3O8O

Structure of phosphofructokinase from Saccharomyces cerevisiae

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.259 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

The Crystal Structures of Eukaryotic Phosphofructokinases from Baker's Yeast and Rabbit Skeletal Muscle.

Banaszak, K., Mechin, I., Obmolova, G., Oldham, M., Chang, S.H., Ruiz, T., Radermacher, M., Kopperschlager, G., Rypniewski, W.

(2011) J.Mol.Biol. 407: 284-297

  • DOI: 10.1016/j.jmb.2011.01.019
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Phosphofructokinase 1 (PFK) is a multisubunit allosteric enzyme that catalyzes the principal regulatory step in glycolysis-the phosphorylation of fructose 6-phosphate to fructose 1,6-bisphosphate by ATP. The activity of eukaryotic PFK is modulated by ...

    Phosphofructokinase 1 (PFK) is a multisubunit allosteric enzyme that catalyzes the principal regulatory step in glycolysis-the phosphorylation of fructose 6-phosphate to fructose 1,6-bisphosphate by ATP. The activity of eukaryotic PFK is modulated by a number of effectors in response to the cell's needs for energy and building blocks for biosynthesis. The crystal structures of eukaryotic PFKs-from Saccharomyces cerevisiae and rabbit skeletal muscle-demonstrate how successive gene duplications and fusion are reflected in the protein structure and how they allowed the evolution of new functionalities. The basic framework inherited from prokaryotes is conserved, and additional levels of structural and functional complexity have evolved around it. Analysis of protein-ligand complexes has shown how PFK is activated by fructose 2,6-bisphosphate (a powerful PFK effector found only in eukaryotes) and reveals a novel nucleotide binding site. Crystallographic results have been used as the basis for structure-based effector design.

    Organizational Affiliation: 

    Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
6-phosphofructokinase subunit alpha
A, C, E, G
787Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PFK1
EC: 2.7.1.11
Find proteins for P16861 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P16861
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
6-phosphofructokinase subunit beta
B, D, F, H
766Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PFK2
EC: 2.7.1.11
Find proteins for P16862 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P16862
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FDP
Query on FDP
Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
FRUCTOSE-2,6-DIPHOSPHATE
C6 H14 O12 P2
YXWOAJXNVLXPMU-ZXXMMSQZSA-N
 Ligand Interaction
F6P
Query on F6P
Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
FRUCTOSE-6-PHOSPHATE
C6 H13 O9 P
BGWGXPAPYGQALX-ARQDHWQXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.259 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 180.046α = 90.00
b = 186.205β = 90.00
c = 236.507γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
SCALEPACKdata scaling
MAR345data collection
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-02-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Advisory, Refinement description