1DKO

CRYSTAL STRUCTURE OF TUNGSTATE COMPLEX OF ESCHERICHIA COLI PHYTASE AT PH 6.6 WITH TUNGSTATE BOUND AT THE ACTIVE SITE AND WITH HG2+ CATION ACTING AS AN INTERMOLECULAR BRIDGE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structures of Escherichia coli phytase and its complex with phytate.

Lim, D.Golovan, S.Forsberg, C.W.Jia, Z.

(2000) Nat Struct Biol 7: 108-113

  • DOI: 10.1038/72371
  • Primary Citation of Related Structures:  
    1DKO, 1DKN, 1DKM, 1DKL, 1DKQ, 1DKP

  • PubMed Abstract: 
  • Phytases catalyze the hydrolysis of phytate and are able to improve the nutritional quality of phytate-rich diets. Escherichia coli phytase, a member of the histidine acid phosphatase family has the highest specific activity of all phytases characterized ...

    Phytases catalyze the hydrolysis of phytate and are able to improve the nutritional quality of phytate-rich diets. Escherichia coli phytase, a member of the histidine acid phosphatase family has the highest specific activity of all phytases characterized. The crystal structure of E. coli phytase has been determined by a two-wavelength anomalous diffraction method using the exceptionally strong anomalous scattering of tungsten. Despite a lack of sequence similarity, the structure closely resembles the overall fold of other histidine acid phosphatases. The structure of E. coli phytase in complex with phytate, the preferred substrate, reveals the binding mode and substrate recognition. The binding is also accompanied by conformational changes which suggest that substrate binding enhances catalysis by increasing the acidity of the general acid.


    Related Citations: 
    • Purification, Crystallization and Preliminary X-ray Analysis of the Escherichia coli Phytase
      Jia, Z., Golovan, S., Ye, Q., Forsberg, C.W.
      (1998) Acta Crystallogr D Biol Crystallogr 54: 647
    • The Complete Nucleotide Sequence of the Escherichia coli Gene appA Reveals Significant Homology Between pH 2.5 Acid Phosphatase and Glucose-1-phosphatase
      Dassa, J., Marck, C., Boquet, P.L.
      (1990) J Bacteriol 172: 5497

    Organizational Affiliation

    Department of Biochemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PHYTASEA410Escherichia coliMutation(s): 1 
EC: 3.1.3.2 (PDB Primary Data), 3.1.3.26 (UniProt)
UniProt
Find proteins for P07102 (Escherichia coli (strain K12))
Explore P07102 
Go to UniProtKB:  P07102
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
WO4
Query on WO4

Download Ideal Coordinates CCD File 
F [auth A]TUNGSTATE(VI)ION
O4 W
PBYZMCDFOULPGH-UHFFFAOYSA-N
 Ligand Interaction
HG
Query on HG

Download Ideal Coordinates CCD File 
B [auth A], C [auth A], D [auth A], E [auth A]MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.642α = 90
b = 74.952β = 90
c = 89.653γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNSrefinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-08-03
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance