, C, D
550Homo sapiensMutation(s): 1 
Gene Names: PKMOIP3PK2PK3PKM2
EC: 2.7.1.40
UniProt & NIH Common Fund Data Resources
Find proteins for P14618 (Homo sapiens)
Explore P14618 
Go to UniProtKB:  P14618
PHAROS:  P14618
GTEx:  ENSG00000067225 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14618
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
JA [auth D]
KA [auth D]
E [auth A],
F [auth A],
G [auth A],
JA [auth D],
KA [auth D],
LA [auth D],
Q [auth B],
R [auth B],
S [auth B],
Y [auth C],
Z [auth C]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

Download Ideal Coordinates CCD File 
CA [auth C]
DA [auth C]
EA [auth C]
FA [auth C]
GA [auth C]
CA [auth C],
DA [auth C],
EA [auth C],
FA [auth C],
GA [auth C],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
QA [auth D],
RA [auth D],
SA [auth D],
TA [auth D],
V [auth B],
W [auth B],
X [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
OXL
Query on OXL

Download Ideal Coordinates CCD File 
J [auth A],
PA [auth D]
OXALATE ION
C2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-L
K
Query on K

Download Ideal Coordinates CCD File 
BA [auth C],
I [auth A],
NA [auth D],
OA [auth D],
U [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
HA [auth C],
IA [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth C],
H [auth A],
MA [auth D],
T [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.167α = 90
b = 132.628β = 112.74
c = 110.128γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
Cootmodel building
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesCLP 1506181

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 1.1: 2020-10-28
    Changes: Database references
  • Version 1.2: 2021-02-24
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Database references, Refinement description