title: Phylogenetic analysis, molecular modeling, substrate-inhibitor specificity, and active site comparison of bacterial, fungal, and plant heme peroxidases.
abstract: Phylogenetic analysis of 40 heme peroxidases, belonging to both prokaryotes and eukaryotes, revealed their clustering into three major classes. Class I represented sequences from plants, bacteria, fungi, and algae, whereas classes II and III exclusively represented plant and fungal peroxidases, respectively. Modeling of three representative classes of peroxidases, belonging to each of bacterial, plant, and fungal categories, revealed a similar kind of folding; however, superimposition analysis revealed relatively more closeness between plant and fungal peroxidases than that of the bacterial peroxidase. The docking analysis of three representative modeled peroxidases with three common substrates, namely, H₂O₂, guaiacol, and ascorbate, and three arginine-specific inhibitors, namely, phenylglyoxal, 1,2-cyclohexanedione, and 2,3-butanedione, revealed that all three inhibitors competed for guaiacol- and ascorbate-binding sites of peroxidases, except for phenylglyoxal binding in the case of plant peroxidase. Phenylglyoxal, 1,2-cyclohexanedione, and 2,3-butanedione were found to be most potent inhibitors of bacterial, fungal, and plant peroxidases, respectively.
authors.affiliation: Department of Biochemistry, Bioinformatics Infrastructure Facility, Center of Excellence in Bioinformatics, University of Lucknow, Lucknow, Uttar Pradesh, India.
authors.forename: Swati
authors.initials: S
authors.lastname: Singh
authors.forename: Veda P
authors.initials: VP
authors.lastname: Pandey
authors.forename: Huma
authors.initials: H
authors.lastname: Naaz
authors.forename: Upendra N
authors.initials: UN
authors.lastname: Dwivedi
mesh_terms: D000595:Amino Acid Sequence; D001419:Bacteria / Q000166:cytology / Q000201:enzymology; D020134:Catalytic Domain; D002462:Cell Membrane / Q000378:metabolism; D003512:Cyclohexanones / Q000378:metabolism / Q000494:pharmacology; D003931:Diacetyl / Q000378:metabolism / Q000494:pharmacology; D004791:Enzyme Inhibitors / Q000378:metabolism / Q000494:pharmacology*; D005658:Fungi / Q000166:cytology / Q000201:enzymology; D006418:Heme / Q000378:metabolism*; D062105:Molecular Docking Simulation; D008969:Molecular Sequence Data; D010544:Peroxidases / Q000037:antagonists & inhibitors* / Q000737:chemistry* / Q000378:metabolism; D010658:Phenylglyoxal / Q000378:metabolism / Q000494:pharmacology; D010802:Phylogeny; D010944:Plants / Q000201:enzymology; D021381:Protein Transport; D012995:Solubility; D013379:Substrate Specificity
chemical_list: D003512:Cyclohexanones; D004791:Enzyme Inhibitors; D006418:Heme; C018031:1,2-cyclohexanedione; D010544:Peroxidases; D003931:Diacetyl; D010658:Phenylglyoxal