3CP8

Crystal structure of GidA from Chlorobium tepidum

3CP8 の概要

• エントリーDOI: 10.2210/pdb3cp8/pdb
• 関連するPDBエントリー: 3CP2
• 分子名称: tRNA uridine 5-carboxymethylaminomethyl modification enzyme gidA, FLAVIN-ADENINE DINUCLEOTIDE (2 entities in total)
• 機能のキーワード: rossmann fold, fad-binding domain, dinucleotide-binding motif, glutathione reductase, oxido-reductase, trna-modification, cytoplasm, flavoprotein, trna processing, oxidoreductase
• 由来する生物種: Chlorobium tepidum
• 細胞内の位置: Cytoplasm (By similarity): Q8KA85
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 284571.01

構造登録者

Meyer, S.,Scrima, A.,Versees, W.,Wittinghofer, A. (登録日: 2008-03-31, 公開日: 2008-06-24, 最終更新日: 2023-11-01)

主引用文献

Meyer, S.,Scrima, A.,Versees, W.,Wittinghofer, A.
Crystal structures of the conserved tRNA-modifying enzyme GidA: implications for its interaction with MnmE and substrate
J.Mol.Biol., 380:532-547, 2008

PubMed Abstract: 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.

PubMed: 18565343
DOI: 10.1016/j.jmb.2008.04.072

実験手法

X-RAY DIFFRACTION (3.2 Å)