8RE3

Crystal Structure determination of Dye-decolorizing Peroxidase (DyP) mutant M190G from Deinoccoccus radiodurans

8RE3 の概要

• エントリーDOI: 10.2210/pdb8re3/pdb
• 分子名称: Peroxidase, putative, PROTOPORPHYRIN IX CONTAINING FE, HYDROXIDE ION, ... (6 entities in total)
• 機能のキーワード: peroxidase, heme, hydrogen peroxide, d.radiodurans, structural protein
• 由来する生物種: Deinococcus radiodurans
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 100898.03

構造登録者

Salgueiro, B.A.,Frade, K.,Frazao, C.,Matias, P.,Moe, E. (登録日: 2023-12-10, 公開日: 2024-01-31)

主引用文献

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

実験手法

X-RAY DIFFRACTION (1.51 Å)