Conserved Cysteine Residues of GidA Are Essential for Biogenesis of 5-Carboxymethylaminomethyluridine at tRNA Anticodon

Takuo Osawa, Koichi Ito, Hideko Inanaga, Osamu Nureki, Kozo Tomita, Tomoyuki Numata

Research output: Contribution to journalArticle

36 Citations (Scopus)

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 Å 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.

Original languageEnglish
Pages (from-to)713-724
Number of pages12
JournalStructure
Volume17
Issue number5
DOIs
Publication statusPublished - May 13 2009
Externally publishedYes

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Anticodon
Transfer RNA
Cysteine
Flavin-Adenine Dinucleotide
Uridine
Codon
Thymidylate Synthase
Structural Models
Binding Sites
Mutation
Enzymes
5-carboxymethylaminomethyluridine

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Molecular Biology

Cite this

Conserved Cysteine Residues of GidA Are Essential for Biogenesis of 5-Carboxymethylaminomethyluridine at tRNA Anticodon. / Osawa, Takuo; Ito, Koichi; Inanaga, Hideko; Nureki, Osamu; Tomita, Kozo; Numata, Tomoyuki.

In: Structure, Vol. 17, No. 5, 13.05.2009, p. 713-724.

Research output: Contribution to journalArticle

Osawa, Takuo ; Ito, Koichi ; Inanaga, Hideko ; Nureki, Osamu ; Tomita, Kozo ; Numata, Tomoyuki. / Conserved Cysteine Residues of GidA Are Essential for Biogenesis of 5-Carboxymethylaminomethyluridine at tRNA Anticodon. In: Structure. 2009 ; Vol. 17, No. 5. pp. 713-724.
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