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Active site determination of novel plant versatile peroxidase extracted from Citrus sinensis and bioconversion of β-naphthol

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Abstract

A ligninolytic peroxidase called versatile peroxidase, VP, (EC 1.11.1.16) is an iron-containing metalloenzyme. The most distinctive feature of this enzyme is its composite molecular framework, which combines lignin peroxidase’s capacity to oxidize compounds with high-redox potential with manganese peroxidase’s capacity to oxidize Mn2+ to Mn3+. In this study, we have extracted amino acid sequences from the Citrus sinensis source and subjected them to various computation tools to visualize the insight secondary and 3D structure, physicochemical properties, and validation of the structure which have not been studied so far to further investigate the catalytic efficiency and effectiveness of VP. The binding energies of HEME and HEME C (HEC) ligands with produced PDB (6rqf.1. A) have been also assessed, analyzed, and confirmed utilizing AutoDock. Binding energies were calculated using the AutoDock and validated by MD simulation using SCHRODINGER DESMOND. Most stable confirmation was achieved through a protein–ligand interaction study. Bio-technological use of VP in the biotransformation of β-naphthol has also been studied. The findings in the current study will have a substantial impact on proteomics, biochemistry, biotechnology, and possible uses of versatile peroxidase in the bio-remediation of different toxic organic compounds.

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Data availability

Data will be provided on request to corresponding author.

Abbreviations

VP:

Versatile peroxidase

LiP:

Lignin peroxidase

MnP:

Manganese peroxidase

WRF:

White rot fungus

NCBI:

National Center for Biotechnology Information

BLAST:

The Basic Local Alignment Search Tool

FASTA:

Fast alignment

pI:

Isoelectric point

SOPMA:

Self-optimized prediction method with alignment

SAVESv6.0:

Structure validation server

PLIP:

Protein–ligand interaction profiler

STRING:

Search tool for the retrieval of interacting genes/proteins

Hh:

Alpha helix

Ee:

Extended strand

Tt:

Beta-turn

Cc:

Random coil

RMSD:

Root-mean-square deviation

RMSF:

Root-mean-square fluctuation

MMGBSA:

Molecular mechanics with generalized born and surface area solvation

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Acknowledgements

The Department of Chemistry and CRF of NERIST is well-acknowledged for providing the necessary facilities. I am very thankful for the GATE fellowship provided by NERIST

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Authors and Affiliations

  1. Department of Chemistry, North Eastern Regional Institute of Science and Technology, Nirjuli, Itanagar, AP, 791109, India

    Rohida Amin Hoque, Meera Yadav, Nivedita Rai & Hardeo Singh Yadav

  2. Department of Physics, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, 273009, India

    Umesh Yadava & Shivani Negi

Authors
  1. Rohida Amin Hoque
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  2. Meera Yadav
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  3. Umesh Yadava
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  4. Nivedita Rai
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  5. Shivani Negi
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  6. Hardeo Singh Yadav
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Contributions

The primary, secondary, and peptide structure analyses and modeling were completed and written manuscript by RAH. The data analysis and interpretation, responsibility, and accountability for the contents of the article were done by MY. MD Simulation and MMGBSA energy calculation has been done by UY and his student SN. NR has done the preliminary study of versatile peroxidase enzymes. HSY was credited for the methodology of the communicated work.

Corresponding author

Correspondence to Meera Yadav.

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Hoque, R.A., Yadav, M., Yadava, U. et al. Active site determination of novel plant versatile peroxidase extracted from Citrus sinensis and bioconversion of β-naphthol. 3 Biotech 13, 345 (2023). https://doi.org/10.1007/s13205-023-03758-x

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