5C2I
Crystal structure of Anabaena sp. DyP-type peroxidese (AnaPX)
Summary for 5C2I
| Entry DOI | 10.2210/pdb5c2i/pdb |
| Descriptor | Alr1585 protein, PROTOPORPHYRIN IX CONTAINING FE, GLYCEROL, ... (6 entities in total) |
| Functional Keywords | dyp-type peroxidase, dye-decolorizing peroxidase, oxidoreductase |
| Biological source | Nostoc sp. (strain PCC 7120 / UTEX 2576) |
| Total number of polymer chains | 4 |
| Total formula weight | 216942.07 |
| Authors | Yoshida, T.,Amano, Y.,Tsuge, H.,Sugano, Y. (deposition date: 2015-06-16, release date: 2015-12-16, Last modification date: 2023-11-08) |
| Primary citation | Yoshida, T.,Ogola, H.J.,Amano, Y.,Hisabori, T.,Ashida, H.,Sawa, Y.,Tsuge, H.,Sugano, Y. Anabaena sp. DyP-type peroxidase is a tetramer consisting of two asymmetric dimers. Proteins, 84:31-42, 2016 Cited by PubMed Abstract: DyP-type peroxidases are a newly discovered family of heme peroxidases distributed from prokaryotes to eukaryotes. Recently, using a structure-based sequence alignment, we proposed the new classes, P, I and V, as substitutes for classes A, B, C, and D [Arch Biochem Biophys 2015;574:49-55]. Although many class V enzymes from eukaryotes have been characterized, only two from prokaryotes have been reported. Here, we show the crystal structure of one of these two enzymes, Anabaena sp. DyP-type peroxidase (AnaPX). AnaPX is tetramer formed from Cys224-Cys224 disulfide-linked dimers. The tetramer of wild-type AnaPX was stable at all salt concentrations tested. In contrast, the C224A mutant showed salt concentration-dependent oligomeric states: in 600 mM NaCl, it maintained a tetrameric structure, whereas in the absence of salt, it dissociated into monomers, leading to a reduction in thermostability. Although the tetramer exhibits non-crystallographic, 2-fold symmetry in the asymmetric unit, two subunits forming the Cys224-Cys224 disulfide-linked dimer are related by 165° rotation. This asymmetry creates an opening to cavities facing the inside of the tetramer, providing a pathway for hydrogen peroxide access. Finally, a phylogenetic analysis using structure-based sequence alignments showed that class V enzymes from prokaryotes, including AnaPX, are phylogenetically closely related to class V enzymes from eukaryotes. PubMed: 26492416DOI: 10.1002/prot.24952 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.89 Å) |
Structure validation
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