Structure of Plasmodium falciparum IMP-nucleotidase

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.236 

wwPDB Validation   3D Report Full Report

This is version 1.1 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 6RNH


Structure and catalytic regulation of Plasmodium falciparum IMP specific nucleotidase.

Carrique, L.Ballut, L.Shukla, A.Varma, N.Ravi, R.Violot, S.Srinivasan, B.Ganeshappa, U.T.Kulkarni, S.Balaram, H.Aghajari, N.

(2020) Nat Commun 11: 3228-3228

  • DOI: https://doi.org/10.1038/s41467-020-17013-x
  • Primary Citation of Related Structures:  
    6RMD, 6RME, 6RMO, 6RMW, 6RN1, 6RNH

  • PubMed Abstract: 

    Plasmodium falciparum (Pf) relies solely on the salvage pathway for its purine nucleotide requirements, making this pathway indispensable to the parasite. Purine nucleotide levels are regulated by anabolic processes and by nucleotidases that hydrolyse these metabolites into nucleosides. Certain apicomplexan parasites, including Pf, have an IMP-specific-nucleotidase 1 (ISN1). Here we show, by comprehensive substrate screening, that PfISN1 catalyzes the dephosphorylation of inosine monophosphate (IMP) and is allosterically activated by ATP. Crystal structures of tetrameric PfISN1 reveal complex rearrangements of domain organization tightly associated with catalysis. Immunofluorescence microscopy and expression of GFP-fused protein indicate cytosolic localization of PfISN1 and expression in asexual and gametocyte stages of the parasite. With earlier evidence on isn1 upregulation in female gametocytes, the structures reported in this study may contribute to initiate the design for possible transmission-blocking agents.

  • Organizational Affiliation

    Molecular Microbiology and Structural Biochemistry, UMR5086 CNRS-University of Lyon, Lyon, 69007, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
IMP-specific 5'-nucleotidase, putative
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
444Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1206100
Find proteins for A0A144A134 (Plasmodium falciparum (isolate 3D7))
Explore A0A144A134 
Go to UniProtKB:  A0A144A134
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A144A134
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.236 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.96α = 90
b = 204.07β = 90.02
c = 149.28γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-17-CE11-0032

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-15
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description