Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 63.76 kDa 
• Atom Count: 4519 
• Modelled Residue Count: 526 
• Deposited Residue Count: 542 
• Unique protein chains: 1

4I3Y

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

• PDB DOI: 10.2210/pdb4I3Y/pdb

• Classification: HYDROLASE
• Organism(s): Staphylococcus aureus subsp. aureus MSSA476
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-11-26 Released: 2013-11-27 
• Deposition Author(s): Dutta, A., Bhattacharyya, S., Dutta, D., Das, A.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 0.248 
• R-Value Work: 0.184 
• R-Value Observed: 0.187 

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 

• PubMed: 25263816 
• DOI: 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inositol monophosphatase family protein	A, B	271	Staphylococcus aureus subsp. aureus MSSA476	Mutation(s): 0  Gene Names: Inositol monophosphatase (SAS2203), SAS2203 EC: 3.1.3.25

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	G [auth A], H [auth A], J [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PO4	C [auth A], L [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	E [auth A], I [auth A], M [auth B], O [auth B], P [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	D [auth A], F [auth A], K [auth B], N [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 60.136	α = 90
b = 62.819	β = 90
c = 141.58	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-11-26 
• Released Date: 2013-11-27 
Deposition Author(s): Dutta, A., Bhattacharyya, S., Dutta, D., Das, A.K.

Revision History  

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