1DKQ

CRYSTAL STRUCTURE OF PHYTATE COMPLEX ESCHERICHIA COLI PHYTASE AT PH 5.0. PHYTATE IS BOUND WITH ITS 3-PHOSPHATE IN THE ACTIVE SITE. HG2+ CATION ACTS AS AN INTERMOLECULAR BRIDGE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.4 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 character ...

    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): 2 
EC: 3.1.3.2 (PDB Primary Data), 3.1.3.26 (UniProt)
Find proteins for P07102 (Escherichia coli (strain K12))
Explore P07102 
Go to UniProtKB:  P07102
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IHP
Query on IHP

Download CCD File 
A
INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
 Ligand Interaction
HG
Query on HG

Download CCD File 
A
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.445α = 90
b = 75.141β = 90
c = 89.957γ = 90
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
XTALVIEWrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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
  • Version 1.3: 2019-07-24
    Changes: Data collection, Refinement description
  • Version 1.4: 2020-10-14
    Changes: Derived calculations, Structure summary