1EW9

ALKALINE PHOSPHATASE (E.C. 3.1.3.1) COMPLEX WITH MERCAPTOMETHYL PHOSPHONATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Alternate modes of binding in two crystal structures of alkaline phosphatase-inhibitor complexes.

Holtz, K.M.Stec, B.Myers, J.K.Antonelli, S.M.Widlanski, T.S.Kantrowitz, E.R.

(2000) Protein Sci. 9: 907-915

  • DOI: 10.1110/ps.9.5.907
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Two high resolution crystal structures of Escherichia coli alkaline phosphatase (AP) in the presence of phosphonate inhibitors are reported. The phosphonate compounds, phosphonoacetic acid (PAA) and mercaptomethylphosphonic acid (MMP), bind competiti ...

    Two high resolution crystal structures of Escherichia coli alkaline phosphatase (AP) in the presence of phosphonate inhibitors are reported. The phosphonate compounds, phosphonoacetic acid (PAA) and mercaptomethylphosphonic acid (MMP), bind competitively to AP with dissociation constants of 5.5 and 0.6 mM, respectively. The structures of the complexes of AP with PAA and MMP were refined at high resolution to crystallographic R-values of 19.0 and 17.5%, respectively. Refinement of the AP-inhibitor complexes was carried out using X-PLOR. The final round of refinement was done using SHELXL-97. Crystallographic analyses of the inhibitor complexes reveal different binding modes for the two phosphonate compounds. The significant difference in binding constants can be attributed to these alternative binding modes observed in the high resolution X-ray structures. The phosphinyl group of PAA coordinates to the active site zinc ions in a manner similar to the competitive inhibitor and product inorganic phosphate. In contrast, MMP binds with its phosphonate moiety directed toward solvent. Both enzyme-inhibitor complexes exhibit close contacts, one of which has the chemical and geometrical potential to be considered an unconventional hydrogen bond of the type C-H...X.


    Related Citations: 
    • Reaction Mechanism of Alkaline Phosphatase Based on Two Crystal Structures. Two-metal Ion Catalysis
      Kim, E.E.,Wyckoff, H.W.
      (1991) J.Mol.Biol. 218: 449
    • A Model of the Transition State in the Alkaline Phosphatase Reaction
      Holtz, K.M.,Stec, B.,Kantrowitz, E.R.
      (1999) J.Biol.Chem. 274: 8351


    Organizational Affiliation

    Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALKALINE PHOSPHATASE
A, B
449Escherichia coli (strain K12)Mutation(s): 0 
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
MMQ
Query on MMQ

Download SDF File 
Download CCD File 
A, B
MERCAPTOMETHYL PHOSPHONATE
C H3 O3 P S
MJZCELCYTRONIX-UHFFFAOYSA-L
 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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MMQKd: 600000 nM BINDINGMOAD
MMQKi: 600000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.175 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 194.830α = 90.00
b = 167.100β = 90.00
c = 76.670γ = 90.00
Software Package:
Software NamePurpose
SDMSdata collection
X-PLORmodel building
SDMSdata reduction
SDMSdata scaling
X-PLORphasing
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-05-01
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2018-01-31
    Type: Experimental preparation