3CQD

Structure of the tetrameric inhibited form of phosphofructokinase-2 from Escherichia coli

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


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

Literature

Crystallographic structure of phosphofructokinase-2 from Escherichia coli in complex with two ATP molecules. Implications for substrate inhibition.

Cabrera, R., Ambrosio, A.L., Garratt, R.C., Guixe, V., Babul, J.

(2008) J.Mol.Biol. 383: 588-602

  • DOI: 10.1016/j.jmb.2008.08.029

  • PubMed Abstract: 

    • Phosphofructokinase-1 and -2 (Pfk-1 and Pfk-2, respectively) from Escherichia coli belong to different homologous superfamilies. However, in spite of the lack of a common ancestor, they share the ability to catalyze the same reaction and are inhibite ...

    Phosphofructokinase-1 and -2 (Pfk-1 and Pfk-2, respectively) from Escherichia coli belong to different homologous superfamilies. However, in spite of the lack of a common ancestor, they share the ability to catalyze the same reaction and are inhibited by the substrate MgATP. Pfk-2, an ATP-dependent 6-phosphofructokinase member of the ribokinase-like superfamily, is a homodimer of 66 kDa subunits whose oligomerization state is necessary for catalysis and stability. The presence of MgATP favors the tetrameric form of the enzyme. In this work, we describe the structure of Pfk-2 in its inhibited tetrameric form, with each subunit bound to two ATP molecules and two Mg ions. The present structure indicates that substrate inhibition occurs due to the sequential binding of two MgATP molecules per subunit, the first at the usual site occupied by the nucleotide in homologous enzymes and the second at the allosteric site, making a number of direct and Mg-mediated interactions with the first. Two configurations are observed for the second MgATP, one of which involves interactions with Tyr23 from the adjacent subunit in the dimer and the other making an unusual non-Watson-Crick base pairing with the adenine in the substrate ATP. The oligomeric state observed in the crystal is tetrameric, and some of the structural elements involved in the binding of the substrate and allosteric ATPs are also participating in the dimer-dimer interface. This structure also provides the grounds to compare analogous features of the nonhomologous phosphofructokinases from E. coli.

    Organizational Affiliation: 

    Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago, Chile.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
6-phosphofructokinase isozyme 2
A, B
309Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: pfkB
EC: 2.7.1.11
Find proteins for P06999 (Escherichia coli (strain K12))
Go to UniProtKB:  P06999
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP
Download SDF File 
Download CCD File 
A, B
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG
Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.186 
  • Space Group: P 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 42.822α = 90.00
b = 86.834β = 90.00
c = 171.308γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
MAR345data collection
REFMACrefinement
SCALAdata scaling
MOSFLMdata 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: 2008-09-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description