4I3Y

Crystal structure of Staphylococcal inositol monophosphatase-1: 100 mM LiCl soaked inhibitory complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Elucidation of the Binding Site and Mode of Inhibition of Li(+) and Mg(2+) in Inositol Monophosphatase

Dutta, A.Bhattacharyya, S.Dutta, D.Das, A.K.

(2014) Febs J. --: --

  • DOI: 10.1111/febs.13070
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Mg(2+) -dependent, Li(+) -sensitive phosphatases are a widely distributed family of enzymes with significant importance throughout the biological kingdom. Inositol monophosphatase (IMPase) is an important target of Li(+) -based therapeutic agents in ...

    Mg(2+) -dependent, Li(+) -sensitive phosphatases are a widely distributed family of enzymes with significant importance throughout the biological kingdom. Inositol monophosphatase (IMPase) is an important target of Li(+) -based therapeutic agents in manic depressive disorders. However, despite decades of intense research efforts, the precise mechanism of Li(+) -induced inhibition of IMPase remains obscured. Here we describe a structural investigation of the Li(+) binding site in staphylococcal IMPase I (SaIMPase I) using X-ray crystallography. The biochemical study indicated common or overlapping binding sites for Mg(2+) and Li(+) in the active site of SaIMPase I. The crystal structure of the SaIMPase I ternary product complex shows the presence of a phosphate and three Mg(2+) ions (namely Mg1, Mg2 and Mg3) in the active site. As Li(+) is virtually invisible in X-ray crystallography, competitive displacement of Mg(2+) ions from the SaIMPase I ternary product complex as a function of increasing LiCl concentration was used to identify the Li(+) binding site. In this approach, the disappearing electron density of Mg(2+) ions due to Li(+) ion binding was traced, and the Mg(2+) ion present at the Mg2 binding site was found to be replaced. Moreover, based on a detailed comparative investigation of the phosphate orientation and coordination states of Mg(2+) binding sites in enzyme-substrate and enzyme-product complexes, inhibition mechanisms for Li(+) and Mg(2+) are proposed.


    Organizational Affiliation

    Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Inositol monophosphatase family protein
A, B
271N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

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A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

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Download CCD File 
A
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.184 
  • Space Group: P 21 2 21
Unit Cell:
Length (Å)Angle (°)
a = 60.136α = 90.00
b = 62.819β = 90.00
c = 141.580γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
MOLREPphasing
StructureStudiodata collection
REFMACrefinement
PDB_EXTRACTdata extraction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-11-27
    Type: Initial release
  • Version 1.1: 2014-10-22
    Type: Database references