4RPP

crystal structure of PKM2-K422R mutant bound with FBP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.274 
  • R-Value Observed: 0.275 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Structural insight into mechanisms for dynamic regulation of PKM2.

Wang, P.Sun, C.Zhu, T.Xu, Y.

(2015) Protein Cell 6: 275-287

  • DOI: https://doi.org/10.1007/s13238-015-0132-x
  • Primary Citation of Related Structures:  
    4QG6, 4QG8, 4QG9, 4QGC, 4RPP

  • 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyruvate kinase PKM
A, B, C, D
535Homo sapiensMutation(s): 1 
Gene Names: PKMPKM2
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.274 
  • R-Value Observed: 0.275 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.674α = 90
b = 152.554β = 104.24
c = 97.676γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-25
    Type: Initial release
  • Version 1.1: 2015-03-25
    Changes: Structure summary
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.3: 2022-08-24
    Changes: Database references, Structure summary
  • Version 2.0: 2023-04-05
    Changes: Advisory, Atomic model, Database references, Polymer sequence, Source and taxonomy, Structure summary