8RE2

Crystal Structure determination of Dye-decolorizing Peroxidase (DyP) from Deinoccoccus radiodurans

Summary for 8RE2

• Entry DOI: 10.2210/pdb8re2/pdb
• Descriptor: Peroxidase, putative, PROTOPORPHYRIN IX CONTAINING FE, GLYCEROL, ... (5 entities in total)
• Functional Keywords: heme protein, peroxidase, ferredoxin like fold, hydrogen peroxide, structural protein
• Biological source: Deinococcus radiodurans
• Total number of polymer chains: 1
• Total formula weight: 50375.45

Authors

Salgueiro, B.A.,Frade, K.,Frazao, C.,Moe, E. (deposition date: 2023-12-10, release date: 2024-01-31)

Primary citation

Frade, K.,Silveira, C.M.,Salgueiro, B.A.,Mendes, S.,Martins, L.O.,Frazao, C.,Todorovic, S.,Moe, E.
Biochemical, Biophysical, and Structural Analysis of an Unusual DyP from the Extremophile Deinococcus radiodurans.
Molecules, 29:-, 2024

PubMed Abstract: Dye-decolorizing peroxidases (DyPs) are heme proteins with distinct structural properties and substrate specificities compared to classical peroxidases. Here, we demonstrate that DyP from the extremely radiation-resistant bacterium is, like some other homologues, inactive at physiological pH. Resonance Raman (RR) spectroscopy confirms that the heme is in a six-coordinated-low-spin (6cLS) state at pH 7.5 and is thus unable to bind hydrogen peroxide. At pH 4.0, the RR spectra of the enzyme reveal the co-existence of high-spin and low-spin heme states, which corroborates catalytic activity towards HO detected at lower pH. A sequence alignment with other DyPs reveals that DyP possesses a Methionine residue in position five in the highly conserved GXXDG motif. To analyze whether the presence of the Methionine is responsible for the lack of activity at high pH, this residue is substituted with a Glycine. UV-vis and RR spectroscopies reveal that the resulting DyPM190G is also in a 6cLS spin state at pH 7.5, and thus the Methionine does not affect the activity of the protein. The crystal structures of DyP and DyPM190G, determined to 2.20 and 1.53 Å resolution, respectively, nevertheless reveal interesting insights. The high-resolution structure of DyPM190G, obtained at pH 8.5, shows that one hydroxyl group and one water molecule are within hydrogen bonding distance to the heme and the catalytic Asparagine and Arginine. This strong ligand most likely prevents the binding of the HO substrate, reinforcing questions about physiological substrates of this and other DyPs, and about the possible events that can trigger the removal of the hydroxyl group conferring catalytic activity to DyP.

PubMed: 38257271
DOI: 10.3390/molecules29020358

Experimental method

X-RAY DIFFRACTION (2.2 Å)