6RN1 | pdb_00006rn1

Structure of N-terminal truncated Plasmodium falciparum IMP-nucleotidase

• PDB DOI: https://doi.org/10.2210/pdb6RN1/pdb

• Classification: HYDROLASE
• Organism(s): Plasmodium falciparum 3D7
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-05-07 Released: 2020-07-15 
• Deposition Author(s): Carrique, L., Ballut, L., Violot, S., Aghajari, N.
• Funding Organization(s): French National Research Agency

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.280 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.252 (Depositor), 0.254 (DCC) 
• R-Value Observed: 
  0.254 (Depositor) 

Starting Model: experimental

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

• PubMed: 32591529 
• DOI: https://doi.org/10.1038/s41467-020-17013-x
• Primary Citation 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.

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Organizational Affiliation: 
• Molecular Microbiology and Structural Biochemistry, UMR5086 CNRS-University of Lyon, Lyon, 69007, France.
Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Oxford, OX3 7BN, UK.
Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru, Karnataka, 560064, India.
Venture Studio, Ahmedabad University, Navrangpura, Ahmedabad, 380009, India.
Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK.
Rubizon Pvt ltd, #783, 10th cross, Mathrushree, Bangalore, 560086, India.
Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru, Karnataka, 560064, India. [e-mail].
Molecular Microbiology and Structural Biochemistry, UMR5086 CNRS-University of Lyon, Lyon, 69007, France. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 89.9 kDa 
• Atom Count: 5,179 
• Modeled Residue Count: 705 
• Deposited Residue Count: 770 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IMP-specific 5'-nucleotidase, putative	A, B	385	Plasmodium falciparum 3D7	Mutation(s): 0  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)) Explore A0A144A134  Go to UniProtKB:  A0A144A134

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.280 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.252 (Depositor), 0.254 (DCC) 
• R-Value Observed: 0.254 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.66	α = 90
b = 140.66	β = 90
c = 86.98	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-07-15 
Deposition Author(s): Carrique, L., Ballut, L., Violot, S., Aghajari, N.

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Funding Organization	Location	Grant Number
French National Research Agency	France	ANR-17-CE11-0032

Revision History  

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