4B2D

human PKM2 with L-serine and FBP bound.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Serine is a natural ligand and allosteric activator of pyruvate kinase M2.

Chaneton, B.Hillmann, P.Zheng, L.Martin, A.C.L.Maddocks, O.D.K.Chokkathukalam, A.Coyle, J.E.Jankevics, A.Holding, F.P.Vousden, K.H.Frezza, C.O'Reilly, M.Gottlieb, E.

(2012) Nature 491: 458-462

  • DOI: 10.1038/nature11540

  • PubMed Abstract: 
  • Cancer cells exhibit several unique metabolic phenotypes that are critical for cell growth and proliferation. Specifically, they overexpress the M2 isoform of the tightly regulated enzyme pyruvate kinase (PKM2), which controls glycolytic flux, and ar ...

    Cancer cells exhibit several unique metabolic phenotypes that are critical for cell growth and proliferation. Specifically, they overexpress the M2 isoform of the tightly regulated enzyme pyruvate kinase (PKM2), which controls glycolytic flux, and are highly dependent on de novo biosynthesis of serine and glycine. Here we describe a new rheostat-like mechanistic relationship between PKM2 activity and serine biosynthesis. We show that serine can bind to and activate human PKM2, and that PKM2 activity in cells is reduced in response to serine deprivation. This reduction in PKM2 activity shifts cells to a fuel-efficient mode in which more pyruvate is diverted to the mitochondria and more glucose-derived carbon is channelled into serine biosynthesis to support cell proliferation.


    Organizational Affiliation

    Cancer Research UK, The Beatson Institute for Cancer Research, Switchback Road, Glasgow, G61 1BD, Scotland, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PYRUVATE KINASE ISOZYMES M1/M2
A, B, C
548Homo sapiensGene 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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PYRUVATE KINASE ISOZYMES M1/M2
D
548Homo sapiensGene 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
MG
Query on MG

Download SDF File 
Download CCD File 
A, C
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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SERKd: 200000 nM BINDINGMOAD
SERKd: 200000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 80.611α = 90.00
b = 151.098β = 102.01
c = 91.791γ = 90.00
Software Package:
Software NamePurpose
CSEARCHphasing
BUSTERrefinement
SCALAdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-10
    Type: Initial release
  • Version 1.1: 2012-10-24
    Type: Database references
  • Version 1.2: 2012-11-21
    Type: Database references
  • Version 1.3: 2013-02-06
    Type: Atomic model, Derived calculations, Other
  • Version 1.4: 2018-02-07
    Type: Database references, Structure summary