6RME

Structure of IMP bound Plasmodium falciparum IMP-nucleotidase mutant D172N


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 

Starting Model: experimental
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Literature

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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
IMP-specific 5'-nucleotidase, putative
A, G
384Plasmodium falciparum 3D7Mutation(s): 1 
Gene Names: PF3D7_1206100
EC: 3.1.3.5 (PDB Primary Data), 3.1.3.99 (UniProt)
UniProt
Find proteins for A0A144A134 (Plasmodium falciparum (isolate 3D7))
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Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A144A134
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
IMP-specific 5'-nucleotidase, putative
B, D
385Plasmodium falciparum 3D7Mutation(s): 1 
Gene Names: PF3D7_1206100
EC: 3.1.3.5 (PDB Primary Data), 3.1.3.99 (UniProt)
UniProt
Find proteins for A0A144A134 (Plasmodium falciparum (isolate 3D7))
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UniProt GroupA0A144A134
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
IMP-specific 5'-nucleotidase, putative394Plasmodium falciparum 3D7Mutation(s): 1 
Gene Names: PF3D7_1206100
EC: 3.1.3.5 (PDB Primary Data), 3.1.3.99 (UniProt)
UniProt
Find proteins for A0A144A134 (Plasmodium falciparum (isolate 3D7))
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Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A144A134
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
IMP-specific 5'-nucleotidase, putative
E, H
386Plasmodium falciparum 3D7Mutation(s): 1 
Gene Names: PF3D7_1206100
EC: 3.1.3.5 (PDB Primary Data), 3.1.3.99 (UniProt)
UniProt
Find proteins for A0A144A134 (Plasmodium falciparum (isolate 3D7))
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UniProt GroupA0A144A134
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
IMP-specific 5'-nucleotidase, putative388Plasmodium falciparum 3D7Mutation(s): 1 
Gene Names: PF3D7_1206100
EC: 3.1.3.5 (PDB Primary Data), 3.1.3.99 (UniProt)
UniProt
Find proteins for A0A144A134 (Plasmodium falciparum (isolate 3D7))
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Go to UniProtKB:  A0A144A134
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UniProt GroupA0A144A134
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IMP (Subject of Investigation/LOI)
Query on IMP

Download Ideal Coordinates CCD File 
I [auth A]
K [auth B]
M [auth C]
O [auth D]
R [auth E]
I [auth A],
K [auth B],
M [auth C],
O [auth D],
R [auth E],
U [auth F],
W [auth G],
Y [auth H]
INOSINIC ACID
C10 H13 N4 O8 P
GRSZFWQUAKGDAV-KQYNXXCUSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
Q [auth D],
T [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
J [auth A]
L [auth B]
N [auth C]
P [auth D]
S [auth E]
J [auth A],
L [auth B],
N [auth C],
P [auth D],
S [auth E],
V [auth F],
X [auth G],
Z [auth H]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.26α = 90
b = 204.61β = 113.19
c = 115.92γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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: 2020-07-08
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description