Crystal structure of Cet1 from Trypanosoma cruzi in complex with manganese ion.

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.241 

Starting Model: experimental
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Crystal structures of the RNA triphosphatase fromTrypanosoma cruziprovide insights into how it recognizes the 5'-end of the RNA substrate.

Takagi, Y.Kuwabara, N.Dang, T.T.Furukawa, K.Ho, C.K.

(2020) J Biol Chem 295: 9076-9086

  • DOI: https://doi.org/10.1074/jbc.RA119.011811
  • Primary Citation of Related Structures:  
    6L7V, 6L7W, 6L7X, 6L7Y

  • PubMed Abstract: 

    RNA triphosphatase catalyzes the first step in mRNA cap formation, hydrolysis of the terminal phosphate from the nascent mRNA transcript. The RNA triphosphatase from the protozoan parasite Trypanosoma cruzi , TcCet1, belongs to the family of triphosphate tunnel metalloenzymes (TTMs). TcCet1 is a promising antiprotozoal drug target because the mechanism and structure of the protozoan RNA triphosphatases are completely different from those of the RNA triphosphatases found in mammalian and arthropod hosts. Here, we report several crystal structures of the catalytically active form of TcCet1 complexed with a divalent cation and an inorganic tripolyphosphate in the active-site tunnel at 2.20-2.51 Å resolutions. The structures revealed that the overall structure, the architecture of the tunnel, and the arrangement of the metal-binding site in TcCet1 are similar to those in other TTM proteins. On the basis of the position of three sulfate ions that cocrystallized on the positively charged surface of the protein and results obtained from mutational analysis, we identified an RNA-binding site in TcCet1. We conclude that the 5'-end of the triphosphate RNA substrate enters the active-site tunnel directionally. The structural information reported here provides valuable insight into designing inhibitors that could specifically block the entry of the triphosphate RNA substrate into the TTM-type RNA triphosphatases of T. cruzi and related pathogens.

  • Organizational Affiliation

    Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
mRNA_triPase domain-containing protein
A, B
209Trypanosoma cruzi strain CL BrenerMutation(s): 1 
Gene Names: Tc00.1047053508479.390
Find proteins for Q4E2I1 (Trypanosoma cruzi (strain CL Brener))
Explore Q4E2I1 
Go to UniProtKB:  Q4E2I1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4E2I1
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.241 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.445α = 90
b = 73.208β = 114.063
c = 63.747γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan16H05180

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-03
    Type: Initial release
  • Version 1.1: 2020-07-15
    Changes: Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references
  • Version 1.3: 2024-04-03
    Changes: Refinement description