Abstract
There are many unspecific peroxygenases (UPOs) or UPO-like extracellular enzymes secreted by fungal species. These enzymes are considered special in their ways of catalyzing a wide variety of reactions such as epoxidation, peroxygenation and electron oxidations. This enzyme family exhibits diverse functions with thousands of UPOs and UPO-like sequences. These sequences are difficult to analyze without proper management tool and therefore desperately calls for a unified platform that can aide with annotation, classification, navigation and easy sequence retrieval. This prompted us to create an online database called Unspecific Peroxygenase Database (UPObase) (upobase.bioinformaticsreview.com) which currently includes 1948 peroxygenase-encoding protein sequences mined from more than 800 available fungal genomes. It provides information such as classification and motifs about each sequence and has functions such as homology search against UPObase sequence analyses such as multiple sequence alignments and phylogenetic trees. It also provides a new sequence submission facility. The database has been made user-friendly facilitating systematic search and filters. UPObase allows users to search for the sequences by organism name, cluster ID and accession number. Notably, in our previous study, 113 UPOs were classified into five subfamilies (I, II, III, IV and V) and an undetermined group (Pog) which remain established. In this study, using 1948 UPOs in our database, we were able to further identify six novel sub-superfamilies (Pog-a, Pog-b, Pog-c, Pog-d, Pog-e and Pog-f) with signature motifs and two distinct groups in Subfamily I and III, Ia and Ib, IIIa and IIIb, respectively. With the novel UPO-like sequences and classification, UPObase may serve for researchers working in the area of enzyme engineering and related fields.
Highlights
Unspecific peroxygenases (UPOs) (EC 1.11.2.1) represent the oxidoreductase sub-subclass of heme-thiolate proteins obtained from fungal species [1]
Some UPOs which are known to date with experimental evidence include Agrocybe aegerita UPO (AaeUPO), Marasmius rotula (MroUPO) and Coprinellus radians (CraUPO), among which the protein crystal structure of AaeUPO (2YOR) and MroUPO (5FUJ) is only available to date
UPOs are classified as heme-thiolate peroxidases (HTPs) due to their heme-ligation bond with cysteine and their similarity with other HTPs known as chloroperoxidases (CPOs)
Summary
Unspecific peroxygenases (UPOs) (EC 1.11.2.1) represent the oxidoreductase sub-subclass of heme-thiolate proteins obtained from fungal species [1]. Fungal UPOs are considered as intriguing enzymes because of their various significant properties such as stability, specificity, catalytic activity, high specific activity, water-soluble nature and capability of catalyzing reactions using inexpensive peroxides and cofactors such as Mg2+. UPOs are classified as heme-thiolate peroxidases (HTPs) due to their heme-ligation bond with cysteine and their similarity with other HTPs known as chloroperoxidases (CPOs). In the preliminary publication, UPOs have been classified on the basis of phylogeny and sequence motifs, into five subfamilies and a superfamily which includes MroUPO and some CPOs showing an intermediate behavior between the peroxygenases and peroxidases [8]. There are many other UPOs or UPO-like sequences which were not included in the previous analysis and thereby not classified under any known subfamilies and superfamily
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