Taxonomic distribution of proteins containing GIDA_assoc_3 domains

The tree below includes only several representative species and genera. The complete taxonomic breakdown of all proteins containing GIDA_assoc_3 domains can be accessed here. Click the counts or percentage values to display the corresponding proteins.

Conserved cysteine residues of GidA are essential for biogenesis of5-carboxymethylaminomethyluridine at tRNA anticodon.

Osawa T, Ito K, Inanaga H, Nureki O, Tomita K, Numata T
Structure. 2009; 17: 713-24

The 5-carboxymethylaminomethyl modification of uridine (cmnm(5)U) at theanticodon first position occurs in tRNAs that read split codon boxes ending with purine. This modification is crucial for correct translation, by restrictingcodon-anticodon wobbling. Two conserved enzymes, GidA and MnmE, participate inthe cmnm(5)U modification process. Here we determined the crystal structure ofAquifex aeolicus GidA at 2.3 A resolution. The structure revealed the tightinteraction of GidA with FAD. Structure-based mutation analyses allowed us toidentify 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 mutationalanalysis of MnmE, we propose a mechanism for the cmnm(5)U modification processwhere GidA, but not MnmE, attacks the C6 atom of uridine by a mechanism analogousto that of thymidylate synthase. We also present a tRNA-docking model thatprovides structural insights into the tRNA recognition mechanism for efficientmodification.

Crystal structures of the conserved tRNA-modifying enzyme GidA: implications for its interaction with MnmE and substrate.

Meyer S, Scrima A, Versees W, Wittinghofer A
J Mol Biol. 2008; 380: 532-47

GidA is a flavin-adenine-dinucleotide (FAD)-binding protein that is conservedamong bacteria and eucarya. Together with MnmE, it is involved in the addition ofa carboxymethylaminomethyl group to the uridine base in the wobble position(nucleotide 34) of tRNAs that read split codon boxes. Here, we report the crystalstructures of the GidA proteins from both Escherichia coli and Chlorobiumtepidum. The structures show that the protein can be divided into three domains: a first FAD-binding domain showing the classical Rossmann fold, a secondalpha/beta domain inserted between two strands of the Rossmann fold, and analpha-helical C-terminal domain. The domain inserted into the Rossmann folddisplays structural similarity to thenicotinamide-adenine-dinucleotide-(phosphate)-binding domains of phenolhydroxylase and 3-hydroxy-3-methylglutaryl-CoA reductase, and, correspondingly,we show that GidA binds NADH with high specificity as an initial donor ofelectrons. GidA behaves as a homodimer in solution. As revealed by the crystalstructures, homodimerization is mediated via both the FAD-binding domain and the NADH-binding domain. Finally, a large patch of highly conserved, positivelycharged residues on the surface of GidA leading to the FAD-binding site suggests a tRNA-binding surface. We propose a model for the interaction between GidA andMnmE, which is supported by site-directed mutagenesis. Our data suggest that thisinteraction is modulated and potentially regulated by the switch function of the G domain of MnmE.