3HIY

Minor Editosome-Associated TUTase 1 with bound UTP and Mg


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the Mitochondrial Editosome-Like Complex Associated TUTase 1 Reveals Divergent Mechanisms of UTP Selection and Domain Organization.

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

(2010) J.Mol.Biol. 399: 464-475

  • DOI: 10.1016/j.jmb.2010.04.021
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • RNA uridylylation reactions catalyzed by terminal uridylyl transferases (TUTases) play critical roles in the formation of the mitochondrial transcriptome in trypanosomes. Two mitochondrial RNA editing TUTases have been described: RNA editing TUTase 1 ...

    RNA uridylylation reactions catalyzed by terminal uridylyl transferases (TUTases) play critical roles in the formation of the mitochondrial transcriptome in trypanosomes. Two mitochondrial RNA editing TUTases have been described: RNA editing TUTase 1 catalyzes guide RNA, ribosomal RNA, and mRNA 3'-uridylylation, and RNA editing TUTase 2 acts as a subunit of the RNA editing core complex (also referred to as the 20S editosome) to perform guided U-insertion mRNA editing. Although RNA editing TUTase 1 and RNA editing TUTase 2 carry out distinct functions and possess dissimilar enzymatic properties, their catalytic N-terminal domain and base recognition C-terminal domain display a high degree of similarity, while their middle domains are less conserved. MEAT1 (mitochondrial editosome-like complex associated TUTase 1), which interacts with an editosome-like assembly and is exclusively U-specific, nonetheless shows limited similarity with editing TUTases and lacks the middle domain. The crystal structures of apo MEAT1 and UTP-bound MEAT1 refined to 1.56 A and 1.95 A, respectively, reveal an unusual mechanism of UTP selection and domain organization previously unseen in TUTases. In addition to established invariant UTP-binding determinants, we have identified and verified critical contributions of MEAT1-specific residues using mutagenesis. Furthermore, MEAT1 possesses a novel bridging domain, which extends from the C-terminal domain and makes hydrophobic contacts with the N-terminal domain, thereby creating a cavity adjacent to the UTP-binding site. Unlike the minimal TUT4 TUTase, MEAT1 shows no appreciable conformational change upon UTP binding and apparently does not require RNA substrate to select a cognate nucleoside triphosphate. Because MEAT1 is essential for the viability of the bloodstream and insect forms of Trypanosoma brucei, the unique organization of its active site renders this protein an attractive target for trypanocide development.


    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
Minor Editosome-Associated TUTase
A, B
384Trypanosoma brucei brucei (strain 927/4 GUTat10.1)Mutation(s): 0 
Find proteins for Q4GZ86 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Go to UniProtKB:  Q4GZ86
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
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 63.093α = 90.00
b = 103.024β = 111.01
c = 63.041γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
DENZOdata reduction
REFMACrefinement
RESOLVEphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-05-20 
  • Released Date: 2010-05-12 
  • Deposition Author(s): Stagno, J., Luecke, H.

Revision History 

  • Version 1.0: 2010-05-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description