Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 37.13 kDa 
• Atom Count: 2797 
• Modelled Residue Count: 328 
• Deposited Residue Count: 337 
• Unique protein chains: 1

1NUW

Fructose-1,6-Bisphosphatase Complex with Magnesium, Fructose-6-Phosphate and Phosphate at pH 9.6

• PDB DOI: 10.2210/pdb1NUW/pdb

• Classification: HYDROLASE
• Organism(s): Sus scrofa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-02-01 Released: 2003-07-08 
• Deposition Author(s): Choe, J., Iancu, C.V., Fromm, H.J., Honzatko, R.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.207 
• R-Value Work: 0.164 
• R-Value Observed: 0.168 

Literature

Metaphosphate in the active site of fructose-1,6-bisphosphatase

Choe, J.Y., Iancu, C.V., Fromm, H.J., Honzatko, R.B.

(2003) J Biol Chem 278: 16015-16020

• PubMed: 12595528 
• DOI: 10.1074/jbc.M212395200
• Primary Citation of Related Structures:  
  1NUW, 1NUX, 1NUY


• PubMed Abstract: 
  

The hydrolysis of a phosphate ester can proceed through an intermediate of metaphosphate (dissociative mechanism) or through a trigonal bipryamidal transition state (associative mechanism). Model systems in solution support the dissociative pathway, whereas most enzymologists favor an associative mechanism for enzyme-catalyzed reactions. Crystals of fructose-1,6-bisphosphatase grow from an equilibrium mixture of substrates and products at near atomic resolution (1.3 A). At neutral pH, products of the reaction (orthophosphate and fructose 6-phosphate) bind to the active site in a manner consistent with an associative reaction pathway; however, in the presence of inhibitory concentrations of K+ (200 mm), or at pH 9.6, metaphosphate and water (or OH-) are in equilibrium with orthophosphate. Furthermore, one of the magnesium cations in the pH 9.6 complex resides in an alternative position, and suggests the possibility of metal cation migration as the 1-phosphoryl group of the substrate undergoes hydrolysis. To the best of our knowledge, the crystal structures reported here represent the first direct observation of metaphosphate in a condensed phase and may provide the structural basis for fundamental changes in the catalytic mechanism of fructose-1,6-bisphosphatase in response to pH and different metal cation activators.

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Organizational Affiliation: 

Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fructose-1,6-bisphosphatase	A	337	Sus scrofa	Mutation(s): 0  Gene Names: FBP1, FBP EC: 3.1.3.11
UniProt
Find proteins for P00636 (Sus scrofa) Explore P00636  Go to UniProtKB:  P00636

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
F6P	B [auth A]	6-O-phosphono-beta-D-fructofuranose C6 H13 O9 P BGWGXPAPYGQALX-ARQDHWQXSA-N
PO3	C [auth A]	PHOSPHITE ION O3 P AQSJGOWTSHOLKH-UHFFFAOYSA-N
MG	D [auth A], E [auth A], F [auth A], G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.207 
• R-Value Work: 0.164 
• R-Value Observed: 0.168 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.6	α = 90
b = 83.017	β = 90
c = 165.378	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
SHELXL-97	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-02-01 
• Released Date: 2003-07-08 
Deposition Author(s): Choe, J., Iancu, C.V., Fromm, H.J., Honzatko, R.B.

Revision History  

• Version 1.0: 2003-07-08
  Type: Initial release
  
• Version 1.1: 2008-04-29
  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: Data collection, Derived calculations, Structure summary