2ZXI
Structure of Aquifex aeolicus GidA in the form II crystal
Summary for 2ZXI
| Entry DOI | 10.2210/pdb2zxi/pdb |
| Related | 2ZXH |
| Descriptor | tRNA uridine 5-carboxymethylaminomethyl modification enzyme mnmG, FLAVIN-ADENINE DINUCLEOTIDE (3 entities in total) |
| Functional Keywords | modification, trna, 5-carboxymethylaminomethyl uridine, wobble uridine, fad, fad-binding protein, trna modification enzyme |
| Biological source | Aquifex aeolicus |
| Cellular location | Cytoplasm (By similarity): O66962 |
| Total number of polymer chains | 4 |
| Total formula weight | 290439.42 |
| Authors | Numata, T.,Osawa, T. (deposition date: 2008-12-24, release date: 2009-05-19, Last modification date: 2023-11-01) |
| Primary citation | Osawa, T.,Ito, K.,Inanaga, H.,Nureki, O.,Tomita, K.,Numata, T. Conserved cysteine residues of GidA are essential for biogenesis of 5-carboxymethylaminomethyluridine at tRNA anticodon Structure, 17:713-724, 2009 Cited by 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. PubMed: 19446527DOI: 10.1016/j.str.2009.03.013 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.3 Å) |
Structure validation
Download full validation report
