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Tartrate Dehydrogenase in Bacillus Species: Deciphering Unique Catalytic Diversity Through Kinetic, Structural and Molecular Docking Analysis

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Abstract

Divergently evolved Tartrate dehydrogenase (TDH) exhibits multiple catalytic activities at a single active site; the enzyme from P. putida (pTDH) being structurally and biochemically well-characterized. Occurrence of TDH-associated ability to aerobically metabolize L-tartrate in Bacillus isolates and limited resemblance of ycsA-encoded protein sequences with pTDH rendered Bacillus TDH as an intriguing enzyme with possible catalytic diversity as well as evolutionary significance. The present study explores substrate interactions of TDHs from B. subtilis 168 (168bTDH) and B. licheniformis DSM-13 (429bTDH) through kinetic, structural and molecular docking-based analysis. Heterologously expressed bTDHs, purified from insoluble fractions of E. coli BL21(DE3) cells, could significantly catalyze L-tartrate and meso-tartrate as substrates in forward reaction. Unlike pTDH, bTDHs distinctly and more efficiently catalyzed the reverse reaction using dihydroxyfumarate substrate following sigmoidal kinetics; the ability being ~ 4 fold higher in 168bTDH. Their binding energies predicted from molecular docking, further substantiated the relative substrate specificities, while revealing major residues involved in protein-ligand interactions at active site. The kinetic analysis and homology modelling validated using Ramachandran Plot analysis predicted a dimeric nature for bTDH. Collectively, the results highlight unique catalytic potential of phylogenetically recent bTDHs, offering an important protein engineering target to mediate efficient enantioselective enzymatic biotransformations.

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Acknowledgements

The authors are thankful to Dr. Darshan Patel, Charotar University of Science and Technology, Gujarat, India, for kind support with respect to experimental resources.

Funding

The work was supported by Science and Engineering Research Board, Department of Science & Technology, Government of India [Grant number: EMR/2016/003524].

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Authors and Affiliations

  1. Department of Biological Sciences, P D Patel Institute of Applied Sciences, Charotar University of Science and Technology, CHARUSAT Campus, Dist. Anand, Changa, Gujarat, 388 421, India

    Manali Chandnani, Disha Patel, Twinkle Patel & Aditi Buch

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  1. Manali Chandnani
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  2. Disha Patel
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  3. Twinkle Patel
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  4. Aditi Buch
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Contributions

Manali Chandnani executed the experiments related to Bacillus licheniformis DSM-13 and in silico analysis, drafted and reviewed the manuscript; Disha Patel and Twinkle Patel executed the Bacillus subtilis 168 related experiments; Aditi Buch designed the experiments, drafted, reviewed and revised the manuscript.

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Correspondence to Aditi Buch.

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Chandnani, M., Patel, D., Patel, T. et al. Tartrate Dehydrogenase in Bacillus Species: Deciphering Unique Catalytic Diversity Through Kinetic, Structural and Molecular Docking Analysis. Protein J 43, 96–114 (2024). https://doi.org/10.1007/s10930-023-10170-0

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