4U1R

ATP-bound structure of human platelet phosphofructokinase in an R-state, crystal form II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of human platelet phosphofructokinase-1 locked in an activated conformation.

Kloos, M.Bruser, A.Kirchberger, J.Schoneberg, T.Strater, N.

(2015) Biochem J 469: 421-432

  • DOI: 10.1042/BJ20150251
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Phosphofructokinase-1 (Pfk) acts as the main control point of flux through glycolysis. It is involved in complex allosteric regulation and Pfk mutations have been linked to cancer development. Whereas the 3D structure and structural basis of alloster ...

    Phosphofructokinase-1 (Pfk) acts as the main control point of flux through glycolysis. It is involved in complex allosteric regulation and Pfk mutations have been linked to cancer development. Whereas the 3D structure and structural basis of allosteric regulation of prokaryotic Pfk has been studied in great detail, our knowledge about the molecular basis of the allosteric behaviour of the more complex mammalian Pfk is still very limited. To characterize the structural basis of allosteric regulation, the subunit interfaces and the functional consequences of modifications in Tarui's disease and cancer, we analysed the physiological homotetramer of human platelet Pfk at up to 2.67 Å resolution in two crystal forms. The crystallized enzyme is permanently activated by a deletion of the 22 C-terminal residues. Complex structures with ADP and fructose-6-phosphate (F6P) and with ATP suggest a role of three aspartates in the deprotonation of the OH-nucleophile of F6P and in the co-ordination of the catalytic magnesium ion. Changes at the dimer interface, including an asymmetry observed in both crystal forms, are the primary mechanism of allosteric regulation of Pfk by influencing the F6P-binding site. Whereas the nature of this conformational switch appears to be largely conserved in bacterial, yeast and mammalian Pfk, initiation of these changes differs significantly in eukaryotic Pfk.


    Related Citations: 
    • Crystallization and preliminary crystallographic analysis of human muscle phosphofructokinase, the main regulator of glycolysis.
      Kloos, M., Brueser, A., Kirchberger, J., Schoeneberg, T., Straeter, N.
      (2014) Acta Crystallogr F Struct Biol Commun 70: 578

    Organizational Affiliation

    Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, University of Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany strater@bbz.uni-leipzig.de.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP-dependent 6-phosphofructokinase, platelet type
A, B, C, D
743Homo sapiensMutation(s): 0 
Gene Names: PFKPPFKF
EC: 2.7.1.11
Find proteins for Q01813 (Homo sapiens)
Go to UniProtKB:  Q01813
NIH Common Fund Data Resources
PHAROS  Q01813
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download CCD File 
A, B, C, D
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A, B, C, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.896α = 90
b = 132.896β = 90
c = 399.105γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
Cootmodel building
XSCALEdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
DFG, SFB610Germany--

Revision History 

  • Version 1.0: 2015-06-03
    Type: Initial release
  • Version 1.1: 2015-07-01
    Changes: Database references
  • Version 1.2: 2015-08-05
    Changes: Database references