A structural and functional perspective of DyP-type peroxidase family

•The structure and function of DyP-type peroxidase family are reviewed.•The adequacy of this family name is discussed.•The amino acid sequences characteristic of each class of this family are revealed.•We propose the new classification of this family. Dye-decolorizing peroxidase from the basidiomyce...

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Bibliographic Details
Published in:Archives of biochemistry and biophysics 2015-05, Vol.574, p.49-55
Main Authors: Yoshida, Toru, Sugano, Yasushi
Format: Article
Language:English
Subjects:
Amino Acid Sequence
Dye-decolorizing peroxidase
DyP
DyP-type peroxidase family
Models, Molecular
Molecular Sequence Data
Peroxidases - chemistry
Peroxidases - metabolism
Protein Conformation
Sequence Homology, Amino Acid
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Summary:•The structure and function of DyP-type peroxidase family are reviewed.•The adequacy of this family name is discussed.•The amino acid sequences characteristic of each class of this family are revealed.•We propose the new classification of this family. Dye-decolorizing peroxidase from the basidiomycete Bjerkandera adusta Dec 1 (DyP) is a heme peroxidase. This name reflects its ability to degrade several anthraquinone dyes. The substrate specificity, the amino acid sequence, and the tertiary structure of DyP are different from those of the other heme peroxidase (super)families. Therefore, many proteins showing the similar amino acid sequences to that of DyP are called DyP-type peroxidase which is a new family of heme peroxidase identified in 2007. In fact, all structures of this family show a similar structure fold. However, this family includes many proteins whose amino acid sequence identity to DyP is lower than 15% and/or whose catalytic efficiency (kcat/Km) is a few orders of magnitude less than that of DyP. A protein showing an activity different from peroxidase activity (dechelatase activity) has been also reported. In addition, the precise physiological roles of DyP-type peroxidases are unknown. These facts raise a question of whether calling this family DyP-type peroxidase is suitable. Here, we review the differences and similarities of structure and function among this family and propose the reasonable new classification of DyP-type peroxidase family, that is, class P, I and V. In this contribution, we discuss the adequacy of this family name.
ISSN:0003-9861
1096-0384
DOI:10.1016/j.abb.2015.01.022