4XZ2

Human platelet phosphofructokinase in an R-state in complex with ADP and F6P, crystal form I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.216 

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
  • Primary Citation of Related Structures:  

  • 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.
      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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP-dependent 6-phosphofructokinase, platelet type
A, B, C, D
761Homo sapiensMutation(s): 0 
Gene Names: PFKP (PFKF)
EC: 2.7.1.11
Find proteins for Q01813 (Homo sapiens)
Go to Gene View: PFKP
Go to UniProtKB:  Q01813
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
B, D
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-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
F6P
Query on F6P

Download SDF File 
Download CCD File 
B, D
FRUCTOSE-6-PHOSPHATE
C6 H13 O9 P
BGWGXPAPYGQALX-ARQDHWQXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.216 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 76.652α = 90.00
b = 164.524β = 102.96
c = 133.200γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XSCALEdata scaling
XDSdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-02-03 
  • Released Date: 2015-06-03 
  • Deposition Author(s): Kloos, M., Strater, N.

Funding OrganizationLocationGrant Number
DFGGermanySFB 610

Revision History 

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