7YZT
Crystal structure of a dye-decolorizing (Dyp) peroxidase from Acinetobacter radioresistens
Summary for 7YZT
| Entry DOI | 10.2210/pdb7yzt/pdb |
| Descriptor | Dyp-type peroxidase family protein, PROTOPORPHYRIN IX CONTAINING FE (3 entities in total) |
| Functional Keywords | biocatalysis; dye-decolorizing; peroxidase; heme, oxidoreductase |
| Biological source | Acinetobacter radioresistens |
| Total number of polymer chains | 3 |
| Total formula weight | 108890.70 |
| Authors | Zhang, C.,Catucci, G.,Gilardi, G.,Sadeghi, S.J.,Di Nardo, G. (deposition date: 2022-02-21, release date: 2023-01-25, Last modification date: 2025-01-29) |
| Primary citation | Catucci, G.,Zhang, C.,Pernaci, A.,Cappa, F.,Sadeghi, S.J.,Di Nardo, G.,Gilardi, G. Crystal structure and functional characterization of a novel bacterial lignin-degrading dye-decolorizing peroxidase. Int.J.Biol.Macromol., 297:139900-139900, 2025 Cited by PubMed Abstract: A new gene coding for an iron-containing enzyme was identified in the genome of Acinetobacter radioresistens. Bioinformatics analysis allowed the assignment of the protein to DyP peroxidases, due to the presence of conserved residues involved in heme binding and catalysis. Moreover, Ar-DyP is located in an operon coding also for other enzymes involved in iron uptake and regulation. The crystal structure of Ar-DyP determined at 1.85 Å resolution shows that the heme pocket Ar-DyP is "wet" forming a continuous hydrogen-bond network that enables the communication between heme and distal residues. Moreover, as shown by the crystal structure and covalent crosslinking experiments, Ar-DyP uses a long-range electron transfer pathway involving His-181 and Tyr-241, in the active site and on the surface of the enzyme, respectively. This pathway allows oxidation of substrates of different sizes, including Kraft lignin. Indeed, the biochemical characterization showed that Ar-Dyp oxidizes ABTS and Reactive Blue 19 (turnover numbers of 500 and 464 min, respectively), but also phenolic compounds such as guaiacol and pyrogallol (turnover numbers of 7.4 and 1.8 min respectively). Overall, the data shows that Ar-DyP is a promising candidate for applications in lignin valorization, bioremediation and industrial processes involving the breakdown of phenolic compounds. PubMed: 39818373DOI: 10.1016/j.ijbiomac.2025.139900 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.85 Å) |
Structure validation
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