1IMA

STRUCTURAL ANALYSIS OF INOSITOL MONOPHOSPHATASE COMPLEXES WITH SUBSTRATES

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history. 

Literature

Structural analysis of inositol monophosphatase complexes with substrates.

Bone, R., Frank, L., Springer, J.P., Pollack, S.J., Osborne, S.A., Atack, J.R., Knowles, M.R., McAllister, G., Ragan, C.I., Broughton, H.B., Baker, R., Fletcher, S.R.

(1994) Biochemistry 33: 9460-9467

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The structures of ternary complexes of human inositol monophosphatase with inhibitory Gd3+ and either D- or L-myo-inositol 1-phosphate have been determined to 2.2-2.3 A resolution using X-ray crystallography. Substrate and metal are bound identically ...

    The structures of ternary complexes of human inositol monophosphatase with inhibitory Gd3+ and either D- or L-myo-inositol 1-phosphate have been determined to 2.2-2.3 A resolution using X-ray crystallography. Substrate and metal are bound identically in each active site of the phosphatase dimer. The substrate is present at full occupancy, while the metal is present at only 35% occupancy, suggesting that Li+ from the crystallization solvent partially replaces Gd3+ upon substrate binding. The phosphate groups of both substrates interact with the phosphatase in the same manner with one phosphate oxygen bound to the octahedrally coordinated active site metal and another oxygen forming hydrogen bonds with the amide groups of residues 94 and 95. The active site orientations of the inositol rings of D- and L-myo-inositol 1-phosphate differ by rotation of nearly 60 degrees about the phosphate ester bond. Each substrate utilizes the same key residues (Asp 93, Ala 196, Glu 213, and Asp 220) to form the same number of hydrogen bonds with the enzyme. Mutagenesis experiments confirm the interaction of Glu 213 with the inositol ring and suggest that interactions with Ser 165 may develop during the transition state. The structural data suggest that the active site nucleophile is a metal-bound water that is activated by interaction with Glu 70 and Thr 95. Expulsion of the ester oxygen appears to be promoted by three aspartate residues acting together (90, 93, and 220), either to donate a proton to the leaving group or to form another metal binding site from which a second Mg2+ coordinates the leaving group during the transition state.

    Related Citations: 
    • Structure of Inositol Monophosphatase, the Putative Target of Lithium Therapy
      Bone, R.,Springer, J.P.,Atack, J.R.
      (1992) Proc.Natl.Acad.Sci.USA 89: 10031
    • Cdna Cloning of Human and Rat Brain Myo-Inositol Monophosphatase. Expression and Characterization of the Human Recombinant Enzyme
      Mcallister, G.,Whiting, P.,Hammond, E.A.,Knowles, M.R.,Atack, J.R.,Bailey, F.J.,Maigetter, R.,Ragan, C.I.
      (1992) Biochem.J. 284: 749

    Organizational Affiliation: 

    Department of Biophysical Chemistry, Merck Research Laboratories, Rahway, New Jersey 07065.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
INOSITOL MONOPHOSPHATASE
A, B
277Homo sapiensMutation(s): 0 
Gene Names: IMPA1 (IMPA)
EC: 3.1.3.25
Find proteins for P29218 (Homo sapiens)
Go to Gene View: IMPA1
Go to UniProtKB:  P29218
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IPD
Query on IPD
Download SDF File 
Download CCD File 
A, B
D-MYO-INOSITOL-1-PHOSPHATE
C6 H11 O9 P
INAPMGSXUVUWAF-UOTPTPDRSA-L
 Ligand Interaction
GD
Query on GD
Download SDF File 
Download CCD File 
A, B
GADOLINIUM ATOM
Gd
UIWYJDYFSGRHKR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Work: 0.181 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 86.900α = 90.00
b = 86.900β = 90.00
c = 154.500γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 1994-02-08 
  • Released Date: 1995-02-27 
  • Deposition Author(s): Bone, R.

Revision History 

  • Version 1.0: 1995-02-27
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2012-02-22
    Type: Database references
  • Version 1.4: 2017-11-29
    Type: Advisory, Derived calculations, Other