1ED8

STRUCTURE OF E. COLI ALKALINE PHOSPHATASE INHIBITED BY THE INORGANIC PHOSPHATE AT 1.75A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A revised mechanism for the alkaline phosphatase reaction involving three metal ions.

Stec, B.Holtz, K.M.Kantrowitz, E.R.

(2000) J.Mol.Biol. 299: 1303-1311

  • DOI: 10.1006/jmbi.2000.3799
  • Primary Citation of Related Structures:  1ED9

  • PubMed Abstract: 
  • Here, X-ray crystallography has been used to investigate the proposed double in-line displacement mechanism of Escherichia coli alkaline phosphatase in which two of the three active-site metal ions have a direct role in catalysis. Two new X-ray cryst ...

    Here, X-ray crystallography has been used to investigate the proposed double in-line displacement mechanism of Escherichia coli alkaline phosphatase in which two of the three active-site metal ions have a direct role in catalysis. Two new X-ray crystal structures of the wild-type enzyme in the absence and presence of inorganic phosphate have been refined at 1.75 A to final working R-factors of 15.4% and 16.4%, respectively. In the refinement of both structures, residues in the active sites were treated anisotropically. The ellipsoids resulting from the partial anisotropic refinement show a clear route for the binding and release of substrate/product. In addition, a direct comparison of the refined structures with and without phosphate reveal a strong correlation between the occupancy of the third metal-binding site and the conformation of the Ser102 nucleophile. These findings clarify two important and unresolved aspects of the previously proposed catalytic mechanism, how Ser102 is activated for nucleophilic attack and why a magnesium ion in the third metal site is required for catalysis. Analysis of these results suggest that three metal-ion assisted catalysis is a more accurate description of the mechanism of the alkaline phosphatase reaction. A revised mechanism for the catalytic reaction of alkaline phosphatase is proposed on the basis of the two new X-ray crystal structures reported.


    Related Citations: 
    • Reaction Mechanism of Alkaline Phosphatase Based on Crystal Structures. Two-metal Ion Catalysis.
      Kim, E.E.,Wyckoff, H.W.
      (1991) J.Mol.Biol. 218: 449


    Organizational Affiliation

    Department of Biochemistry and Cell Biology, W. M. Keck Center for Computational Biology, Rice University, Houston, TX, 77005, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALKALINE PHOSPHATASE
A, B
449Escherichia coli (strain K12)Gene Names: phoA
EC: 3.1.3.1
Find proteins for P00634 (Escherichia coli (strain K12))
Go to UniProtKB:  P00634
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.196 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 195.150α = 90.00
b = 167.340β = 90.00
c = 76.800γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
SDMSdata scaling
X-PLORphasing
SHELXL-97refinement
SDMSdata collection
SDMSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-09-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance