1FBH

CRYSTALLOGRAPHIC STUDIES OF THE CATALYTIC MECHANISM OF THE NEUTRAL FORM OF FRUCTOSE-1,6-BISPHOSPHATASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Crystallographic studies of the catalytic mechanism of the neutral form of fructose-1,6-bisphosphatase.

Zhang, Y.Liang, J.Y.Huang, S.Ke, H.Lipscomb, W.N.

(1993) Biochemistry 32: 1844-1857

  • DOI: https://doi.org/10.1021/bi00058a019
  • Primary Citation of Related Structures:  
    1FBC, 1FBD, 1FBE, 1FBF, 1FBG, 1FBH

  • PubMed Abstract: 

    The crystal structures of fructose-1,6-bisphosphatase (EC 3.1.3.11) complexed with substrate alone or with substrate analogues in the presence of divalent metal ions have been determined. The substrate analogues, 2,5-anhydro-D-glucitol-1,6-bisphosphate (AhG-1,6-P2) and 2,5-anhydro-D-mannitol-1,6-bisphosphate (AhM-1,6-P2), differ from the alpha and beta anomers of fructose-1,6-bisphosphate (Fru-1,6-P2), respectively, in that the OH on C2 is replaced by a hydrogen atom. Structures have been refined at resolutions of 2.5 to 3.0 A to R factors of 0.172 to 0.195 with root-mean-square deviations of 0.012-0.018 A and 2.7-3.8 degrees from the ideal geometries of bond lengths and bond angles, respectively. In addition, the complex of substrate with the enzyme has been determined in the absence of metal. The electron density at 2.5-A resolution does not distinguish between alpha and beta anomers, which differ for the most part only in the position of the 1-phosphate group and the orientation of the C2-hydroxyl group. The positions of the 6-phosphate and the sugar ring of the substrate analogues are almost identical to those of the respective anomer of the substrate. In the presence of metal ions the positions of the 1-phosphate groups of both alpha and beta analogues differ significantly (0.8-1.0 A) from those of anomers of the substrate in the metal-free complex. Two metal ions (Mn2+ or Zn2+) are located at the enzyme active site of complexes of the alpha analogue AhG-1,6-P2. Metal site 1 is coordinated by the carboxylate groups of Glu-97, Asp-118, and Glu-280 and the 1-phosphate group of substrate analogue, while the metal site 2 is coordinated by the carboxylate groups of Glu-97, Asp-118, the 1-phosphate group of substrate analogue, and the carbonyl oxygen of Leu-120. Both metal sites have a distorted tetrahedral geometry. However, only one metal ion (Mg2+ or Mn2+) is found very near the metal site 1 in the enzyme's active site in complexes of the beta analogue AhM-1,6-P2 or for Mg2+ in the complex of the alpha analogue AhG-1,6-P2. This single metal ion is coordinated by the carboxylate groups of Glu-97, Asp-118, Asp-121, and Glu-280 and the 1-phosphate group of substrate analogue in a distorted square pyramidal geometry.(ABSTRACT TRUNCATED AT 400 WORDS)


  • Organizational Affiliation

    Gibbs Chemical Laboratory, Harvard University, Cambridge, Massachusetts 02138.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FRUCTOSE 1,6-BISPHOSPHATASE
A, B
335Sus scrofaMutation(s): 0 
EC: 3.1.3.11
UniProt
Find proteins for P00636 (Sus scrofa)
Explore P00636 
Go to UniProtKB:  P00636
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00636
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FBP
Query on FBP

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
1,6-di-O-phosphono-beta-D-fructofuranose
C6 H14 O12 P2
RNBGYGVWRKECFJ-ARQDHWQXSA-N
AFP
Query on AFP

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
1,6-di-O-phosphono-alpha-D-fructofuranose
C6 H14 O12 P2
RNBGYGVWRKECFJ-ZXXMMSQZSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.2α = 90
b = 131.2β = 90
c = 69.3γ = 120
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 2.1: 2024-02-07
    Changes: Data collection, Database references, Structure summary