5KAL

Terminal uridylyl transferase 4 from Trypanosoma brucei with bound UTP and UpU


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

RNA Editing TUTase 1: structural foundation of substrate recognition, complex interactions and drug targeting.

Rajappa-Titu, L.Suematsu, T.Munoz-Tello, P.Long, M.Demir, O.Cheng, K.J.Stagno, J.R.Luecke, H.Amaro, R.E.Aphasizheva, I.Aphasizhev, R.Thore, S.

(2016) Nucleic Acids Res 44: 10862-10878

  • DOI: https://doi.org/10.1093/nar/gkw917
  • Primary Citation of Related Structures:  
    5HZD, 5I49, 5IDO, 5KAL

  • PubMed Abstract: 

    Terminal uridyltransferases (TUTases) execute 3' RNA uridylation across protists, fungi, metazoan and plant species. Uridylation plays a particularly prominent role in RNA processing pathways of kinetoplastid protists typified by the causative agent of African sleeping sickness, Trypanosoma brucei In mitochondria of this pathogen, most mRNAs are internally modified by U-insertion/deletion editing while guide RNAs and rRNAs are U-tailed. The founding member of TUTase family, RNA editing TUTase 1 (RET1), functions as a subunit of the 3' processome in uridylation of gRNA precursors and mature guide RNAs. Along with KPAP1 poly(A) polymerase, RET1 also participates in mRNA translational activation. RET1 is divergent from human TUTases and is essential for parasite viability in the mammalian host and the insect vector. Given its robust in vitro activity, RET1 represents an attractive target for trypanocide development. Here, we report high-resolution crystal structures of the RET1 catalytic core alone and in complex with UTP analogs. These structures reveal a tight docking of the conserved nucleotidyl transferase bi-domain module with a RET1-specific C2H2 zinc finger and RNA recognition (RRM) domains. Furthermore, we define RET1 region required for incorporation into the 3' processome, determinants for RNA binding, subunit oligomerization and processive UTP incorporation, and predict druggable pockets.


  • Organizational Affiliation

    Department of Molecular Biology, University of Geneva, 1211 Geneva, Switzerland.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA uridylyltransferase 4
A, B
353Trypanosoma bruceiMutation(s): 0 
Gene Names: TUT4
UniProt
Find proteins for Q381M1 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Explore Q381M1 
Go to UniProtKB:  Q381M1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ381M1
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(*UP*U)-3')C [auth Y],
D [auth Z]
2Trypanosoma brucei
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.688α = 90
b = 42.876β = 94.05
c = 109.618γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
d*TREKdata scaling
PDB_EXTRACTdata extraction
d*TREKdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2016-12-28
    Changes: Database references
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description