5B37

Crystal structure of L-tryptophan dehydrogenase from Nostoc punctiforme

5B37 の概要

• エントリーDOI: 10.2210/pdb5b37/pdb
• 分子名称: Tryptophan dehydrogenase (2 entities in total)
• 機能のキーワード: dehydrogenase, oxidoreductase
• 由来する生物種: Nostoc punctiforme NIES-2108
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 237540.68

構造登録者

Wakamatsu, T.,Sakuraba, H.,Kitamura, M.,Hakumai, Y.,Ohnishi, K.,Ashiuchi, M.,Ohshima, T. (登録日: 2016-02-11, 公開日: 2016-11-23, 最終更新日: 2023-11-08)

主引用文献

Wakamatsu, T.,Sakuraba, H.,Kitamura, M.,Hakumai, Y.,Fukui, K.,Ohnishi, K.,Ashiuchi, M.,Ohshima, T.
Structural Insights into l-Tryptophan Dehydrogenase from a Photoautotrophic Cyanobacterium, Nostoc punctiforme.
Appl. Environ. Microbiol., 83:-, 2017

PubMed Abstract: l-Tryptophan dehydrogenase from Nostoc punctiforme NIES-2108 (NpTrpDH), despite exhibiting high amino acid sequence identity (>30%)/homology (>50%) with NAD(P)-dependent l-Glu/l-Leu/l-Phe/l-Val dehydrogenases, exclusively catalyzes reversible oxidative deamination of l-Trp to 3-indolepyruvate in the presence of NAD Here, we determined the crystal structure of the apo form of NpTrpDH. The structure of the NpTrpDH monomer, which exhibited high similarity to that of l-Glu/l-Leu/l-Phe dehydrogenases, consisted of a substrate-binding domain (domain I, residues 3 to 133 and 328 to 343) and an NAD/NADH-binding domain (domain II, residues 142 to 327) separated by a deep cleft. The apo-NpTrpDH existed in an open conformation, where domains I and II were apart from each other. The subunits dimerized themselves mainly through interactions between amino acid residues around the β-1 strand of each subunit, as was observed in the case of l-Phe dehydrogenase. The binding site for the substrate l-Trp was predicted by a molecular docking simulation and validated by site-directed mutagenesis. Several hydrophobic residues, which were located in the active site of NpTrpDH and possibly interacted with the side chain of the substrate l-Trp, were arranged similarly to that found in l-Leu/l-Phe dehydrogenases but fairly different from that of an l-Glu dehydrogenase. Our crystal structure revealed that Met-40, Ala-69, Ile-74, Ile-110, Leu-288, Ile-289, and Tyr-292 formed a hydrophobic cluster around the active site. The results of the site-directed mutagenesis experiments suggested that the hydrophobic cluster plays critical roles in protein folding, l-Trp recognition, and catalysis. Our results provide critical information for further characterization and engineering of this enzyme.

PubMed: 27815281
DOI: 10.1128/AEM.02710-16

実験手法

X-RAY DIFFRACTION (3.4 Å)