PeroxiBase: a database with new tools for peroxidase family classification

Abstract

Peroxidases (EC 1.11.1.x), which are encoded by small or large multigenic families, are involved in several important physiological and developmental processes. They use various peroxides as electron acceptors to catalyse a number of oxidative reactions and are present in almost all living organisms. We have created a peroxidase database (http://peroxibase.isb-sib.ch) that contains all identified peroxidase-encoding sequences (about 6000 sequences in 940 organisms). They are distributed between 11 superfamilies and about 60 subfamilies. All the sequences have been individually annotated and checked. PeroxiBase can be consulted using six major interlink sections ‘Classes’, ‘Organisms’, ‘Cellular localisations’, ‘Inducers’, ‘Repressors’ and ‘Tissue types’. General documentation on peroxidases and PeroxiBase is accessible in the ‘Documents’ section containing ‘Introduction’, ‘Class description’, ‘Publications’ and ‘Links’. In addition to the database, we have developed a tool to classify peroxidases based on the PROSITE profile methodology. To improve their specificity and to prevent overlaps between closely related subfamilies the profiles were built using a new strategy based on the silencing of residues. This new profile construction method and its discriminatory capacity have been tested and validated using the different peroxidase families and subfamilies present in the database. The peroxidase classification tool called PeroxiScan is accessible at the following address: http://peroxibase.isb-sib.ch/peroxiscan.php.

Characterization of Dye-decolorizing Peroxidase (DyP) from Thermomonospora curvata Reveals Unique Catalytic Properties of A-type DyPs

“…Analysis of the genome sequence has revealed that DyPs are mostly present in bacteria, whereas only a limited number exists in fungi and higher eukaryotes (14). DyPs can be subdivided into four types, A, B, C, and D, based on their primary sequences (15). Identities between different types are at most 15%, each having a unique characteristic sequence.…”

Predicting the functionally distinct residues in the heme, cation, and substrate-binding sites of peroxidase from stress-tolerant mangrove specie, Avicennia marina

“…Homology sequence searches were performed using BLAST (Altschul et al 1997) against non-redundant (nr) database and class III PeroxiBase (Koua et al 2009). Multiple sequence alignment of plant peroxidases was performed using Clustal X program (Thompson et al 1997).…”

“…Analysis of the amino acid sequence deduced for AP using the databank, PeroxiBase (Koua et al 2009), revealed that A. marina has the highest homology with that of Triphysaria versicolor, N. tabacum, C. roseus, and Capsicum annum. AP also shares significant identity with barley grain peroxidase (BGP) whose 3D structure has been determined (Henriksen et al 1998a).…”

“…A number of plant peroxidases have been either structurally elucidated or their 3D structures were predicted (Koua et al 2009;Passardi et al 2007). They consist of highly conserved domains as well as variable regions.…”

Nuclear Magnetic Resonance Spectroscopic and Computational Investigations of Chloroperoxidase Catalyzed Regio- and Enantio-Selective Transformations

“…Out of 10630 peroxidase sequences were recorded in PeroxiBase, and more than 78% of peroxidases are coded for heme peroxidases [4]. According to the phylogenetic trees, heme peroxidases are distributed into 9 In the heme-containing peroxidases, cytochrome c peroxidase, horseradish peroxidase, lactoperoxidase, and myeloperoxidase are of interest due to their wide applications or unique reactions, and thus are intensively studied.…”