6YRD

SFX structure of dye-type peroxidase DtpB in the ferryl state

6YRD の概要

• エントリーDOI: 10.2210/pdb6yrd/pdb
• 分子名称: Putative iron-dependent peroxidase, PROTOPORPHYRIN IX CONTAINING FE, MAGNESIUM ION, ... (6 entities in total)
• 機能のキーワード: peroxidase; dye-decolourising; serial femtosecond crystallography; damage-free; ferryl, oxidoreductase
• 由来する生物種: Streptomyces lividans 1326
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 209071.09

構造登録者

Lucic, M.,Axford, D.A.,Owen, R.L.,Worrall, J.A.R.,Hough, M.A. (登録日: 2020-04-20, 公開日: 2021-01-13, 最終更新日: 2024-05-01)

主引用文献

Lucic, M.,Svistunenko, D.A.,Wilson, M.T.,Chaplin, A.K.,Davy, B.,Ebrahim, A.,Axford, D.,Tosha, T.,Sugimoto, H.,Owada, S.,Dworkowski, F.S.N.,Tews, I.,Owen, R.L.,Hough, M.A.,Worrall, J.A.R.
Serial Femtosecond Zero Dose Crystallography Captures a Water-Free Distal Heme Site in a Dye-Decolorising Peroxidase to Reveal a Catalytic Role for an Arginine in Fe IV =O Formation.
Angew.Chem.Int.Ed.Engl., 59:21656-21662, 2020

PubMed Abstract: Obtaining structures of intact redox states of metal centers derived from zero dose X-ray crystallography can advance our mechanistic understanding of metalloenzymes. In dye-decolorising heme peroxidases (DyPs), controversy exists regarding the mechanistic role of the distal heme residues aspartate and arginine in the heterolysis of peroxide to form the catalytic intermediate compound I (Fe =O and a porphyrin cation radical). Using serial femtosecond X-ray crystallography (SFX), we have determined the pristine structures of the Fe and Fe =O redox states of a B-type DyP. These structures reveal a water-free distal heme site that, together with the presence of an asparagine, imply the use of the distal arginine as a catalytic base. A combination of mutagenesis and kinetic studies corroborate such a role. Our SFX approach thus provides unique insight into how the distal heme site of DyPs can be tuned to select aspartate or arginine for the rate enhancement of peroxide heterolysis.

PubMed: 32780931
DOI: 10.1002/anie.202008622

実験手法

X-RAY DIFFRACTION (1.75 Å)