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 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1093/nar/gkw917
  • Primary Citation of Related Structures:  

  • 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 ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA uridylyltransferase 4
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
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*UP*U)-3')Y,Z2Trypanosoma brucei
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UTP
Query on UTP

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.214 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 82.688α = 90.00
b = 42.876β = 94.05
c = 109.618γ = 90.00
Software Package:
Software NamePurpose
d*TREKdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement
PHASERphasing
d*TREKdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2016-12-28
    Type: Database references