Terminal uridylyl transferase 4 from Trypanosoma brucei with bound GTP

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 

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Dual role of the RNA substrate in selectivity and catalysis by terminal uridylyl transferases.

Stagno, J.Aphasizheva, I.Aphasizhev, R.Luecke, H.

(2007) Proc Natl Acad Sci U S A 104: 14634-14639

  • DOI: https://doi.org/10.1073/pnas.0704259104
  • Primary Citation of Related Structures:  
    2Q0C, 2Q0D, 2Q0E, 2Q0F, 2Q0G

  • PubMed Abstract: 

    Terminal RNA uridylyltransferases (TUTases) catalyze template-independent UMP addition to the 3' hydroxyl of RNA. TUTases belong to the DNA polymerase beta superfamily of nucleotidyltransferases that share a conserved catalytic domain bearing three metal-binding carboxylate residues. We have previously determined crystal structures of the UTP-bound and apo forms of the minimal trypanosomal TUTase, TbTUT4, which is composed solely of the N-terminal catalytic and C-terminal base-recognition domains. Here we report crystal structures of TbTUT4 with bound CTP, GTP, and ATP, demonstrating nearly perfect superposition of the triphosphate moieties with that of the UTP substrate. Consequently, at physiological nucleoside 5'-triphosphate concentrations, the protein-uracil base interactions alone are not sufficient to confer UTP selectivity. To resolve this ambiguity, we determined the crystal structure of a prereaction ternary complex composed of UTP, TbTUT4, and UMP, which mimics an RNA substrate, and the postreaction complex of TbTUT4 with UpU dinucleotide. The UMP pyrimidine ring stacks against the uracil base of the bound UTP, which on its other face also stacks with an essential tyrosine. In contrast, the different orientation of the purine bases observed in cocrystals with ATP and GTP prevents this triple stacking, precluding productive binding of the RNA. The 3' hydroxyl of the bound UMP is poised for in-line nucleophilic attack while contributing to the formation of a binding site for a second catalytic metal ion. We propose a dual role for RNA substrates in TUTase-catalyzed reactions: contribution to selective incorporation of the cognate nucleoside and shaping of the catalytic metal binding site.

  • Organizational Affiliation

    Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA uridylyl transferase
A, B
353Trypanosoma bruceiMutation(s): 0 
Gene Names: TUT4
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
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.788α = 90
b = 41.917β = 93.34
c = 106.388γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
PDB_EXTRACTdata extraction
Blu-Icedata collection
d*TREKdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-08-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-18
    Changes: Refinement description
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description