1ANI

ALKALINE PHOSPHATASE (D153H, K328H)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mutations at positions 153 and 328 in Escherichia coli alkaline phosphatase provide insight towards the structure and function of mammalian and yeast alkaline phosphatases.

Murphy, J.E.Tibbitts, T.T.Kantrowitz, E.R.

(1995) J.Mol.Biol. 253: 604-617

  • DOI: 10.1006/jmbi.1995.0576
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In order to understand some of the differences between human placental, human, Saccharomyces cerevisiae and Escherichia coli alkaline phosphatases in specific activity, activation by magnesium, and pH versus activity profiles, the X-ray crystal struc ...

    In order to understand some of the differences between human placental, human, Saccharomyces cerevisiae and Escherichia coli alkaline phosphatases in specific activity, activation by magnesium, and pH versus activity profiles, the X-ray crystal structures of three mutant E. coli alkaline phosphatases have been determined. The aligned sequences of alkaline phosphatases from mammalian, yeast and E. coli show that 25 to 30% of the amino acids are absolutely conserved and the active site residues are completely conserved with the exception of residues 153, 328 and 155. The bacterial enzyme has a salt-bridge, Asp153/Lys328, near the third metal binding site which, based on sequence homology, is apparently absent in the yeast and mammalian enzymes. The human enzymes have histidine at positions 153 and 328, and the yeast enzyme has histidine at position 328. In the E. coli enzyme, Asp153 was replaced by histidine (D153H), Lys328 was replaced by histidine (K328H), and a double mutant (DM) was constructed containing both mutations. The structure of the K328H enzyme was refined using cross-validation to a resolution of 2.3 A with a working R-factor of 0.181 and a free R-factor of 0.249. The DM structure was determined to a resolution of 2.5 A with a working R-factor of 0.166 and a free R-factor of 0.233. The structure of the D135H enzyme, which has been reported to a resolution of 2.4 A, has been re-refined using cross-validation to a working R-factor of 0.179 and a free R-factor of 0.239 for controlled comparisons with the two new structures. In all three structures the most significant changes are related to the bound phosphate inhibitor and the identity of the metal ion in the third binding site. The changes in the position of the phosphate group and the alterations at the third metal binding site indicate the structural basis for the variations in the steady-state kinetic parameters previously reported for these enzymes.


    Related Citations: 
    • Magnesium in the Active Site of Escherichia Coli Alkaline Phosphatase is Important for Both Structural Stabilization and Catalysis
      Janeway, C.M.L.,Xu, X.,Murphy, J.E.,Chaidaroglou, A.,Kantrowitz, E.R.
      (1993) Biochemistry 32: 1601
    • Conversion of a Magnesium Binding Site Into a Zinc Binding Site by a Single Amino Acid Substitution in Escherichia Coli Alkaline Phosphatase
      Murphy, J.E.,Xu, X.,Kantrowitz, E.R.
      (1993) J.Biol.Chem. 268: 21497
    • 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

    Boston College, Department of Chemistry, Merkert Chemistry Center, Chestnut Hill, MA 02167-3860, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALKALINE PHOSPHATASE
A, B
446Escherichia coli (strain K12)Mutation(s): 2 
Gene Names: phoA
EC: 3.1.3.1
Find proteins for P00634 (Escherichia coli (strain K12))
Go to UniProtKB:  P00634
Small Molecules
Ligands 2 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.176 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 194.600α = 90.00
b = 167.300β = 90.00
c = 76.300γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORphasing
TIBBITTSrefinement
IMPLORrefinement
POLYVISIONrefinement
SANdata collection
X-PLORrefinement
SDMSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-01-29
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance