7E5Q

Crystal Structure of Dye Decolorizing peroxidase from Bacillus subtilis at acidic pH

Summary for 7E5Q

• Entry DOI: 10.2210/pdb7e5q/pdb
• Descriptor: Deferrochelatase/peroxidase, PROTOPORPHYRIN IX CONTAINING FE, OXYGEN MOLECULE, ... (10 entities in total)
• Functional Keywords: dye-decolorizing peroxidase, ferredoxin like fold, oxidoreductase, heme, acidic
• Biological source: Bacillus subtilis
• Total number of polymer chains: 2
• Total formula weight: 84182.54

Authors

Dhankhar, P.,Dalal, V.,Kumar, P. (deposition date: 2021-02-19, release date: 2022-08-24, Last modification date: 2023-11-29)

Primary citation

Dhankhar, P.,Dalal, V.,Sharma, A.K.,Kumar, P.
Structural insights at acidic pH of dye-decolorizing peroxidase from Bacillus subtilis.
Proteins, 2022

PubMed 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.

PubMed: 36345957
DOI: 10.1002/prot.26444

Experimental method

X-RAY DIFFRACTION (1.9 Å)