Modeling of the protein structure of the α-subunit of biphenyl 2,3- dioxygenase (BphA1) of the R. wratislaviensis strain CH628

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Published: Apr 2, 2025
DOI: https://doi.org/10.17072/1994-9952-2025-1-32-42
Keywords:
AlphaFold MODELLER trRosetta Rhodococcus biphenyl dioxygenase protein modeling active site

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Tatyana D. Kir’yanova
Institute of Ecology and Genetics of Microorganisms, PFRC Ural Branch of the RAS, Perm, Russia

Abstract

Three-dimensional modeling of the α-subunit of biphenyl dioxygenase (BphA1) from the Rhodococcus wratislaviensis strain CH628 was performed using MODELLER, AlphaFold, and trRosetta software. The nucleotide sequence of the bphA gene was determined through an analysis of the whole-genome sequence of the strain in the RAST system. Phylogenetic analysis of bphACH628 revealed a high degree of similarity with the α-subunit of naphthalene dioxygenase (narA). To assess the quality of the generated models, ERRAT, VERIFY3D, and PROCHECK programs were employed. The BphA1CH628 model constructed with MODELLER demonstrated the highest structural accuracy, while the BphA1CH628 model from AlphaFold provided a better prediction of the enzyme's active site. Analysis of the active site indicated the conservation of key amino acids involved in catalysis, which supports the functional similarity to naphthalene dioxygenase. These findings open up new avenues for further investigation of BphA1 in the context of its application in the bioremediation.

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How to Cite
Kir’yanova Т. Д. (2025). Modeling of the protein structure of the α-subunit of biphenyl 2,3- dioxygenase (BphA1) of the R. wratislaviensis strain CH628. Bulletin of Perm University. Biology, (1), 32–42. https://doi.org/10.17072/1994-9952-2025-1-32-42
Issue
No. 1 (2025): Bulletin of Perm University. BIOLOGY
Section
Микробиология

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Tatyana D. Kir’yanova, Institute of Ecology and Genetics of Microorganisms, PFRC Ural Branch of the RAS, Perm, Russia

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