4OMT | pdb_00004omt

Crystal structure of human muscle phosphofructokinase (dissociated homodimer)

• PDB DOI: https://doi.org/10.2210/pdb4OMT/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2014-01-27 Released: 2014-05-14 
• Deposition Author(s): Kloos, M., Straeter, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 6.00 Å
• R-Value Free: 
  0.274 (Depositor), 0.291 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.263 (DCC) 
• R-Value Observed: 
  0.242 (Depositor) 

Starting Model: experimental

Literature

Crystallization and preliminary crystallographic analysis of human muscle phosphofructokinase, the main regulator of glycolysis.

Kloos, M., Bruser, A., Kirchberger, J., Schoneberg, T., Strater, N.

(2014) Acta Crystallogr Sect F Struct Biol Cryst Commun 70: 578-582

• PubMed: 24817713 
• DOI: https://doi.org/10.1107/S2053230X14008723
• Primary Citation Related Structures: 
  4OMT


• PubMed Abstract: 
  

  Whereas the three-dimensional structure and the structural basis of the allosteric regulation of prokaryotic 6-phosphofructokinases (Pfks) have been studied in great detail, knowledge of the molecular basis of the allosteric behaviour of the far more complex mammalian Pfks is still very limited. The human muscle isozyme was expressed heterologously in yeast cells and purified using a five-step purification protocol. Protein crystals suitable for diffraction experiments were obtained by the vapour-diffusion method. The crystals belonged to space group P6222 and diffracted to 6.0 Å resolution. The 3.2 Å resolution structure of rabbit muscle Pfk (rmPfk) was placed into the asymmetric unit and optimized by rigid-body and group B-factor refinement. Interestingly, the tetrameric enzyme dissociated into a dimer, similar to the situation observed in the structure of rmPfk.

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Organizational Affiliation: 
• Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, University of Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany.
Institute of Biochemistry, Medical Faculty, University of Leipzig, Johannisallee 30, 04103 Leipzig, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 85.29 kDa 
• Atom Count: 5,715 
• Modeled Residue Count: 748 
• Deposited Residue Count: 780 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-phosphofructokinase, muscle type	A	780	Homo sapiens	Mutation(s): 0  Gene Names: PFKM, PFKX EC: 2.7.1.11
UniProt & NIH Common Fund Data Resources
Find proteins for P08237 (Homo sapiens) Explore P08237  Go to UniProtKB:  P08237
PHAROS:  P08237 GTEx:  ENSG00000152556

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 6.00 Å
• R-Value Free:  0.274 (Depositor), 0.291 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.263 (DCC) 
• R-Value Observed: 0.242 (Depositor) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 229.7	α = 90
b = 229.7	β = 90
c = 133	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MxCuBE	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-05-14 
Deposition Author(s): Kloos, M., Straeter, N.

Revision History  

• Version 1.0: 2014-05-14
  Type: Initial release
  
• Version 1.1: 2014-09-24
  Changes: Database references
• Version 1.2: 2014-12-10
  Changes: Structure summary
• Version 1.3: 2019-07-17
  Changes: Data collection, Refinement description
• Version 1.4: 2023-09-20
  Changes: Data collection, Database references, Refinement description