7KIR

Crystal structure of inositol polyphosphate 1-phosphatase (INPP1) D54A mutant in complex with inositol (1,4)-bisphosphate

  • Classification: HYDROLASE
  • Organism(s): Bos taurus
  • Expression System: Spodoptera frugiperda
  • Mutation(s): Yes 

  • Deposited: 2020-10-24 Released: 2020-11-25 
  • Deposition Author(s): Dollins, D.E., Xiong, J.-P., Ren, Y., York, J.D.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.196 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

A structural basis for lithium and substrate binding of an inositide phosphatase.

Dollins, D.E.Xiong, J.P.Endo-Streeter, S.Anderson, D.E.Bansal, V.S.Ponder, J.W.Ren, Y.York, J.D.

(2020) J Biol Chem 296: 100059-100059

  • DOI: https://doi.org/10.1074/jbc.RA120.014057
  • Primary Citation of Related Structures:  
    6WRO, 6WRR, 6WRY, 6X25, 7KIO, 7KIR

  • PubMed Abstract: 

    Inositol polyphosphate 1-phosphatase (INPP1) is a prototype member of metal-dependent/lithium-inhibited phosphomonoesterase protein family defined by a conserved three-dimensional core structure. Enzymes within this family function in distinct pathways including inositide signaling, gluconeogenesis, and sulfur assimilation. Using structural and biochemical studies, we report the effect of substrate and lithium on a network of metal binding sites within the catalytic center of INPP1. We find that lithium preferentially occupies a key site involved in metal-activation only when substrate or product is added. Mutation of a conserved residue that selectively coordinates the putative lithium-binding site results in a dramatic 100-fold reduction in the inhibitory constant as compared with wild-type. Furthermore, we report the INPP1/inositol 1,4-bisphosphate complex which illuminates key features of the enzyme active site. Our results provide insights into a structural basis for uncompetitive lithium inhibition and substrate recognition and define a sequence motif for metal binding within this family of regulatory phosphatases.


  • Organizational Affiliation

    Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inositol polyphosphate 1-phosphatase400Bos taurusMutation(s): 1 
Gene Names: INPP1
EC: 3.1.3.57
UniProt
Find proteins for P21327 (Bos taurus)
Explore P21327 
Go to UniProtKB:  P21327
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21327
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.196 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.437α = 90
b = 51.437β = 90
c = 142.938γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
SCALEPACKdata scaling
PHASERphasing
DENZOdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM124404
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesR01-HL055672
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-25
    Type: Initial release
  • Version 1.1: 2021-07-14
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description