3W9Z

Crystal structure of DusC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of dihydrouridine synthase C (DusC) from Escherichia coli

Chen, M.Yu, J.Tanaka, Y.Tanaka, M.Tanaka, I.Yao, M.

(2013) Acta Crystallogr.,Sect.F 69: 834-838

  • DOI: 10.1107/S1744309113019489

  • PubMed Abstract: 
  • Dihydrouridine (D) is one of the most widely conserved tRNA modifications. Dihydrouridine synthase (Dus) is responsible for introducing D modifications into RNA by the reduction of uridine. Recently, a unique substrate-recognition mechanism using a s ...

    Dihydrouridine (D) is one of the most widely conserved tRNA modifications. Dihydrouridine synthase (Dus) is responsible for introducing D modifications into RNA by the reduction of uridine. Recently, a unique substrate-recognition mechanism using a small adapter molecule has been proposed for Thermus thermophilus Dus (TthDusC). To acquire insight regarding its substrate-recognition mechanism, the crystal structure of DusC from Escherichia coli (EcoDusC) was determined at 2.1 Å resolution. EcoDusC was shown to be composed of two domains: an N-terminal catalytic domain and a C-terminal tRNA-binding domain. An L-shaped electron density surrounded by highly conserved residues was found in the active site, as observed for TthDus. Structure comparison with TthDus indicated that the N-terminal region has a similar structure, whereas the C-terminal domain has marked differences in its relative orientation to the N-terminal domain as well as in its own structure. These observations suggested that Dus proteins adopt a common substrate-recognition mechanism using an adapter molecule, whereas the manner of tRNA binding is diverse.


    Organizational Affiliation

    Graduate School of Life Sciences, Hokkaido University, Sapporo 060-0810, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
tRNA-dihydrouridine synthase C
A
322Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: dusC (yohI)
EC: 1.3.1.-
Find proteins for P33371 (Escherichia coli (strain K12))
Go to UniProtKB:  P33371
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.221 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 93.252α = 90.00
b = 93.252β = 90.00
c = 115.499γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SHELXphasing
SHELXDphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-31
    Type: Initial release
  • Version 1.1: 2013-08-21
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Refinement description