4WFS

Crystal Structure of tRNA-dihydrouridine(20) synthase catalytic domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

An extended dsRBD is required for post-transcriptional modification in human tRNAs.

Bou-Nader, C.Pecqueur, L.Bregeon, D.Kamah, A.Guerineau, V.Golinelli-Pimpaneau, B.Guimaraes, B.G.Fontecave, M.Hamdane, D.

(2015) Nucleic Acids Res. 43: 9446-9456

  • DOI: 10.1093/nar/gkv989
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In tRNA, dihydrouridine is a conserved modified base generated by the post-transcriptional reduction of uridine. Formation of dihydrouridine 20, located in the D-loop, is catalyzed by dihydrouridine synthase 2 (Dus2). Human Dus2 (HsDus2) expression i ...

    In tRNA, dihydrouridine is a conserved modified base generated by the post-transcriptional reduction of uridine. Formation of dihydrouridine 20, located in the D-loop, is catalyzed by dihydrouridine synthase 2 (Dus2). Human Dus2 (HsDus2) expression is upregulated in lung cancers, offering a growth advantage throughout its ability to interact with components of the translation apparatus and inhibit apoptosis. Here, we report the crystal structure of the individual domains of HsDus2 and their functional characterization. HsDus2 is organized into three major modules. The N-terminal catalytic domain contains the flavin cofactor involved in the reduction of uridine. The second module is the conserved α-helical domain known as the tRNA binding domain in HsDus2 homologues. It is connected via a flexible linker to an unusual extended version of a dsRNA binding domain (dsRBD). Enzymatic assays and yeast complementation showed that the catalytic domain binds selectively NADPH but cannot reduce uridine in the absence of the dsRBD. While in Dus enzymes from bacteria, plants and fungi, tRNA binding is essentially achieved by the α-helical domain, we showed that in HsDus2 this function is carried out by the dsRBD. This is the first reported case of a tRNA-modifying enzyme carrying a dsRBD used to bind tRNAs.


    Organizational Affiliation

    Institut de Chimie des Substances Naturelles, Centre de Recherche de Gif, CNRS, 1 avenue de la Terrasse, 91198 Gif-sur-Yvette, France.,Sorbonne Universités, UPMC Univ. Paris 06, IBPS, UMR8256, Biology of Aging and Adaptation, F-75005 Paris, France.,Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, France, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France.,Université de Lille-Nord de France, CNRS UMR 8576, Institut Fédératif de Recherches 147, Villeneuve d'Ascq, France.,Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, 91190 Gif-sur-Yvette, France.,Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, France, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France djemel.hamdane@college-de-france.fr.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
tRNA-dihydrouridine(20) synthase [NAD(P)+]-like
A
327Homo sapiensMutation(s): 0 
Gene Names: DUS2 (DUS2L)
EC: 1.3.1.91
Find proteins for Q9NX74 (Homo sapiens)
Go to Gene View: DUS2
Go to UniProtKB:  Q9NX74
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FMN
Query on FMN

Download SDF File 
Download CCD File 
A
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.197 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 71.570α = 90.00
b = 85.260β = 90.00
c = 144.230γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-10-07
    Type: Initial release
  • Version 1.1: 2015-10-14
    Type: Database references
  • Version 1.2: 2015-11-11
    Type: Database references