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3WWO

S-selective hydroxynitrile lyase from Baliospermum montanum (apo1)

3WWO の概要
エントリーDOI10.2210/pdb3wwo/pdb
関連するPDBエントリー3wwp
分子名称(S)-hydroxynitrile lyase, CALCIUM ION, (4S)-2-METHYL-2,4-PENTANEDIOL, ... (4 entities in total)
機能のキーワードalpha/beta hydrolase fold, lyase
由来する生物種Baliospermum montanum
タンパク質・核酸の鎖数2
化学式量合計65584.09
構造登録者
Nakano, S.,Dadashipour, M.,Asano, Y. (登録日: 2014-06-23, 公開日: 2014-10-22, 最終更新日: 2024-03-20)
主引用文献Nakano, S.,Dadashipour, M.,Asano, Y.
Structural and functional analysis of hydroxynitrile lyase from Baliospermum montanum with crystal structure, molecular dynamics and enzyme kinetics
Biochim.Biophys.Acta, 1844:2059-2067, 2014
Cited by
PubMed Abstract: Hydroxynitrile lyases (HNLs) catalyze degradation of cyanohydrins to hydrogen cyanide and the corresponding ketone or aldehyde. HNLs can also catalyze the reverse reaction, i.e., synthesis of cyanohydrins. Although several crystal structures of S-selective hydroxynitrile lyases (S-HNLs) have been reported, it remains unknown whether and how dynamics at the active site of S-HNLs influence their broad substrate specificity and affinity. In this study, we analyzed the structure, dynamics and function of S-HNL from Baliospermum montanum (BmHNL), which has an α/β hydrolase fold. Two crystal structures of BmHNL, apo1 and apo2, were determined at 2.55 and 1.9Å, respectively. Structural comparison between BmHNL (apo2) and S-HNL from Hevea brasiliensis with (S)-mandelonitrile bound to the active site revealed that hydrophobic residues at the entrance region of BmHNL formed hydrophobic interactions with the benzene ring of the substrate. The flexible structures of these hydrophobic residues were confirmed by a 15ns molecular dynamics simulation. This flexibility regulated the size of the active site cavity, enabling binding of various substrates to BmHNL. The high affinity of BmHNL toward substrates containing a benzene ring was also confirmed by comparing the kinetics of BmHNL and S-HNL from Manihot esculenta. Taken together, the results indicated that the flexibility and placement of the residues are important for the broad substrate specificity of S-HNLs.
PubMed: 25220808
DOI: 10.1016/j.bbapap.2014.09.004
主引用文献が同じPDBエントリー
実験手法
X-RAY DIFFRACTION (2.55 Å)
構造検証レポート
Validation report summary of 3wwo
検証レポート(詳細版)ダウンロードをダウンロード

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件を2026-04-22に公開中

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