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Structural insights at acidic <scp>pH</scp> of dye‐decolorizing peroxidase from Bacillus subtilis

Authors :
Poonam Dhankhar
Vikram Dalal
Ashwani Kumar Sharma
Pravindra Kumar
Source :
Proteins: Structure, Function, and Bioinformatics. 91:508-517
Publication Year :
2022
Publisher :
Wiley, 2022.

Abstract

Dye-decolorizing peroxidases (DyPs), a type of heme-containing oxidoreductase enzymes, catalyze the peroxide-dependent oxidation of various industrial dyes as well as lignin and lignin model compounds. In our previous work, we have recently reported the crystal structures of class A-type DyP from Bacillus subtilis at pH 7.0 (BsDyP7), exposing the location of three binding sites for small substrates and high redox-potential substrates. The biochemical studies revealed the optimum acidic pH for enzyme activity. In the present study, the crystal structure of BsDyP at acidic pH (BsDyP4) reveals two-monomer units stabilized by intermolecular salt bridges and a hydrogen bond network in a homo-dimeric unit. Based on the monomeric structural comparison of BsDyP4 and BsDyP7, minor differences were observed in the loop regions, that is, LI (Ala64-Gln71), LII (Glu96-Lys108), LIII (Pro117-Leu124), and LIV (Leu295-Asp303). Despite these differences, BsDyP4 adopts similar heme architecture as well as three substrate-binding sites to BsDyP7. In BsDyP4, a shift in Asp187, heme pocket residue discloses the plausible reason for optimal acidic pH for BsDyP activity. This study provides insight into the structural changes in BsDyP at acidic pH, where BsDyP is biologically active.

Details

ISSN :
10970134 and 08873585
Volume :
91
Database :
OpenAIRE
Journal :
Proteins: Structure, Function, and Bioinformatics
Accession number :
edsair.doi.dedup.....4ad164b8582ec0b8e11c6398e53b1e44
Full Text :
https://doi.org/10.1002/prot.26444