Structure of Aquifex aeolicus GidA in the form I crystal

Experimental Data Snapshot

  • Resolution: 3.20 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.242 

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Conserved cysteine residues of GidA are essential for biogenesis of 5-carboxymethylaminomethyluridine at tRNA anticodon

Osawa, T.Ito, K.Inanaga, H.Nureki, O.Tomita, K.Numata, T.

(2009) Structure 17: 713-724

  • DOI: https://doi.org/10.1016/j.str.2009.03.013
  • Primary Citation of Related Structures:  
    2ZXH, 2ZXI

  • PubMed Abstract: 

    The 5-carboxymethylaminomethyl modification of uridine (cmnm(5)U) at the anticodon first position occurs in tRNAs that read split codon boxes ending with purine. This modification is crucial for correct translation, by restricting codon-anticodon wobbling. Two conserved enzymes, GidA and MnmE, participate in the cmnm(5)U modification process. Here we determined the crystal structure of Aquifex aeolicus GidA at 2.3 A resolution. The structure revealed the tight interaction of GidA with FAD. Structure-based mutation analyses allowed us to identify two conserved Cys residues in the vicinity of the FAD-binding site that are essential for the cmnm(5)U modification in vivo. Together with mutational analysis of MnmE, we propose a mechanism for the cmnm(5)U modification process where GidA, but not MnmE, attacks the C6 atom of uridine by a mechanism analogous to that of thymidylate synthase. We also present a tRNA-docking model that provides structural insights into the tRNA recognition mechanism for efficient modification.

  • Organizational Affiliation

    Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA uridine 5-carboxymethylaminomethyl modification enzyme mnmG
A, B
637Aquifex aeolicusMutation(s): 0 
Gene Names: aq_761
Find proteins for O66962 (Aquifex aeolicus (strain VF5))
Explore O66962 
Go to UniProtKB:  O66962
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO66962
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.20 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.242 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.638α = 90
b = 213.272β = 90
c = 231.737γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-05-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-04-04
    Changes: Database references
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations