1FPG

STRUCTURAL ASPECTS OF THE ALLOSTERIC INHIBITION OF FRUCTOSE-1,6-BISPHOSPHATASE BY AMP: THE BINDING OF BOTH THE SUBSTRATE ANALOGUE 2,5-ANHYDRO-D-GLUCITOL-1,6-BISPHOSPHATE AND CATALYTIC METAL IONS MONITORED BY X-RAY CRYSTALLOGRAPHY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural aspects of the allosteric inhibition of fructose-1,6-bisphosphatase by AMP: the binding of both the substrate analogue 2,5-anhydro-D-glucitol 1,6-bisphosphate and catalytic metal ions monitored by X-ray crystallography.

Villeret, V.Huang, S.Zhang, Y.Lipscomb, W.N.

(1995) Biochemistry 34: 4307-4315

  • DOI: 10.1021/bi00013a020
  • Primary Citation of Related Structures:  
    1FPG, 1FPF, 1FPE, 1FPD

  • PubMed Abstract: 
  • The crystal structures of the T form pig kidney fructose-1,6-bisphosphatase (EC 3.1.3.11) complexed with AMP, the substrate analogue 2,5-anhydro-D-glucitol 1,6-bisphosphate (AhG-1,6-P2), and Mn2+ at concentrations of 5, 15, 100, and 300 microM have been determined and refined at resolutions of 2 ...

    The crystal structures of the T form pig kidney fructose-1,6-bisphosphatase (EC 3.1.3.11) complexed with AMP, the substrate analogue 2,5-anhydro-D-glucitol 1,6-bisphosphate (AhG-1,6-P2), and Mn2+ at concentrations of 5, 15, 100, and 300 microM have been determined and refined at resolutions of 2.1-2.3 A to R factors which range from 0.180 to 0.195, respectively. Two metal ions per active site have been identified, one at a binding site of high affinity (metal site 1'), the second in a low affinity site (metal site 2'). The 1-phosphate group of the substrate analogue coordinates to the metal ion at site 1', but not at site 2'. In these four complexes, the distances between the two metal ions are all within 0.2 A of 4.3 A. In the previously determined R form structure of Fru-1,6-Pase complexed with AhG-1,6-P2 and Mn2+, there are also two metal ions in the active site at metal sites 1 and 2. The metal ion at site 1 is only 0.6 A displaced from the metal ion at site 1' in the T form and is also coordinated to the 1-phosphate group of AhG-1,6-P2. However, the second metal ion is located in two distinct sites which are 1.4 A apart in the T and R form structures. In the R form the Mn2+ at site 2 is coordinated to the 1-phosphate group of the substrate analogue. This metal ion is apparently required to orient the phosphate group for nucleophilic attack at the phosphorus center.(ABSTRACT TRUNCATED AT 250 WORDS)


    Related Citations: 
    • Toward a Mechanism for the Allosteric Transition of Pig Kidney Fructose-1,6-Bisphosphatase
      Zhang, Y., Liang, J.-Y., Huang, S., Lipscomb, W.N.
      (1994) J Mol Biol 244: 609
    • 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
    • Conformational Transition of Fructose-1,6-Bisphosphatase: Structure Comparison between the AMP Complex (T Form) and the Fructose 6-Phosphate Complex (R Form)
      Ke, H., Liang, J.-Y., Zhang, Y., Lipscomb, W.N.
      (1991) Biochemistry 30: 4412

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FRUCTOSE 1,6-BISPHOSPHATASE AB335Sus scrofaMutation(s): 0 
Gene Names: FBP1FBP
EC: 3.1.3.11
Find proteins for P00636 (Sus scrofa)
Explore P00636 
Go to UniProtKB:  P00636
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AMPIC50:  1300   nM  BindingDB
AMPIC50:  9800   nM  BindingDB
AMPIC50:  800   nM  BindingDB
AMPIC50:  3200   nM  BindingDB
AMPIC50:  440   nM  BindingDB
AMPIC50:  140   nM  BindingDB
AMPIC50:  1000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.1α = 90
b = 166.5β = 90
c = 80γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1995-02-27
    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: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Database references, Derived calculations, Other, Structure summary