1IME

STRUCTURAL STUDIES OF METAL BINDING BY INOSITOL MONOPHOSPHATASE: EVIDENCE FOR TWO-METAL ION CATALYSIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural studies of metal binding by inositol monophosphatase: evidence for two-metal ion catalysis.

Bone, R.Frank, L.Springer, J.P.Atack, J.R.

(1994) Biochemistry 33: 9468-9476

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The structure of inositol monophosphatase has been determined to 2.60 A resolution in complexes with Mn2+ and with Mn2+ and phosphate. In the Mn2+ complex, three metal cations and one Cl were bound in the active site on each of the two subunits of th ...

    The structure of inositol monophosphatase has been determined to 2.60 A resolution in complexes with Mn2+ and with Mn2+ and phosphate. In the Mn2+ complex, three metal cations and one Cl were bound in the active site on each of the two subunits of the enzyme. Ligands to the three metals include the side chains of Glu 70, Asp 90, Asp 93, and Asp 220, t he carbonyl group of Ile 92, several solvent molecules and the chloride, which is a ligand to each of the cations. When phosphate is soaked into these Mn2+ cocrystals, one of the three Mn2+ ions is expelled from the active site, leaving metal ions with octahedral and tetrahedral coordination geometry. In addition, the structure of apoinositol monophosphatase was determined to 2.5 A resolution. Residues 70-75, a two-turn helical segment which is involved in metal coordination, moves away from the metal binding site by 2-3 A in the absence of cations. Residues 30-40, which wrap around the metal binding site and interact with the metal indirectly through solvent molecules and protein ligands to the metal, become disordered in the absence of metal. In various metal complexes, segmental mobility is also observed in the residues which form the metal binding sites. The results of these studies of the interaction of inositol monophosphatase with cations suggest that the enzyme accomplishes phosphate ester hydrolysis using two metal ions, one with octahedral and one with tetrahedral coordination geometry. Broad metal-binding specificity appears to result from extensive flexibility in several of the protein segments which contribute metal ligands, from the presence of alternate metal ligands and from metal coordination spheres which include water molecules.


    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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Work: 0.184 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 86.000α = 90.00
b = 86.000β = 90.00
c = 154.100γ = 120.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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: 2017-11-29
    Type: Advisory, Derived calculations, Other