1ALK

REACTION MECHANISM OF ALKALINE PHOSPHATASE BASED ON CRYSTAL STRUCTURES. TWO METAL ION CATALYSIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Reaction mechanism of alkaline phosphatase based on crystal structures. Two-metal ion catalysis.

Kim, E.E.Wyckoff, H.W.

(1991) J.Mol.Biol. 218: 449-464


  • PubMed Abstract: 
  • Alkaline phosphatase (AP) is a widely distributed non-specific phosphomonoesterase that functions through formation of a covalent phosphoseryl intermediate (E-P). The enzyme also catalyzes phosphoryl transfer reaction to various alcohols. Escherichia ...

    Alkaline phosphatase (AP) is a widely distributed non-specific phosphomonoesterase that functions through formation of a covalent phosphoseryl intermediate (E-P). The enzyme also catalyzes phosphoryl transfer reaction to various alcohols. Escherichia coli AP is a homodimer with 449 residues per monomer. It is a metalloenzyme with two Zn2+ and one Mg2+ at each active site. The crystal structure of native E. coli AP complexed with inorganic phosphate (Pi), which is a strong competitive inhibitor as well as a substrate for the reverse reaction, has been refined at 2.0 A resolution. Some parts of the molecular have been retraced, starting from the previous 2.8 A study. The active site has been modified substantially and is described in this paper. The changes in the active site region suggest the need to reinterpret earlier spectral data, and suggestions are made. Also presented are the structures of the Cd-substituted enzyme complexed with inorganic phosphate at 2.5 A resolution, and the phosphate-free native enzyme at 2.8 A resolution. At pH 7.5, where the X-ray data were collected, the Cd-substituted enzyme is predominantly the covalent phosphoenzyme (E-P) while the native Zn/Mg enzyme exists in predominantly noncovalent (E.P) form. Implication of these results for the catalytic mechanism of the enzyme is discussed. APs from other sources are believed to function in a similar manner.


    Related Citations: 
    • Refined Structure of Alkaline Phosphatase
      Sowadski, J.M.,Handschumacher, M.D.,Murthy, H.M.K.,Foster, B.A.,Wyckoff, H.W.
      (1985) J.Mol.Biol. 186: 417
    • Structure of Alkaline Phosphatases
      Kim, E.E.,Wyckoff, H.W.
      (1989) Clin.Chim.Acta 186: 175
    • Bacillus Subtilis Alkaline Phosphatases III and Iv. Cloning, Sequencing, and Comparisons of Deduced Amino Acid Sequence with Escherichia Coli Alkaline Phosphatase Three-Dimensional Structure
      Hulett, F.M.,Kim, E.E.,Bookstein, C.,Kapp, N.V.,Edwards, C.W.,Wyckoff, H.W.
      (1991) J.Biol.Chem. 266: 1077


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511.




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 3 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
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: 2 Å
  • R-Value Work: 0.177 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 195.300α = 90.00
b = 167.400β = 90.00
c = 76.700γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
PROFFTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1993-03-03 
  • Released Date: 1994-01-31 
  • Deposition Author(s): Kim, E.E., Wyckoff, W.

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance