2D1P

crystal structure of heterohexameric TusBCD proteins, which are crucial for the tRNA modification


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis for Sulfur Relay to RNA Mediated by Heterohexameric TusBCD Complex

Numata, T.Fukai, S.Ikeuchi, Y.Suzuki, T.Nureki, O.

(2006) Structure 14: 357-366

  • DOI: 10.1016/j.str.2005.11.009

  • PubMed Abstract: 
  • Uridine at wobble position 34 of tRNA(Lys), tRNA(Glu), and tRNA(Gln) is exclusively modified into 2-thiouridine (s2U), which is crucial for both precise codon recognition and recognition by the cognate aminoacyl-tRNA synthetases. Recent Escherichia c ...

    Uridine at wobble position 34 of tRNA(Lys), tRNA(Glu), and tRNA(Gln) is exclusively modified into 2-thiouridine (s2U), which is crucial for both precise codon recognition and recognition by the cognate aminoacyl-tRNA synthetases. Recent Escherichia coli genetic studies revealed that the products of five novel genes, tusABCDE, function in the s2U modification. Here, we solved the 2.15 angstroms crystal structure of the E. coli TusBCD complex, a sulfur transfer mediator, forming a heterohexamer composed of a dimer of the heterotrimer. Structure-based sequence alignment suggested two putative active site Cys residues, Cys79 (in TusC) and Cys78 (in TusD), which are exposed on the hexameric complex. In vivo mutant analyses revealed that only Cys78, in the TusD subunit, participates in sulfur transfer during the s2U modification process. Since the single Cys acts as a catalytic residue, we proposed that TusBCD mediates sulfur relay via a putative persulfide state of the TusD subunit.


    Organizational Affiliation

    Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama-shi, Kanagawa 226-8501, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hypothetical UPF0163 protein yheN
A, D, G
140Escherichia coli (strain K12)Gene Names: tusD (yheN)
EC: 2.8.1.-
Find proteins for P45532 (Escherichia coli (strain K12))
Go to UniProtKB:  P45532
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hypothetical UPF0116 protein yheM
B, E, H
119Escherichia coli (strain K12)Gene Names: tusC (yheM)
Find proteins for P45531 (Escherichia coli (strain K12))
Go to UniProtKB:  P45531
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Hypothetical protein yheL
C, F, I
95Escherichia coli (strain K12)Gene Names: tusB (yheL)
Find proteins for P45530 (Escherichia coli (strain K12))
Go to UniProtKB:  P45530
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
H
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.209 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 141.392α = 90.00
b = 141.392β = 90.00
c = 135.686γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
HKL-2000data scaling
SHARPphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-02-28
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance