Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 327615.75 
• Atom Count: 22567 
• Residue Count: 2972 
• Unique protein chains: 1

4U1R

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

• DOI: 10.2210/pdb4U1R/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2014-07-16 Released: 2015-06-03 
• Deposition Author(s): Kloos, M., Straeter, N.
• Funding Organization(s): DFG, SFB610 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.198 
• R-Value Work: 0.162 

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

• PubMed: 26205495 
• DOI: 10.1042/BJ20150251
• Primary Citation of Related Structures:  
  4WL0, 4XZ2, 4RH3


• 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.

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Related Citations: 

• Crystallization and preliminary crystallographic analysis of human muscle phosphofructokinase, the main regulator of glycolysis.
  Kloos, M.,Brueser, A.,Kirchberger, J.,Schoeneberg, T.,Straeter, N.
  (2014) Acta Crystallogr F Struct Biol Commun 70: 578




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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
Molecule	Chains	Sequence Length	Organism	Details
ATP-dependent 6-phosphofructokinase, platelet type	A, B, C, D	743	Homo sapiens	Mutation(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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ATP	A, B, C, D	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
PO4	A, B, C, D	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.198 
• R-Value Work: 0.162 
• Space Group: P 3₂ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 132.896	α = 90.00
b = 132.896	β = 90.00
c = 399.105	γ = 120.00

Software Package:

Software Name	Purpose
XSCALE	data reduction
XDS	data reduction
PDB_EXTRACT	data extraction
XSCALE	data scaling
PHASER	phasing
Coot	model building
REFMAC	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2014-07-16 
• Released Date: 2015-06-03 
• Deposition Author(s): Kloos, M., Straeter, N.

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Funding Organization	Location	Grant Number
DFG, SFB610	Germany	--

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