1. Chen, Y., Zhu, L. & Zhou, R. Characterization and distribution of polycyclic aromatic hydrocarbon in surface water and sediment from Qiantang River, China. J. Hazard. Mater. 141, 148-155 (2007).
2. Qi, J. et al. Genetic determinants involved in the biodegradation of naphthalene and phenanthrene in Pseudomonas aeruginosa PAO1. Environ. Sci. Pollut. Res. 22, 6743-6755 (2015).
3. Duan, L., Naidu, R., Thavamani, P., Meaklim, J. & Megharaj, M. Managing long-term polycyclic aromatic hydrocarbon contaminated soils: a risk-based approach. Environ. Sci. Pollut. Res. 22, 8927-8941 (2015).
4. Yuan, Z., Liu, G., Da, C., Wang, J. & Liu, H. Occurrence, sources, and potential toxicity of polycyclic aromatic hydrocarbons in surface soils from the Yellow river delta natural reserve, China. Arch. Environ. Contam. Toxicol. 68, 330-341 (2015).
5. Cao, J., Lai, Q., Yuan, J. & Shao, Z. Genomic and metabolic analysis of fluoranthene degradation pathway in Celeribacter indicus P73T. Sci. Rep. 5, 7741 (2015).
6. He, C., Li, Y., Huang, C., Chen, F. & Ma, Y. Genome sequence and metabolic analysis of a fluoranthene-degrading strain Pseudomonas aeruginosa DN1. Front. Microbiol. 9 (2018).
7. Kweon, O. et al. A polyomic approach to elucidate the fluoranthene-degradativepathway in Mycobacterium vanbaalenii PYR-1,. J. Bacteriol. 189, 4635–4647 (2007).
8. Kanaly, R. A. & Harayama, S. Biodegradation of high-molecular-weight polycyclic aromatic hydrocarbons by bacteria. J. Bacteriol. 182, 2059-2067 (2000).
9. Brzeszcz, J. & Kaszycki, P. Aerobic bacteria degrading both n-alkanes and aromatic hydrocarbons: an undervalued strategy for metabolic diversity and flexibility. Biodegradation. 29, 359-407 (2018).
10. Ławniczak, Ł., Woźniak-Karczewska, M., Loibner, A. P., Heipieper, H. J. & Chrzanowski, Ł. Microbial degradation of hydrocarbons—basic principles for bioremediation: A review. Molecules. 25, 856 (2020).
11. Doyle, E., Muckian L, Hickey AM & N, C. Microbial PAH degradation. Adv Appl Microbiol. 65, 27-66 (2008).
12. Karlsson, A. et al. Crystal structure of naphthalene dioxygenase: Side-on binding of dioxygen to Iron. Science. 299, 1039-1042 (2003).
13. Parales, R. E. et al. Substrate specificity of naphthalene dioxygenase: Effect of specific amino acids at the active site of the enzyme. J. Bacteriol. 182, 1641-1649 (2000).
14. Kim, S. J. et al. Molecular cloning and expression of genes encoding a novel dioxygenase involved in low- and high-molecular-weight polycyclic aromatic hydrocarbon degradation in Mycobacterium vanbaalenii PYR-1. Appl. Environ. Microbiol. 72, 1045-1054 (2006).
15. Weissenfels, W. D., Beyer, M., Klein, J. & Rehm, H. J. Microbial metabolism of fluoranthene: Isolation and identification of ring fission products. Appl. Microbiol. Biotechnol. 34, 528-535 (1991).
16. Wargo, M. J., Szwergold, B. S. & Hogan, D. A. Identification of two gene clusters and a transcriptional regulator required for Pseudomonas aeruginosa glycine betaine catabolism. J. Bacteriology. 190, 2690-2699 (2008).
17. Shao, Y.-H. et al. Glycine betaine monooxygenase, an unusual Rieske-type oxygenase system, catalyzes the oxidative N-demethylation of glycine betaine in Chromohalobacter salexigens DSM 3043. Appl. Environ. microbiol. 84 (2018).
18. Christopher Perry, L., E., C. de los Santos, Alkhalaf, L. M. & Challis., G. L. Rieske non-heme iron-dependent oxygenases catalyse diverse reactions in natural product biosynthesis. Nat. Prod. Rep. 35, 622-632 (2018).
19. Parales, R. E. & Resnick, S. M. Aromatic ring hydroxylating dioxygenases. J.L. Ramos, and R.C. Levesque, eds. (Springer), 287-340 (2006).
20. Peng, R. H. et al. Microbial biodegradation of polyaromatic hydrocarbons. FEMS. Microbiol. Rev. 32, 927-955 (2008).
21. Isaac, P., Lozada, M., Dionisi, H. M., Estévez, M. C. & Ferrero, M. A. Differential expression of the catabolic nahAc gene and its effect on PAH degradation in Pseudomonas strains isolated from contaminated Patagonian coasts. Int. Biodeterior. Biodegr. 105, 1-6 (2015).
22. Jakoncic, J., Jouanneau, Y., Meyer, C. & Stojanoff, V. The catalytic pocket of the ring-hydroxylating dioxygenase from Sphingomonas CHY-1. Biochem. Biophys. Res. Commun. 352, 861-866 (2007).
23. Kovaleva, E. G. & Lipscomb, J. D. Versatility of biological non-heme Fe(II) centers in oxygen activation reactions. Nature. Chem. Biol. 4, 186-193 (2008).
24. Singh, S. N., Kumari, B., Upadhyay, S. K., Mishra, S. & Kumar, D. Bacterial degradation of pyrene in minimal salt medium mediated by catechol dioxygenases: Enzyme purification and molecular size determination. Contam. Toxicol. 133, 293-300 (2013).
25. Han, X. M., Liu, Y. R., Zheng, Y. M., Zhang, X. X. & He, J. Z. Response of bacterial pdo1, nah, and C12O genes to aged soil PAH pollution in a coke factory area. Environ. Sci. Pollut. Res. 21, 9754-9763 (2014).
26. Kweon, O. et al. A new classification system for bacterial Rieske non-heme iron aromatic ring-hydroxylating oxygenases. BMC Biochemistry. 9, 11 (2008).
27. Boyd, D. R. et al. Bacterial dioxygenase-catalysed dihydroxylation and chemical resolutionroutes to enantiopure cis-dihydrodiols of chrysene. J. Chem. Soc. Perkin Trans. 28, 1715-1724 (1997).
28. Boyd, D. R. & Bugg, T. D. H. Arene cis-Dihydrodiol Formation: From Biology to Application. Org. Biomol. Chem. 4, 181-192 (2006).
29. Dong, W. et al. Complete genome sequence of a versatile hydrocarbon degrader, Pseudomonas aeruginosa DN1 isolated from petroleum-contaminated soil. Gene. Rep. 7, 123-126 (2017).
30. Jin, J. N. et al. An integrated approach of bioassay and molecular docking to study the dihydroxylation mechanism of pyrene by naphthalene dioxygenase in Rhodococcus sp. ustb-1. Chemosphere. 128, 307-313 (2015).
31. Daughtry, K. D. et al. Quaternary ammonium oxidative demethylation: X-ray crystallographic, resonance raman, and UV–Visible spectroscopic analysis of a Rieske-type demethylase. J. Am. Chem. Soc. 134, 2823-2834 (2012).
32. Martí-Renom, M. A. et al. Comparative protein structure modeling of genes and genomes. Annu. Rev. Bioph. Biom. 29, 291-325 (2000).
33. Min, J., Lin, D., Zhang, Q., Zhang, J. & Yu, Z. Structure-based virtual screening of novel inhibitors of the uridyltransferase activity of Xanthomonas oryzae pv. oryzae GlmU. Eur. J. Med. Chem. 53, 150-158 (2012).
34. Ferraro, D. J., Gakhar, L. & Ramaswamy, S. Rieske business: Structure–function of Rieske non-heme oxygenases. Biochem. Biophys. Res. Commun. 338, 175-190 (2005).
35. Zeng, X. H., Du, H., Zhao, H. M., Xiang, L. & He, Z. L. Insights into the binding interaction of substrate with catechol 2,3-dioxygenase from biophysics point of view. J. Hazard. Mater. 391, 122211 (2020).
36. Maïté, N. et al. Both Cycloclasticus spp. and Pseudomonas spp. as PAH-degrading bacteria in the Seine estuary (France). FEMS Microbiol. Ecol. 71, 137-147 (2010).
37. Ma, J., Xu, L. & Jia, L. Characterization of pyrene degradation by Pseudomonas sp. strain Jpyr-1 isolated from active sewage sludge. Bioresour. Technol. 140, 15-21 (2013).
38. Jin, J., Yao, J., Zhang, Q. & Liu, J. Biodegradation of pyrene by Pseudomonas sp. JPN2 and its initial degrading mechanism study by combining the catabolic nahAc gene and structure-based analyses. Chemosphere. 164, 379-386 (2016).
39. Liu, Z. et al. Application of molecular docking for the degradation of organic pollutants in the environmental remediation: A review. Chemosphere. 203, 139-150 (2018).
40. de Visser, S. P., Rohde, J. U., Lee, Y. M., Cho, J. & Nam, W. Intrinsic properties and reactivities of mononuclear nonheme iron–oxygen complexes bearing the tetramethylcyclam ligand. Coordin. Chem. Rev. 257, 381-393 (2013).
41. Quesne, M. G., Borowski, T. & Visser, S. P. d. Quantum mechanics/molecular mechanics modeling of enzymatic processes: Caveats and breakthroughs. Chem. Eur. J. 22, 2562 – 2581 (2016).
42. Amy, T., Quesne, M. G., Tomasz, B. & De, V. S. P. Group transfer to an aliphatic bond: A biomimetic study inspired by nonheme iron halogenases. ACS Catalysis. 8, 8685-8698 (2018).
43. Que, L. & Ho, R. Y. N. Dioxygen activation by enzymes with mononuclear non-heme iron active sites. Chem. Rev. 96, 2607-2624 (1996).
44. Ferraro, D. J., Okerlund, A. L., Mowers, J. C. & Ramaswamy, S. Structural basis for regioselectivity and stereoselectivity of product formation by naphthalene 1,2-Dioxygenase. J. Bacteriol. 188, 6986-6994 (2006).
45. Borowski, T., Bassan, A. & Siegbahn, P. E. Mechanism of dioxygen activation in 2-oxoglutarate-dependent enzymes: a hybrid DFT study. Chemistry (Weinheim an der Bergstrasse, Germany). 10, 1031-1041 (2004).
46. DÖLker, N., Maseras, F. & Siegbahn, P. E. M. Stabilization of the adenosyl radical in coenzyme B12 - A theoretical study. Chem. Phys. Lett. 386, 174-178 (2004).
47. Ashikawa, Y. et al. Electron transfer complex formation between oxygenase and ferredoxin components in rieske nonheme iron oxygenase system. Structure. 14, 1779-1789 (2006).
48. Chi, Z., Zhao, J., You, H. & Wang, M. Study on the mechanism of interaction between phthalate acid esters and bovine hemoglobin. J. Agr. Food. Chem. 64, 6035-6041 (2016).
49. Tang, B., Huang, Y., Yang, H., Tang, P. & Li, H. Molecular mechanism of the binding of 3,4,5-tri-O-caffeoylquinic acid to human serum albumin: Saturation transfer difference NMR, multi-spectroscopy, and docking studies. J. Photoch. Photobio. B. 165, 24-33 (2016).
50. Li, Y., Pan, J. & Ma, Y. Elucidation of multiple alkane hydroxylase systems in biodegradation of crude oil n-alkane pollution by Pseudomonas aeruginosa DN1. J. App Microbiol. 128, 151-160 (2019).
51. Hoang, T. T., Karkhoff-Schweizer, R. R., Kutchma, A. J. & Schweizer, H. P. A broad-host-range Flp-FRT recombination system for site-specific excision of chromosomally-located DNA sequences: application for isolation of unmarked Pseudomonas aeruginosa mutants. Gene. Rep. 212, 77-86 (1998).
52. Zhang, Z. et al. Degradation of n-alkanes and polycyclic aromatic hydrocarbons in petroleum by a newly isolated Pseudomonas aeruginosa DQ8. Bioresource. Technol. 102, 4111-4116 (2011).
53. Lovell, S. C. et al. Structure validation by Cα geometry: ϕ, ψ and Cβ deviation. Proteins: Struct, Funct, Bioinf. 50, 437-450 (2003).
54. Arnold, K., Bordoli, L., Kopp, J. & Schwede, T. The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics. 22, 195-201 (2006).
55. Benkert, P., Biasini, M. & Schwede, T. Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics. 27, 343-350 (2011).
56. Porter, L. L. & Rose, G. D. Redrawing the Ramachandran plot after inclusion of hydrogen-bonding constraints. PNAS 108, 109-113 (2011).
57. Jin, J., Yao, J., Liu, W., Zhang, Q. & Liu, J. Fluoranthene degradation and binding mechanism study based on the active-site structure of ring-hydroxylating dioxygenase inMicrobacterium paraoxydansJPM1. Environ. Sci. Pollut. Res. 24, 363-371 (2017).
58. Morris, G. M. et al. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J. Comput. Chem. 30, 2785-2791 (2009).
59. Sun, J., Wang, W., Ying, Y. & Hao, J. A novel glucose-tolerant GH1 β-Glucosidase and improvement of its glucose tolerance using site-directed mutation. Appl. Biochem. Biotech (2020).
60. Wu, H., Zeng, W., Chen, L., Yu, B. & Liang, Z. Integrated multi-spectroscopic and molecular docking techniques to probe the interaction mechanism between maltase and 1-deoxynojirimycin, an α-glucosidase inhibitor. nt J. Biol. 114, 1194-1202 (2018).