4RH3

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.148 

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Ligand Structure Quality Assessment 


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: https://doi.org/10.1042/BJ20150251
  • Primary Citation of Related Structures:  
    4RH3, 4U1R, 4WL0, 4XZ2

  • 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 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.


  • 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent 6-phosphofructokinase, platelet type
A, B, C, D
743Homo sapiensMutation(s): 0 
Gene Names: PFKFPFKP
EC: 2.7.1.11
UniProt & NIH Common Fund Data Resources
Find proteins for Q01813 (Homo sapiens)
Explore Q01813 
Go to UniProtKB:  Q01813
PHAROS:  Q01813
GTEx:  ENSG00000067057 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ01813
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACP
Query on ACP

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
K [auth C],
N [auth D]
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth B]
I [auth B]
L [auth C]
F [auth A],
G [auth A],
H [auth B],
I [auth B],
L [auth C],
M [auth C],
O [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.148 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.911α = 90
b = 132.911β = 90
c = 397.168γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MxCuBEdata collection

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2015-06-24 
  • Deposition Author(s): Kloos, M.

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-24
    Type: Initial release
  • Version 1.1: 2015-08-05
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations, Refinement description