5WRT | pdb_00005wrt

Crystal structure of type I inorganic pyrophosphatase from Toxoplasma gondii.

• PDB DOI: https://doi.org/10.2210/pdb5WRT/pdb

• Classification: HYDROLASE
• Organism(s): Toxoplasma gondii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-12-03 Released: 2017-10-11 
• Deposition Author(s): Jamwal, A., Yogavel, M., Sharma, A.
• Funding Organization(s): Department of Biotechnology, Govt. of India

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.232 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Literature

Structural and Biochemical Characterization of Apicomplexan Inorganic Pyrophosphatases

Jamwal, A., Yogavel, M., Abdin, M.Z., Jain, S.K., Sharma, A.

(2017) Sci Rep 7: 5255-5255

• PubMed: 28701714 
• DOI: https://doi.org/10.1038/s41598-017-05234-y
• Primary Citation Related Structures: 
  5WRT, 5WRU


• PubMed Abstract: 
  

  Inorganic pyrophosphatases (PPase) participate in energy cycling and they are essential for growth and survival of organisms. Here we report extensive structural and functional characterization of soluble PPases from the human parasites Plasmodium falciparum (PfPPase) and Toxoplasma gondii (TgPPase). Our results show that PfPPase is a cytosolic enzyme whose gene expression is upregulated during parasite asexual stages. Cambialistic PfPPase actively hydrolyzes linear short chain polyphosphates like PP _i , polyP ₃ and ATP in the presence of Zn ²⁺ . A remarkable new feature of PfPPase is the low complexity asparagine-rich N-terminal region that mediates its dimerization. Deletion of N-region has an unexpected and substantial effect on the stability of PfPPase domain, resulting in aggregation and significant loss of enzyme activity. Significantly, the crystal structures of PfPPase and TgPPase reveal unusual and unprecedented dimeric organizations and provide new fundamental insights into the variety of oligomeric assemblies possible in eukaryotic inorganic PPases.

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Organizational Affiliation: 
• Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
Department of Biotechnology, Jamia Hamdard, New Delhi, 110063, India.
Department of Biochemistry, Hamdard Institute of Medical Sciences, 110063, New Delhi, India.
Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 53.67 kDa 
• Atom Count: 3,959 
• Modeled Residue Count: 467 
• Deposited Residue Count: 470 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble inorganic pyrophosphatase	A, B	235	Toxoplasma gondii	Mutation(s): 0  Gene Names: sPP1 EC: 3.6.1.1
UniProt
Find proteins for Q4VUZ3 (Toxoplasma gondii) Explore Q4VUZ3  Go to UniProtKB:  Q4VUZ3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A], D [auth A], E [auth B], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.232 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.957	α = 90
b = 88.957	β = 90
c = 158.665	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
AutoSol	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-10-11 
Deposition Author(s): Jamwal, A., Yogavel, M., Sharma, A.

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Funding Organization	Location	Grant Number
Department of Biotechnology, Govt. of India	India	--

Revision History  

• Version 1.0: 2017-10-11
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references, Derived calculations, Refinement description