3MBF

Crystal structure of fructose bisphosphate aldolase from Encephalitozoon cuniculi, bound to fructose 1,6-bisphosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of fructose bisphosphate aldolase from Encephalitozoon cuniculi.

Gardberg, A.Sankaran, B.Davies, D.Bhandari, J.Staker, B.Stewart, L.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 1055-1059

  • DOI: 10.1107/S1744309111021841
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Fructose bisphosphate aldolose (FBPA) enzymes have been found in a broad range of eukaryotic and prokaryotic organisms. FBPA catalyses the cleavage of fructose 1,6-bisphosphate into glyceraldehyde 3-phosphate and dihydroxyacetone phosphate. The SSGCI ...

    Fructose bisphosphate aldolose (FBPA) enzymes have been found in a broad range of eukaryotic and prokaryotic organisms. FBPA catalyses the cleavage of fructose 1,6-bisphosphate into glyceraldehyde 3-phosphate and dihydroxyacetone phosphate. The SSGCID has reported several FBPA structures from pathogenic sources. Bioinformatic analysis of the genome of the eukaryotic microsporidian parasite Encephalitozoon cuniculi revealed an FBPA homolog. The structures of this enzyme in the presence of the native substrate FBP and also with the partial substrate analog phosphate are reported. The purified enzyme crystallized in 90 mM Bis-Tris propane pH 6.5, 18% PEG 3350, 18 mM NaKHPO(4), 10 mM urea for the phosphate-bound form and 100 mM Bis-Tris propane pH 6.5, 20% PEG 3350, 20 mM fructose 1,6-bisphosphate for the FBP-bound form. In both cases protein was present at 25 mg ml(-1) and the sitting-drop vapour-diffusion method was used. For the FBP-bound form, a data set to 2.37 Å resolution was collected from a single crystal at 100 K. The crystal belonged to the orthorhombic space group C222(1), with unit-cell parameters a=121.46, b=135.82, c=61.54 Å. The structure was refined to a final free R factor of 20.8%. For the phosphate-bound form, a data set was collected to 2.00 Å resolution. The space group was also C222(1) and the unit-cell parameters were a=121.96, b=137.61, c=62.23 Å. The structure shares the typical barrel tertiary structure reported for previous FBPA structures and exhibits the same Schiff base in the active site. The quaternary structure is dimeric. This work provides a direct experimental result for the substrate-binding conformation of the product state of E. cuniculi FBPA.


    Organizational Affiliation

    Emerald BioStructures, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA. agardberg@embios.com



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fructose-bisphosphate aldolase
A
342Encephalitozoon cuniculiMutation(s): 0 
Gene Names: ECU01_0240
EC: 4.1.2.13
Find proteins for Q8SSM8 (Encephalitozoon cuniculi (strain GB-M1))
Go to UniProtKB:  Q8SSM8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2FP
Query on 2FP

Download CCD File 
A
1,6-FRUCTOSE DIPHOSPHATE (LINEAR FORM)
C6 H14 O12 P2
XPYBSIWDXQFNMH-PYWDMBMJSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 
  • Space Group: C 2 2 21
  • Diffraction Data DOI: 3MBF Protein Diffraction
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.46α = 90
b = 135.82β = 90
c = 61.54γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-04-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-09-21
    Changes: Database references