5JXU

Structural basis for the catalytic activity of Thermomonospora curvata heme-containing DyP-type peroxidase.

5JXU の概要

• エントリーDOI: 10.2210/pdb5jxu/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: oxidoreductase, heme-containing
• 由来する生物種: Thermomonospora curvata
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 88589.02

構造登録者

Ramyar, K.X.,Carlson, E.A.,Li, P.,Geisbrecht, B.V. (登録日: 2016-05-13, 公開日: 2016-10-19, 最終更新日: 2023-09-27)

主引用文献

Shrestha, R.,Chen, X.,Ramyar, K.X.,Hayati, Z.,Carlson, E.A.,Bossmann, S.H.,Song, L.,Geisbrecht, B.V.,Li, P.
Identification of Surface-Exposed Protein Radicals and A Substrate Oxidation Site in A-Class Dye-Decolorizing Peroxidase from Thermomonospora curvata.
ACS Catal, 6:8036-8047, 2016

PubMed Abstract: Dye-decolorizing peroxidases (DyPs) are a family of heme peroxidases, in which a catalytic distal aspartate is involved in HO activation to catalyze oxidations in acidic conditions. They have received much attention due to their potential applications in lignin compound degradation and biofuel production from biomass. However, the mode of oxidation in bacterial DyPs remains unknown. We have recently reported that the bacterial DyP from is among the most active DyPs and shows activity toward phenolic lignin model compounds (, , 23447). Based on the X-ray crystal structure solved at 1.75 Å, sigmoidal steady-state kinetics with Reactive Blue 19 (RB19), and formation of compound II-like product in the absence of reducing substrates observed with stopped-flow spectroscopy and electron paramagnetic resonance (EPR), we hypothesized that the DyP catalyzes oxidation of large-size substrates multiple surface-exposed protein radicals. Among 7 tryptophans and 3 tyrosines in DyP consisting of 376 residues for the matured protein, W263, W376, and Y332 were identified as surface-exposed protein radicals. Only the W263 was also characterized as one of surface-exposed oxidation sites. SDS-PAGE and size-exclusion chromatography demonstrated that W376 represents an off-pathway destination for electron transfer, resulting in the crosslinking of proteins in the absence of substrates. Mutation of W376 improved compound I stability and overall catalytic efficiency toward RB19. While Y332 is highly conserved across all four classes of DyPs, its catalytic function in A-class DyP is minimal possibly due to its extremely small solvent accessible areas. Identification of surface-exposed protein radicals and substrate oxidation sites is important for understanding DyP mechanism and modulating its catalytic functions for improved activity on phenolic lignin.

PubMed: 29308294
DOI: 10.1021/acscatal.6b01952

実験手法

X-RAY DIFFRACTION (1.751 Å)