3ABI

Crystal Structure of L-Lysine Dehydrogenase from Hyperthermophilic Archaeon Pyrococcus horikoshii

「3A63」から置き換えられました 「2Z2V」から置き換えられました

3ABI の概要

• エントリーDOI: 10.2210/pdb3abi/pdb
• 分子名称: Putative uncharacterized protein PH1688, SULFATE ION, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, ... (4 entities in total)
• 機能のキーワード: l-lysine dehydrogenase, pyrococcus horikoshii, oxidoreductase
• 由来する生物種: Pyrococcus horikoshii
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 85131.44

構造登録者

Yoneda, K.,Sakuraba, H.,Fukuda, J.,Ohshima, T. (登録日: 2009-12-14, 公開日: 2009-12-29, 最終更新日: 2024-03-13)

主引用文献

Yoneda, K.,Fukuda, J.,Sakuraba, H.,Ohshima, T.
First crystal structure of L-lysine 6-dehydrogenase as an NAD-dependent amine dehydrogenase.
J.Biol.Chem., 285:8444-8453, 2010

PubMed Abstract: A gene encoding an L-lysine dehydrogenase was identified in the hyperthermophilic archaeon Pyrococcus horikoshii. The gene was overexpressed in Escherichia coli, and its product was purified and characterized. The expressed enzyme is the most thermostable L-lysine dehydrogenase yet described, with a half-life of 180 min at 100 degrees C. The product of the enzyme's catalytic activity is Delta(1)-piperideine-6-carboxylate, which makes this enzyme an L-lysine 6-dehydrogenase (EC 1.4.1.18) that catalyzes the reductive deamination of the epsilon- amino group and a type of NAD-dependent amine dehydrogenase. The three-dimensional structure of the enzyme was determined using the mercury-based multiple-wavelength anomalous dispersion method at a resolution of 2.44 A in the presence of NAD and sulfate ion. The asymmetric unit consisted of two subunits, and a crystallographic 2-fold axis generated the functional dimer. Each monomer consisted of a Rossmann fold domain and a C-terminal catalytic domain, and the fold of the catalytic domain showed similarity to that of saccharopine reductase. Notably, the structures of subunits A and B differed significantly. In subunit A, the active site contained a sulfate ion that was not seen in subunit B. Consequently, subunit A adopted a closed conformation, whereas subunit B adopted an open one. In each subunit, one NAD molecule was bound to the active site in an anti-conformation, indicating that the enzyme makes use of pro-R-specific hydride transfer between the two hydrides at C-4 of NADH (type A specificity). This is the first description of the three-dimensional structure of l-lysine 6-dehydrogenase as an NAD-dependent amine dehydrogenase.

PubMed: 20056607
DOI: 10.1074/jbc.M109.084384

実験手法

X-RAY DIFFRACTION (2.44 Å)