5VJ0

Crystal Structure of heme-containing DyP Type Peroxidase from Enterobacter lignolyticus

5VJ0 の概要

• エントリーDOI: 10.2210/pdb5vj0/pdb
• 分子名称: Dyp-type peroxidase family, PROTOPORPHYRIN IX CONTAINING FE (3 entities in total)
• 機能のキーワード: enterobacter lignolyticus, peroxidase, heme, lignin, oxidoreductase
• 由来する生物種: Enterobacter lignolyticus
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 144149.03

構造登録者

Meekins, D.A.,Li, P.,Geisbrecht, B.V. (登録日: 2017-04-17, 公開日: 2017-08-16, 最終更新日: 2023-10-04)

主引用文献

Shrestha, R.,Huang, G.,Meekins, D.A.,Geisbrecht, B.V.,Li, P.
Mechanistic Insights into Dye-Decolorizing Peroxidase Revealed by Solvent Isotope and Viscosity Effects.
ACS Catal, 7:6352-6364, 2017

PubMed Abstract: Dye-decolorizing peroxidases (DyPs) are a family of HO-dependent heme peroxidases, which have shown potential applications in lignin degradation and valorization. However, the DyP kinetic mechanism remains underexplored. Using structural biology and solvent isotope (sKIE) and viscosity effects, many mechanistic characteristics have been uncovered for the B-class DyP from . Its structure revealed that a water molecule acts as the sixth axial ligand with two channels at diameters of ~3.0 and 8.0 Å leading to the heme center. A conformational change of ERS to ERS, which have identical spectral characteristics, was proposed as the final step in DyPs' bisubstrate Ping-Pong mechanism. This step is also the rate-determining step in ABTS oxidation. The normal KIE of wild-type DyP with DO at pH 3.5 suggested that cmpd 0 deprotonation by the distal aspartate is rate-limiting in the formation of cmpd I, which is more reactive under acidic pH than under neutral or alkaline pH. The viscosity effects and other biochemical methods implied that the reducing substrate binds with cmpd I instead of the free enzyme. The significant inverse sKIEs of / and suggested that the aquo release in DyPs is mechanistically important and may explain the enzyme's adoption of two-electron reduction for cmpd I. The distal aspartate is catalytically more important than the distal arginine and plays key roles in determining DyPs' acidic pH optimum. The kinetic mechanism of D143H-DyP was also briefly studied. The results obtained will pave the way for future protein engineering to improve DyPs' lignolytic activity.

PubMed: 29308295
DOI: 10.1021/acscatal.7b01861

実験手法

X-RAY DIFFRACTION (1.93 Å)