1TIP | pdb_00001tip

THE BISPHOSPHATASE DOMAIN OF THE BIFUNCTIONAL RAT LIVER 6-PHOSPHOFRUCTO-2-KINASE/FRUCTOSE-2,6-BISPHOSPHATASE

• PDB DOI: https://doi.org/10.2210/pdb1TIP/pdb
• BMRB: 5935

• Classification: HYDROLASE
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1997-05-28 Released: 1998-01-28 
• Deposition Author(s): Lee, Y.-H., Olson, T.W., Ogata, C.M., Levitt, D.G., Banaszak, L.J., Lange, A.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.286 (Depositor) 
• R-Value Work: 
  0.204 (Depositor) 
• R-Value Observed: 
  0.204 (Depositor) 

Literature

Crystal structure of a trapped phosphoenzyme during a catalytic reaction.

Lee, Y.H., Olson, T.W., Ogata, C.M., Levitt, D.G., Banaszak, L.J., Lange, A.J.

(1997) Nat Struct Biol 4: 615-618

• PubMed: 9253407 
• DOI: https://doi.org/10.1038/nsb0897-615
• Primary Citation Related Structures: 
  1TIP


• PubMed Abstract: 
  

  The crystal structure of the fructose-2,6-bisphosphatase domain trapped during the reaction reveal a phosphorylated His 258, and a water molecule immobilized by the product, fructose-6-phosphate. The geometry suggests that the dephosphorylation step requires prior removal of the product for an 'associative in-line' phosphoryl transfer to the catalytic water.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 45.04 kDa 
• Atom Count: 3,434 
• Modeled Residue Count: 382 
• Deposited Residue Count: 382 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHOENZYME INTERMEDIATE OF FRU-2,6-BISPHOSPHATASE	A, B	191	Rattus norvegicus	Mutation(s): 1  Gene Names: A CODING REGION WHICH COVERS EC: 3.1.3.46 (PDB Primary Data), 2.7.1.105 (UniProt)
UniProt
Find proteins for P07953 (Rattus norvegicus) Explore P07953  Go to UniProtKB:  P07953

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
F6P	C [auth A], D [auth B]	6-O-phosphono-beta-D-fructofuranose C6 H13 O9 P BGWGXPAPYGQALX-ARQDHWQXSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NEP	A, B	L-PEPTIDE LINKING	C6 H10 N3 O5 P		HIS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.286 (Depositor) 
• R-Value Work:  0.204 (Depositor) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.23	α = 90
b = 56.52	β = 94.48
c = 90.9	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-01-28 
Deposition Author(s): Lee, Y.-H., Olson, T.W., Ogata, C.M., Levitt, D.G., Banaszak, L.J., Lange, A.J.

Revision History  

• Version 1.0: 1998-01-28
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary
• Version 1.4: 2025-03-26
  Changes: Data collection, Database references, Structure summary