1UMG

Crystal structure of fructose-1,6-bisphosphatase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

The first crystal structure of the novel class of fructose-1,6-bisphosphatase present in thermophilic archaea.

Nishimasu, H.Fushinobu, S.Shoun, H.Wakagi, T.

(2004) Structure 12: 949-959

  • DOI: 10.1016/j.str.2004.03.026
  • Primary Citation of Related Structures:  
    1UMG

  • PubMed Abstract: 
  • As the first structure of the novel class of fructose-1,6-bisphosphatase (FBPase) present in thermophilic archaea, we solved the crystal structure of the ST0318 gene product (St-Fbp) of Sulfolobus tokodaii strain 7. The St-Fbp structure comprises a homooctamer of the 422 point-group ...

    As the first structure of the novel class of fructose-1,6-bisphosphatase (FBPase) present in thermophilic archaea, we solved the crystal structure of the ST0318 gene product (St-Fbp) of Sulfolobus tokodaii strain 7. The St-Fbp structure comprises a homooctamer of the 422 point-group. The protein folds as a four-layer alpha-beta-beta-alpha sandwich with a novel topology, which is completely different from the sugar phosphatase fold. The structure contains an unhydrolyzed FBP molecule in the open-keto form, as well as four hexacoordinated magnesium ions around the 1-phosphoryl group of FBP. The arrangement of the catalytic side chains and metal ligands is consistent with the three-metal ion assisted catalysis proposed for conventional FBPases. The structure provides an insight into the structural basis of the strict substrate specificity of St-Fbp.


    Organizational Affiliation

    Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
385aa long conserved hypothetical proteinA362Sulfurisphaera tokodaii str. 7Mutation(s): 0 
Gene Names: ST0318fbpSTK_03180
EC: 3.1.3.11 (PDB Primary Data), 4.1.2.13 (UniProt)
UniProt
Find proteins for F9VMT6 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7))
Explore F9VMT6 
Go to UniProtKB:  F9VMT6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2FP (Subject of Investigation/LOI)
Query on 2FP

Download Ideal Coordinates CCD File 
F [auth A]1,6-FRUCTOSE DIPHOSPHATE (LINEAR FORM)
C6 H14 O12 P2
XPYBSIWDXQFNMH-PYWDMBMJSA-N
 Ligand Interaction
MPD
Query on MPD

Download Ideal Coordinates CCD File 
G [auth A](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A], C [auth A], D [auth A], E [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.778α = 90
b = 111.778β = 90
c = 153.174γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-07-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2016-12-21
    Changes: Structure summary