2B3J

Crystal Structure of Staphylococcus aureus tRNA Adenosine Deaminase, TadA, in Complex with RNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Crystal structure of Staphylococcus aureus tRNA adenosine deaminase TadA in complex with RNA.

Losey, H.C., Ruthenburg, A.J., Verdine, G.L.

(2006) Nat Struct Mol Biol 13: 153-159

  • DOI: https://doi.org/10.1038/nsmb1047
  • Primary Citation of Related Structures:  
    2B3J

  • PubMed Abstract: 

    Bacterial tRNA adenosine deaminases (TadAs) catalyze the hydrolytic deamination of adenosine to inosine at the wobble position of tRNA(Arg2), a process that enables this single tRNA to recognize three different arginine codons in mRNA. In addition, inosine is also introduced at the wobble position of multiple eukaryotic tRNAs. The genes encoding these deaminases are essential in bacteria and yeast, demonstrating the importance of their biological activity. Here we report the crystallization and structure determination to 2.0 A of Staphylococcus aureus TadA bound to the anticodon stem-loop of tRNA(Arg2) bearing nebularine, a non-hydrolyzable adenosine analog, at the wobble position. The cocrystal structure reveals the basis for both sequence and structure specificity in the interactions of TadA with RNA, and it additionally provides insight into the active site architecture that promotes efficient hydrolytic deamination.

    • Organizational Affiliation: 

    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.


Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA adenosine deaminaseE [auth A],
F [auth B],
G [auth C],
H [auth D]		159Staphylococcus aureus subsp. aureus Mu50Mutation(s): 0 
Gene Names: TADA
EC: 3.5.4
UniProt
Find proteins for Q99W51 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Explore Q99W51 
Go to UniProtKB:  Q99W51
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99W51
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
anticodon stem-loop of t-RNA-Arg2 (nucleotides 27-42)A [auth E],
B [auth F],
C [auth G],
D [auth H]		16N/A
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.055α = 90
b = 89.029β = 90
c = 119.133γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations