2Q0F

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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.Usa 104: 14634-14639

  • DOI: 10.1073/pnas.0704259104
  • Primary Citation of Related Structures:  

  • 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 m ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA uridylyl transferase
A, B
353Trypanosoma brucei brucei (strain 927/4 GUTat10.1)Mutation(s): 0 
Find proteins for Q381M1 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Go to UniProtKB:  Q381M1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UTP
Query on UTP

Download SDF File 
Download CCD File 
A
URIDINE 5'-TRIPHOSPHATE
C9 H15 N2 O15 P3
PGAVKCOVUIYSFO-XVFCMESISA-N
 Ligand Interaction
U5P
Query on U5P

Download SDF File 
Download CCD File 
A, B
URIDINE-5'-MONOPHOSPHATE
C9 H13 N2 O9 P
DJJCXFVJDGTHFX-XVFCMESISA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.223 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 80.620α = 90.00
b = 41.924β = 94.37
c = 106.017γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing
d*TREKdata reduction
Blu-Icedata collection
d*TREKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-05-21 
  • Released Date: 2007-08-28 
  • Deposition Author(s): Stagno, J., Luecke, H.

Revision History 

  • Version 1.0: 2007-08-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-18
    Type: Refinement description