An integrated approach of bioassay and molecular docking to study the dihydroxylation mechanism of pyrene by naphthalene dioxygenase in Rhodococcus sp. ustb-1.
Naphthalene dioxygenase (NDO) is the initial enzyme catalyzing the biodegradation of aromatic compounds, and it plays a key role in microbial remediation of polluting sites. In this study, Rhodococcus sp. ustb-1 derived from crude oil was selected to investigate the biodegradation characters and dihydroxylation mechanism of pyrene by an integrated approach of bioassay and molecular docking. The biodegradation experiment proved that the strain ustb-1 shows high effective biodegradability to pyrene with a 70.8% degradation on the 28th day and the metabolite pyrene cis-4,5-dihydrodiol was found. The results of molecular docking indicated that the regions surrounding pyrene are defined by hydrophobic amino acids which are favorable for the binding of dioxygen molecule at C4 and C5 positions of pyrene in a side-on mode. The binding positions of dioxygen are in agreement with the mass spectral analysis of the metabolite pyrene cis-4,5-dihydrodiol. In summary, this study provides a promising explanation for the possible binding behavior between pyrene and active site of NDO.
School of Civil and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China.
Jing-Nan
JN
Jin
School of Civil and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China; State Key Laboratory of Biogeology and Environmental Geology of Chinese Ministry of Education, Sino-Hungarian Joint Laboratory of Environmental Science and Health, China University of Geoscience, Wuhan 430074, China. Electronic address: yaojun@ustb.edu.cn.
Jun
J
Yao
College of Science, Huazhong Agricultural University, Wuhan 430070, China.
Qing-Ye
QY
Zhang
School of Civil and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China.
Chan
C
Yu
School of Civil and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China.
Peng
P
Chen
School of Civil and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China.
Wen-Juan
WJ
Liu
School of Civil and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China.
Dan-Ning
DN
Peng
School of Civil and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China. Electronic address: mmfchoi@gmail.com.
Martin M F
MM
Choi
D001673:Biodegradation, Environmental; D001681:Biological Assay / Q000379:methods*; D049308:Dioxygenases / Q000378:metabolism*; D006900:Hydroxylation; D009097:Multienzyme Complexes / Q000378:metabolism*; D010578:Petroleum / Q000382:microbiology*; D011485:Protein Binding; D011721:Pyrenes / Q000378:metabolism*; D012240:Rhodococcus / Q000201:enzymology* / Q000378:metabolism
D009097:Multienzyme Complexes; D010578:Petroleum; D011721:Pyrenes; C030984:pyrene; D049308:Dioxygenases; C038703:naphthalene dioxygenase
Biodegradation; Molecular docking; NDO; Pyrene