7DLK

Crystal Structure of veratryl alcohol bound Dye Decolorizing peroxidase from Bacillus subtilis

Summary for 7DLK

• Entry DOI: 10.2210/pdb7dlk/pdb
• Descriptor: Deferrochelatase/peroxidase, PROTOPORPHYRIN IX CONTAINING FE, OXYGEN MOLECULE, ... (10 entities in total)
• Functional Keywords: dye-decolorizing peroxidase, ferredoxin like fold, oxidoreductase, veratryl alcohol
• Biological source: Bacillus subtilis
• Total number of polymer chains: 6
• Total formula weight: 247689.71

Authors

Dhankhar, P.,Dalal, V.,Kumar, P. (deposition date: 2020-11-27, release date: 2021-11-03, Last modification date: 2023-11-29)

Primary citation

Dhankhar, P.,Dalal, V.,Singh, V.,Sharma, A.K.,Kumar, P.
Structure of dye-decolorizing peroxidase from Bacillus subtilis in complex with veratryl alcohol.
Int.J.Biol.Macromol., 193:601-608, 2021

PubMed Abstract: Dye-decolorizing peroxidases (DyPs) are heme-containing peroxidases, which have promising application in biodegradation of phenolic lignin compounds and in detoxification of dyes. In this study, the crystal structure of BsDyP- veratryl alcohol (VA) complex delves deep into the binding of small substrate molecules within the DyP heme cavity. The biochemical analysis shows that BsDyP oxidizes the VA with a turnover number of 0.065 s, followed by the oxidation of 2,6-dimethoxyphenol (DMP) and guaiacol with a comparable turnover number (k) of 0.07 s and 0.07 s, respectively. Moreover, biophysical and computational studies reveal the comparable binding affinity of substrates to BsDyP and produce lower-energy stable BsDyP-ligand(s) complexes. All together with our previous findings, we are providing a complete structural description of substrate-binding sites in DyP. The structural insight of BsDyP helps to modulate its engineering to enhance the activity towards the oxidation of a wide range of substrates.

PubMed: 34687768
DOI: 10.1016/j.ijbiomac.2021.10.100

Experimental method

X-RAY DIFFRACTION (2.1 Å)