3CP2
Crystal structure of GidA from E. coli
PDB DOI: 10.2210/pdb3CP2/pdb
Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli
Deposition Author(s): Scrima, A., Meyer, S., Versees, W., Wittinghofer, A.
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.
(2008) J Mol Biol 380: 532-547
PubMed: 18565343 Search on PubMed
DOI: 10.1016/j.jmb.2008.04.072
3CP2, 3CP8
GidA is a flavin-adenine-dinucleotide (FAD)-binding protein that is conserved among bacteria and eucarya. Together with MnmE, it is involved in the addition of a carboxymethylaminomethyl group to the uridine base in the wobble position (nucleotide 34) of tRNAs that read split codon boxes ...
GidA is a flavin-adenine-dinucleotide (FAD)-binding protein that is conserved among bacteria and eucarya. Together with MnmE, it is involved in the addition of a carboxymethylaminomethyl group to the uridine base in the wobble position (nucleotide 34) of tRNAs that read split codon boxes. Here, we report the crystal structures of the GidA proteins from both Escherichia coli and Chlorobium tepidum. The structures show that the protein can be divided into three domains: a first FAD-binding domain showing the classical Rossmann fold, a second alpha/beta domain inserted between two strands of the Rossmann fold, and an alpha-helical C-terminal domain. The domain inserted into the Rossmann fold displays structural similarity to the nicotinamide-adenine-dinucleotide-(phosphate)-binding domains of phenol hydroxylase and 3-hydroxy-3-methylglutaryl-CoA reductase, and, correspondingly, we show that GidA binds NADH with high specificity as an initial donor of electrons. GidA behaves as a homodimer in solution. As revealed by the crystal structures, homodimerization is mediated via both the FAD-binding domain and the NADH-binding domain. Finally, a large patch of highly conserved, positively charged 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 and MnmE, which is supported by site-directed mutagenesis. Our data suggest that this interaction is modulated and potentially regulated by the switch function of the G domain of MnmE.
Department of Structural Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany.
tRNA uridine 5-carboxymethylaminomethyl modification enzyme gidA A 649 Escherichia coli Mutation(s): 0
Gene Names: gidA
EC: 1
Find proteins for P0A6U3 (Escherichia coli (strain K12))
Explore P0A6U3
Go to UniProtKB: P0A6U3
UniProt Group P0A6U3
B [auth A] SULFATE ION
Space Group: P 65 2 2
a = 197.6 α = 90
b = 197.6 β = 90
c = 69.16 γ = 120