6YRC

Spectroscopically-validated structure of DtpB from Streptomyces lividans in the ferric state

Summary for 6YRC

• Entry DOI: 10.2210/pdb6yrc/pdb
• Descriptor: Putative iron-dependent peroxidase, PROTOPORPHYRIN IX CONTAINING FE, 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL, ... (6 entities in total)
• Functional Keywords: peroxidase; dye-decolourising; spectroscopically-validated, ferric, oxidoreductase
• Biological source: Streptomyces lividans 1326
• Total number of polymer chains: 6
• Total formula weight: 212786.47

Authors

Lucic, M.,Dworkowski, F.S.N.,Worrall, J.A.R.,Hough, M.A. (deposition date: 2020-04-20, release date: 2021-01-13, Last modification date: 2024-05-01)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.99 Å)