Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 233584.89 
• Atom Count: 13991 
• Residue Count: 2140 
• Unique protein chains: 1

4QG6

crystal structure of PKM2-Y105E mutant

• DOI: 10.2210/pdb4QG6/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 1 


• Deposited: 2014-05-22 Released: 2015-02-25 
• Deposition Author(s): Wang, P., Sun, C., Zhu, T., Xu, Y.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.207 Å
• R-Value Free: 0.265 
• R-Value Work: 0.220 

Literature

Structural insight into mechanisms for dynamic regulation of PKM2

Wang, P., Sun, C., Zhu, T., Xu, Y.

(2015) Protein Cell --: --

• PubMed: 25645022 
• DOI: 10.1007/s13238-015-0132-x
• Primary Citation of Related Structures:  
  4RPP, 4QGC, 4QG9, 4QG8


• PubMed Abstract: 
  

Pyruvate kinase isoform M2 (PKM2) converts phosphoenolpyruvate (PEP) to pyruvate and plays an important role in cancer metabolism. Here, we show that post-translational modifications and a patient-derived mutation regulate pyruvate kinase activity of PKM2 through modulating the conformation of the PKM2 tetramer. We determined crystal structures of human PKM2 mutants and proposed a "seesaw" model to illustrate conformational changes between an inactive T-state and an active R-state tetramers of PKM2. Biochemical and structural analyses demonstrate that PKM2(Y105E) (phosphorylation mimic of Y105) decreases pyruvate kinase activity by inhibiting FBP (fructose 1,6-bisphosphate)-induced R-state formation, and PKM2(K305Q) (acetylation mimic of K305) abolishes the activity by hindering tetramer formation. K422R, a patient-derived mutation of PKM2, favors a stable, inactive T-state tetramer because of strong intermolecular interactions. Our study reveals the mechanism for dynamic regulation of PKM2 by post-translational modifications and a patient-derived mutation and provides a structural basis for further investigation of other modifications and mutations of PKM2 yet to be discovered.

---

Organizational Affiliation: 

Fudan University Shanghai Cancer Center and Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032 China.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Pyruvate kinase PKM	A, B, C, D	535	Homo sapiens	Mutation(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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PRO	A, B, C, D	PROLINE C5 H9 N O2 ONIBWKKTOPOVIA-BYPYZUCNSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.207 Å
• R-Value Free: 0.265 
• R-Value Work: 0.220 
• Space Group: P 3₁

Unit Cell:

Length (Å)	Angle (°)
a = 124.455	α = 90.00
b = 124.455	β = 90.00
c = 257.049	γ = 120.00

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
ADSC	data collection
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-05-22 
• Released Date: 2015-02-25 
• Deposition Author(s): Wang, P., Sun, C., Zhu, T., Xu, Y.

Revision History 

• Version 1.0: 2015-02-25
  Type: Initial release
• Version 1.1: 2015-03-25
  Type: Structure summary