8H0M

Crystal structure of VioD

8H0M の概要

• エントリーDOI: 10.2210/pdb8h0m/pdb
• 分子名称: VioD, FLAVIN-ADENINE DINUCLEOTIDE, FORMIC ACID, ... (5 entities in total)
• 機能のキーワード: complex, flavoprotein
• 由来する生物種: Duganella sp. ZLP-XI
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 45597.34

構造登録者

Xu, M.,Ran, T.,Wang, W. (登録日: 2022-09-29, 公開日: 2023-04-12, 最終更新日: 2023-11-29)

主引用文献

Xu, M.,Xu, D.,Gao, M.,Zhuang, X.,Wang, W.,Sun, B.,Ran, T.
Structural basis for substrate binding and catalytic mechanism of the key enzyme VioD in the violacein synthesis pathway.
Proteins, 91:956-966, 2023

PubMed Abstract: Violacein is a pigment synthesized by gram-negative bacteria with various biological activities such as antimicrobial, antiviral, and anticancer activities. VioD is a key oxygenase converting protodeoxyviolaceinic acid to protoviolaceinic acid in violacein biosynthesis. To elucidate the catalytic mechanism of VioD, here, we resolved two crystal structures of VioD, a binary complex structure containing VioD and a FAD and a ternary complex structure composed of VioD, a FAD and a 2-ethyl-1-hexanol (EHN). Structural analysis revealed a deep funnel like binding pocket with wide entrance, this pocket is positively charged. The EHN is located at the deep bottom of the binding pocket near isoalloxazine ring. Further docking simulation help us to propose the mechanism of the hydroxylation of the substrate catalyzed by VioD. Bioinformatic analysis suggested and emphasized the importance of the conserved residues involved in substrate binding. Our results provide a structural basis for the catalytic mechanism of VioD.

PubMed: 36869636
DOI: 10.1002/prot.26484

実験手法

X-RAY DIFFRACTION (1.702 Å)