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 
  • R-Value Observed: 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
  • Primary Citation of Related Structures:  
    2D1P

  • 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 coli genetic studies revealed that the products of five novel genes, tusABCDE, function in the s2U modification ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hypothetical UPF0163 protein yheNA, D, G140Escherichia coliMutation(s): 0 
Gene Names: yheN
EC: 2.8.1
UniProt
Find proteins for P45532 (Escherichia coli (strain K12))
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Go to UniProtKB:  P45532
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Hypothetical UPF0116 protein yheMB, E, H119Escherichia coliMutation(s): 0 
Gene Names: yheM
UniProt
Find proteins for P45531 (Escherichia coli (strain K12))
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Go to UniProtKB:  P45531
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Hypothetical protein yheLC, F, I95Escherichia coliMutation(s): 0 
Gene Names: yheL
UniProt
Find proteins for P45530 (Escherichia coli (strain K12))
Explore P45530 
Go to UniProtKB:  P45530
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
J [auth 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 
  • R-Value Observed: 0.209 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.392α = 90
b = 141.392β = 90
c = 135.686γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
SHARPphasing
CNSrefinement
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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