1UMC

branched-chain 2-oxo acid dehydrogenase (E1) from Thermus thermophilus HB8 with 4-methylpentanoate

1UMC の概要

• エントリーDOI: 10.2210/pdb1umc/pdb
• 関連するPDBエントリー: 1UM9 1UMB 1UMD
• 分子名称: 2-oxo acid dehydrogenase alpha subunit, 2-oxo acid dehydrogenase beta subunit, MAGNESIUM ION, ... (6 entities in total)
• 機能のキーワード: alpha(2)beta(2) tetramer, structural genomics, riken structural genomics/proteomics initiative, rsgi, oxidoreductase
• 由来する生物種: Thermus thermophilus; 詳細
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 154392.61

構造登録者

Nakai, T.,Nakagawa, N.,Maoka, N.,Masui, R.,Kuramitsu, S.,Kamiya, N.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (登録日: 2003-09-25, 公開日: 2004-03-30, 最終更新日: 2023-10-25)

主引用文献

Nakai, T.,Nakagawa, N.,Maoka, N.,Masui, R.,Kuramitsu, S.,Kamiya, N.
Ligand-induced Conformational Changes and a Reaction Intermediate in Branched-chain 2-Oxo Acid Dehydrogenase (E1) from Thermus thermophilus HB8, as Revealed by X-ray Crystallography
J.Mol.Biol., 337:1011-1033, 2004

PubMed Abstract: The alpha(2)beta(2) tetrameric E1 component of the branched-chain 2-oxo acid (BCOA) dehydrogenase multienzyme complex is a thiamin diphosphate (ThDP)-dependent enzyme. E1 catalyzes the decarboxylation of a BCOA concomitant with the formation of the alpha-carbanion/enamine intermediate, 2-(1-hydroxyalkyl)-ThDP, followed by transfer of the 1-hydroxyalkyl group to the distal sulfur atom on the lipoamide of the E2 component. In order to elucidate the catalytic mechanism of E1, the alpha- and beta-subunits of E1 from Thermus thermophilus HB8 have been co-expressed in Escherichia coli, purified and crystallized as a stable complex, and the following crystal structures have been analyzed: the apoenzyme (E1(apo)), the holoenzyme (E1(holo)), E1(holo) in complex with the substrate analogue 4-methylpentanoate (MPA) as an ES complex model, and E1(holo) in complex with 4-methyl-2-oxopentanoate (MOPA) as the alpha-carbanion/enamine intermediate (E1(ceim)). Binding of cofactors to E1(apo) induces a disorder-order transition in two loops adjacent to the active site. Furthermore, upon binding of MPA to E1(holo), the loop comprised of Gly121beta-Gln131beta moves close to the active site and interacts with MPA. The carboxylate group of MPA is recognized mainly by Tyr86beta and N4' of ThDP. The hydrophobic moiety of MPA is recognized by Phe66alpha, Tyr95alpha, Met128alpha and His131alpha. As an intermediate, MOPA is decarboxylated and covalently linked to ThDP, and the conformation of the protein loop is almost the same as in the substrate-free (holoenzyme) form. These results suggest that E1 undergoes an open-closed conformational change upon formation of the ES complex with a BCOA, and the mobile region participates in the recognition of the carboxylate group of the BCOA. ES complex models of E1(holo).MOPA and of E1(ceim).lipoamide built from the above structures suggest that His273alpha and His129beta' are potential proton donors to the carbonyl group of a BCOA and to the proximal sulfur atom on the lipoamide, respectively.

PubMed: 15033367
DOI: 10.1016/j.jmb.2004.02.011

実験手法

X-RAY DIFFRACTION (2.4 Å)