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

Experimental Data Snapshot

  • Resolution: 2.04 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 

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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 281: 5309-5324

  • DOI: https://doi.org/10.1111/febs.13070
  • Primary Citation of Related Structures:  
    4G61, 4I3Y, 4I40, 4PTK

  • 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 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. The atomic coordinates for the SaIMPase I ternary complex, SaIMPase I in 50 mm LiCl, SaIMPase I in 100 mm LiCl and SaIMPase I in 0 mm MgCl2 have been submitted to the Protein Data Bank under accession numbers 4G61, 4I40, 4I3Y and 4PTK, respectively.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inositol monophosphatase family protein
A, B
271Staphylococcus aureus subsp. aureus MSSA476Mutation(s): 0 
Gene Names: Inositol monophosphatase (SAS2203)SAS2203
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PG4

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
J [auth A]
C8 H18 O5
Query on PO4

Download Ideal Coordinates CCD File 
C [auth A],
L [auth B]
O4 P
Query on GOL

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E [auth A],
I [auth A],
M [auth B],
O [auth B],
P [auth B]
C3 H8 O3
Query on MG

Download Ideal Coordinates CCD File 
D [auth A],
F [auth A],
K [auth B],
N [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.04 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.136α = 90
b = 62.819β = 90
c = 141.58γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
StructureStudiodata collection
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-27
    Type: Initial release
  • Version 1.1: 2014-10-22
    Changes: Database references
  • Version 1.2: 2022-08-24
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-11-08
    Changes: Data collection, Refinement description