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Phylogenetic analysis, molecular modeling, substrate–inhibitor specificity, and active site comparison of bacterial, fungal, and plant heme peroxidases
Author(s) -
Singh Swati,
Pandey Veda P.,
Naaz Huma,
Dwivedi Upendra N.
Publication year - 2012
Publication title -
biotechnology and applied biochemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.468
H-Index - 70
eISSN - 1470-8744
pISSN - 0885-4513
DOI - 10.1002/bab.1025
Subject(s) - peroxidase , guaiacol , biochemistry , heme , phenylglyoxal , lactoperoxidase , biology , chemistry , enzyme , amino acid , arginine
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, H 2 O 2 , 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.