7E5Q

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

7E5Q の概要

• エントリーDOI: 10.2210/pdb7e5q/pdb
• 分子名称: Deferrochelatase/peroxidase, PROTOPORPHYRIN IX CONTAINING FE, OXYGEN MOLECULE, ... (10 entities in total)
• 機能のキーワード: dye-decolorizing peroxidase, ferredoxin like fold, oxidoreductase, heme, acidic
• 由来する生物種: Bacillus subtilis
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 84182.54

構造登録者

Dhankhar, P.,Dalal, V.,Kumar, P. (登録日: 2021-02-19, 公開日: 2022-08-24, 最終更新日: 2023-11-29)

主引用文献

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

実験手法

X-RAY DIFFRACTION (1.9 Å)