6YRC image
Entry Detail
PDB ID:
6YRC
Keywords:
Title:
Spectroscopically-validated structure of DtpB from Streptomyces lividans in the ferric state
Biological Source:
PDB Version:
Deposition Date:
2020-04-20
Release Date:
2021-01-13
Method Details:
Experimental Method:
Resolution:
1.99 Å
R-Value Free:
0.21
R-Value Work:
0.17
R-Value Observed:
0.17
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Putative iron-dependent peroxidase
Chain IDs:A, B, C, D, E, F
Chain Length:316
Number of Molecules:6
Biological Source:Streptomyces lividans 1326
Primary Citation
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)
PMID: 32780931 DOI: 10.1002/anie.202008622

Abstact

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 (FeIV =O and a porphyrin cation radical). Using serial femtosecond X-ray crystallography (SFX), we have determined the pristine structures of the FeIII and FeIV =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.

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