5J84

Crystal structure of L-arabinonate dehydratase in holo-form

5J84 の概要

• エントリーDOI: 10.2210/pdb5j84/pdb
• 分子名称: Dihydroxy-acid dehydratase, MAGNESIUM ION, FE2/S2 (INORGANIC) CLUSTER, ... (4 entities in total)
• 機能のキーワード: l-arabinonate dehydratase, l-arabonate dehydratase, pentonate dehydratase, 2fe2s cluster, lyase
• 由来する生物種: Rhizobium leguminosarum bv. trifolii (strain WSM2304); 詳細
• タンパク質・核酸の鎖数: 8
• 化学式量合計: 512472.50

構造登録者

Rahman, M.M.,Rouvinen, J.,Hakulinen, N. (登録日: 2016-04-07, 公開日: 2017-06-21, 最終更新日: 2024-01-10)

主引用文献

Rahman, M.M.,Andberg, M.,Thangaraj, S.K.,Parkkinen, T.,Penttila, M.,Janis, J.,Koivula, A.,Rouvinen, J.,Hakulinen, N.
The Crystal Structure of a Bacterial l-Arabinonate Dehydratase Contains a [2Fe-2S] Cluster.
ACS Chem. Biol., 12:1919-1927, 2017

PubMed Abstract: We present a novel crystal structure of the IlvD/EDD family enzyme, l-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii (RlArDHT, EC 4.2.1.25), which catalyzes the conversion of l-arabinonate to 2-dehydro-3-deoxy-l-arabinonate. The enzyme is a tetramer consisting of a dimer of dimers, where each monomer is composed of two domains. The active site contains a catalytically important [2Fe-2S] cluster and Mg ion and is buried between two domains, and also at the dimer interface. The active site Lys129 was found to be carbamylated. Ser480 and Thr482 were shown to be essential residues for catalysis, and the S480A mutant structure showed an unexpected open conformation in which the active site was more accessible for the substrate. This structure showed the partial binding of l-arabinonate, which allowed us to suggest that the alkoxide ion form of the Ser480 side chain functions as a base and the [2Fe-2S] cluster functions as a Lewis acid in the elimination reaction.

PubMed: 28574691
DOI: 10.1021/acschembio.7b00304

実験手法

X-RAY DIFFRACTION (2.4 Å)