3UQD

Crystal structure of the Phosphofructokinase-2 from Escherichia coli in complex with substrates and products


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Studying the phosphoryl transfer mechanism of theE. coliphosphofructokinase-2: from X-ray structure to quantum mechanics/molecular mechanics simulations.

Murillo-Lopez, J.Zinovjev, K.Pereira, H.Caniuguir, A.Garratt, R.Babul, J.Recabarren, R.Alzate-Morales, J.Caballero, J.Tunon, I.Cabrera, R.

(2019) Chem Sci 10: 2882-2892

  • DOI: 10.1039/c9sc00094a
  • Primary Citation of Related Structures:  
    3UQD

  • PubMed Abstract: 
  • Phosphofructokinases (Pfks) catalyze the ATP-dependent phosphorylation of fructose-6-phosphate (F6P) and they are regulated in a wide variety of organisms. Although numerous aspects of the kinetics and regulation have been characterized for Pfks, the ...

    Phosphofructokinases (Pfks) catalyze the ATP-dependent phosphorylation of fructose-6-phosphate (F6P) and they are regulated in a wide variety of organisms. Although numerous aspects of the kinetics and regulation have been characterized for Pfks, the knowledge about the mechanism of the phosphoryl transfer reaction and the transition state lags behind. In this work, we describe the X-ray crystal structure of the homodimeric Pfk-2 from E. coli , which contains products in one site and reactants in the other, as well as an additional ATP molecule in the inhibitory allosteric site adjacent to the reactants. This complex was previously predicted when studying the kinetic mechanism of ATP inhibition. After removing the allosteric ATP, molecular dynamic (MD) simulations revealed conformational changes related to domain packing, as well as stable interactions of Lys27 and Asp256 with donor (ATP) and acceptor (fructose-6-) groups, and of Asp166 with Mg 2+ . The phosphoryl transfer reaction mechanism catalyzed by Pfk-2 was investigated through Quantum Mechanics/Molecular Mechanics (QM/MM) simulations using a combination of the string method and a path-collective variable for the exploration of its free energy surface. The calculated activation free energies showed that a dissociative mechanism, occurring with a metaphosphate intermediate formation followed by a proton transfer to Asp256, is more favorable than an associative one. The structural analysis reveals the role of Asp256 acting as a catalytic base and Lys27 stabilizing the transition state of the dissociative mechanism.


    Organizational Affiliation

    Departamento de Biología , Facultad de Ciencias , Universidad de Chile , Santiago , Chile . Email: ricabrer@uchile.cl.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
6-phosphofructokinase isozyme 2ABCD309Escherichia coli K-12Mutation(s): 0 
Gene Names: b1723JW5280PFK2pfkB
EC: 2.7.1.11
Find proteins for P06999 (Escherichia coli (strain K12))
Explore P06999 
Go to UniProtKB:  P06999
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 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
ADP
Query on ADP

Download CCD File 
B, C
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
FBP
Query on FBP

Download CCD File 
B, C
1,6-di-O-phosphono-beta-D-fructofuranose
C6 H14 O12 P2
RNBGYGVWRKECFJ-ARQDHWQXSA-N
 Ligand Interaction
F6P
Query on F6P

Download CCD File 
A, D
6-O-phosphono-beta-D-fructofuranose
C6 H13 O9 P
BGWGXPAPYGQALX-ARQDHWQXSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.885α = 90
b = 155.189β = 90
c = 224.989γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
DMphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-28
    Type: Initial release
  • Version 1.1: 2019-03-27
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-13
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary