3WWX

Crystal structure of D-stereospecific amidohydrolase from Streptomyces sp. 82F2

3WWX の概要

• エントリーDOI: 10.2210/pdb3wwx/pdb
• 分子名称: S12 family peptidase, OCTANE 1,8-DIAMINE (3 entities in total)
• 機能のキーワード: amidohydrolase, hydrolase
• 由来する生物種: Streptomyces sp. 82F2
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 37585.20

構造登録者

Arima, J.,Nagano, S.,Hino, T.,Shimone, K.,Isoda, Y.,Mori, N. (登録日: 2014-07-03, 公開日: 2015-07-08, 最終更新日: 2024-10-30)

主引用文献

Arima, J.,Shimone, K.,Miyatani, K.,Tsunehara, Y.,Isoda, Y.,Hino, T.,Nagano, S.
Crystal structure of D-stereospecific amidohydrolase from Streptomyces sp. 82F2 - insight into the structural factors for substrate specificity.
Febs J., 283:337-349, 2016

PubMed Abstract: D-Stereospecific amidohydrolase (DAH) from Streptomyces sp. 82F2, which catalyzes amide bond formation from d-aminoacyl esters and l-amino acids (aminolysis), can be used to synthesize short peptides with a dl-configuration. We found that DAH can use 1,8-diaminooctane and other amino compounds as acyl acceptors in the aminolysis reaction. Low concentrations of 1,8-diaminooctane inhibited acyl-DAH intermediate formation. By contrast, excess 1,8-diaminooctane promoted aminolysis by DAH, producing d-Phe-1,8-diaminooctane via nucleophilic attack of the diamine on enzyme-bound d-Phe. To clarify the mechanism of substrate specificity and amide bond formation by DAH, the crystal structure of the enzyme that binds 1,8-diaminooctane was determined at a resolution of 1.49 Å. Comparison of the DAH crystal structure with those of other members of the S12 peptidase family indicated that the substrate specificity of DAH arises from its active site structure. The 1,8-diaminooctane molecule binds at the entrance of the active site pocket. The electrkon density map showed that another potential 1,8-diaminooctane binding site, probably with lower affinity, is present close to the active site. The enzyme kinetics and structural comparisons suggest that the location of enzyme-bound diamine can explain the inhibition of the acyl-enzyme intermediate formation, although the bound diamine is too far from the active site for aminolysis. Despite difficulty in locating the diamine binding site for aminolysis definitively, we propose that the excess diamine also binds at or near the second binding site to attack the acyl-enzyme intermediate during aminolysis.

PubMed: 26513520
DOI: 10.1111/febs.13579

実験手法

X-RAY DIFFRACTION (1.49 Å)