DyP, a unique dye-decolorizing enzyme from the fungus Thanatephorus cucumeris Dec 1, has been classified as a peroxidase but lacks homology to almost all other known plant peroxidases. The primary structure of DyP shows moderate sequence homology to only two known proteins: the peroxidedependent phenol oxidase, TAP, and the hypothetical peroxidase, cpop21. Here, we show the first crystal structure of DyP and reveal that this protein has a unique tertiary structure with a distal heme region that differs from that of most other peroxidases. DyP lacks an important histidine residue known to assist in the formation of a Fe 4؉ oxoferryl center and a porphyrinbased cation radical intermediate (compound I) during the action of ubiquitous peroxidases. Instead, our tertiary structural and spectrophotometric analyses of DyP suggest that an aspartic acid and an arginine are involved in the formation of compound I. Sequence analysis reveals that the important aspartic acid and arginine mentioned above and histidine of the heme ligand are conserved among DyP, TAP, and cpop21, and structural and phylogenetic analyses confirmed that these three enzymes do not belong to any other families of peroxidase. These findings, which strongly suggest that DyP is a representative heme peroxidase from a novel family, should facilitate the identification of additional new family members and accelerate the classification of this novel peroxidase family.Peroxidases have been systematically researched for more than 70 years. Fifteen years ago, Welinder (1) proposed the concept of a "plant peroxidase superfamily" comprising classes I, II, and III, based on primary sequence alignments and isolation from prokaryotes, fungi, and plants, respectively. Using this strategy, yeast cytochrome c peroxidase (2) and chloroplast ascorbate peroxidase (3) were classified as class I peroxidases on account of their prokaryotic source. Representatives of class II include lignin peroxidase (LiP) 2 (4), manganese peroxidase (MnP) (5), and versatile peroxidase (6, 7), whereas class III contains horseradish peroxidase (HRP) (8) and barley grain peroxidase (BGP) (9). This classification has been widely applied to most known peroxidases, with the exception of chloroperoxidase (CPO) isolated from the fungus, Caldariomyces fumago, which lacks primary structural homology with other peroxidases (10, 11). However, in contrast to the plant peroxidases, those from animals, including mammals, are yet to be categorized. To date, most of these enzymes have been grouped into the plant or animal peroxidase superfamily (12).So far, we isolated and characterized a novel extracellular peroxidase, DyP, from the fungus Thanatephorus cucumeris Dec 1 (13-16). DyP, a glycoprotein having one heme as a cofactor, has a molecular mass of 58 kDa and requires H 2 O 2 for all enzyme reactions, indicating that it functions as a peroxidase. DyP has several characteristics that distinguish it from all other peroxidases, including a particularly wide substrate specificity, a lack of homology to m...