Computational-based insights into the phylogeny, structure, and function of Rhodococcus alkane-1-monooxygenase
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ORIGINAL ARTICLE
Computational‑based insights into the phylogeny, structure, and function of Rhodococcus alkane‑1‑monooxygenase Siddhartha Pal1 · Kriti Sengupta2 Received: 25 May 2020 / Accepted: 10 August 2020 © King Abdulaziz City for Science and Technology 2020
Abstract Alkane-1-monooxygenase of alkanotrophic Rhodococcus species has been characterized using standard bioinformatics tools to investigate phylogenetic relationships, and three-dimensional structure and functions. Results revealed that activity of the Rhodococcus alkane-1-monooxygenase would be optimum in alkaline pH as their isoelectric points were in the range of 7.5 to 9. Higher aliphatic index (87 to 95) indicated that these enzymes are thermostable. Extinction coefficient of the enzyme varied from 68,793 to 1,25,820 M−1 cm−1 and average molecular weight was 45 kDa. Secondary structures predicted maximum alpha-helical content rather than the other conformations such as sheets or turns. The instability index (II) of most stable query protein was 39.7% which was lowest among all 76 proteins analysed in this study. Predicted 3D structure of query protein revealed that it contains homodimer polypeptides. The suitable template for query protein was Flavin-dependent luciferase-type alkane monooxygenase. The presence of 98.3% amino acid residues in Ramachandran plot was determined in 3-D protein model which confirmed the model feasibility. The predicted model contains 12% more α-helix than template protein which indicated towards membrane localization of the protein. The protein interactome partners of predicted model were determined as FMN-dependent oxidoreductase, molybdopterin, nuclear transport factor, and peroxiredoxin. The predicted tertiary model of R. rhodochrous alkane-1-monooxygenase (OOL33526.1) was deposited in Protein Model Database (Accession No.: PM0083166). The overall report is unique to best of our knowledge, and the importance of this study is to understand the theoretical aspects of structure and functions of alkane-1-monooxygenase of hydrocarbonoclastic strains of Rhodococcus. Keywords Rhodococcus · Alkane-1-monooxygenase · Luciferase monooxygenase · Homology modelling · Protein interactome
Introduction Use of excessive crude oil in the recent decades to meet the worldwide energy demand and its accidental spillage during transportation and storage has led to introduction of huge amount of petroleum hydrocarbons in the environment, Electronic supplementary material The online version of this article (https://doi.org/10.1007/s13205-020-02388-x) contains supplementary material, which is available to authorized users. * Kriti Sengupta [email protected] 1
National Centre for Cell Science, Ganeshkhind, Pune 411007, India
Bioenergy Group, Agharkar Research Institute, Gopal Ganesh Agarkar Road, Pune 411004, India
2
especially alkanes (Singh et al. 2012). Alkanes constitute nearly 20–50% of crude oil which makes it the most abundant hydrocarbon fraction (Liu et al. 2014). Even the oily sludge produced after crude
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