Anabaena sp. DyP-type peroxidase is a tetramer consisting of two asymmetric dimers.
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.
Department of Bioresource and Environmental Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto, 603-8555, Japan.
Toru
T
Yoshida
School of Agricultural and Food Sciences, Jaramogi Oginga Odinga University of Science and Technology, Bondo, Kenya.
Henry Joseph Oduor
HJ
Ogola
Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta 4259-R1-8, Midori-Ku, Yokohama, 226-8503, Japan.
Yoshimi
Y
Amano
Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta 4259-R1-8, Midori-Ku, Yokohama, 226-8503, Japan.
Toru
T
Hisabori
Department of Molecular and Functional Genomics, Interdisciplinary Center for Science Research, Shimane University, Nishikawatsu 1060, Matsue, Shimane, 690-8504, Japan.
Hiroyuki
H
Ashida
Department of Life Science and Biotechnology, Faculty of Life and Environmental Science, Shimane University, Matsue, Shimane, 690-8504, Japan.
Yoshihiro
Y
Sawa
Department of Bioresource and Environmental Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto, 603-8555, Japan.
Hideaki
H
Tsuge
Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, 2-8-1 Mejirodai, Bunkyo-Ku, Tokyo, 112-8681, Japan.
Yasushi
Y
Sugano
D000595:Amino Acid Sequence; D017033:Anabaena / Q000737:chemistry / Q000201:enzymology* / Q000235:genetics; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D004795:Enzyme Stability; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010544:Peroxidases / Q000737:chemistry* / Q000235:genetics; D010802:Phylogeny; D017354:Point Mutation; D055503:Protein Multimerization; D016415:Sequence Alignment; D013696:Temperature
D010544:Peroxidases
AnaPX; DyP-type peroxidase; structural asymmetry; structure-based sequence alignment; thermostability