6WRY

CRYSTAL STRUCTURE OF INOSITOL POLYPHOSPHATE 1-PHOSPHATASE INPP1 IN COMPLEX GADOLINIUM AFTER ADDITION OF INOSITOL 1,3,4-TRISPHOSPHATE AT 2.5 ANGSTROM RESOLUTION

  • Classification: SIGNALING PROTEIN
  • Organism(s): Bos taurus
  • Expression System: Baculoviridae sp.
  • Mutation(s): No 

  • Deposited: 2020-04-30 Released: 2020-11-25 
  • Deposition Author(s): Dollins, D.R., Endo-Streeter, S., York, J.D.
  • Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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-phosphatase389Bos taurusMutation(s): 0 
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: 2.80 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.64α = 90
b = 51.64β = 90
c = 143.33γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
UCSD-systemdata reduction
UCSD-systemdata scaling
SQUASHphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL055672
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM124404
Howard Hughes Medical Institute (HHMI)United Statesyork investigator

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