In Silico Approach to Support that p-Nitrophenol Monooxygenase from Arthrobacter sp. Strain JS443 Catalyzes the Initial Two Sequential Monooxygenations

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• 作者：Monika Kallubai ; Umamaheswari Amineni…
• 关键词：PNP monooxygenase ; Arthrobacter sp. strain JS443 ; Bacillus sphaericus JS905 ; Homology modeling ; Molecular docking ; Molecular dynamics simulations
• 刊名：Interdisciplinary Sciences: Computational Life Sciences
• 出版年：2015
• 出版时间：June 2015
• 年：2015
• 卷：7
• 期：2
• 页码：157-167
• 全文大小：4,164 KB
• 参考文献：1.Markle RA, Fentiman AF, Steadman JR, Mayer RA (1980) Potentially toxic and hazardous substances in the industrial organic chemicals and organic dyes in pigment industries. National Technical Information Service, Springfield, VA. EPA600/2-80056
  2.Barik S, Sethunathan N (1978) Metabolism of \(p\) -nitrophenol in flooded soils. J Environ Qual 7:349-52CrossRef
  3.Ramakrishnan B, Megharaj M, Venkateswarlu K, Naidu R, Sethunathan N (2010) The impacts of environmental pollutants on microalgae and cyanobacteria. Crit Rev Environ Sci Technol 40:699-21CrossRef
  4.Ramakrishnan B, Megharaj M, Venkateswarlu K, Sethunathan N, Naidu R (2011) Mixtures of environmental pollutants: effects on microorganisms and their activities. Rev Environ Contam Toxicol 211:63-20PubMed
  5.Bruhn C, Lenke H, Hooper DJ (1987) Nitrosubstituted aromatic compounds as nitrogen source for bacteria. Appl Environ Microbiol 7:208-10
  6.Jones SH, Alexander M (1986) Kinetics of mineralization of phenol in lake water. Appl Environ Microbiol 51:891-97PubMed Central PubMed
  7.Keith LH (1980) EPA priority pollutants: where they come from, where they are going? AIChE Symp Ser 77:209-49
  8.Spain JC (1995) Biodegradation of nitroaromatic compounds. Annu Rev Microbiol 49:523-55CrossRef PubMed
  9.Spain JC, Gibson DT (1991) Pathway for biodegradation for \(p\) -nitrophenol in Moraxella sp. Appl Environ Microbiol 57:812-19PubMed Central PubMed
  10.Kadiyala V, Spain JC (1998) A two-component monooxygenase catalyzes both the hydroxylation of \(p\) -nitrophenol and the oxidative release of nitrite from 4-nitrocatechol in Bacillus sphaericus JS905. Appl Environ Microbiol 64:2479-484PubMed Central PubMed
  11.Perry LL, Zylstra GJ (2007) Cloning of a gene cluster involved in the catabolism of \(p\) -nitrophenol by Arthrobacter sp. strain JS443 and characterization of the \(p\) -nitrophenol monooxygenase. J Bacteriol 189:7563-572PubMed Central CrossRef PubMed
  12.Zhang S, Sun W, Xu L, Zheng X, Chu X, Tian J, Wu N, Fan Y (2012) Identification of the para-nitrophenol catabolic pathway, and characterization of three enzymes involved in the hydroquinone pathway, in Pseudomonas sp. 1-. BMC Microbiol 12:27PubMed Central CrossRef PubMed
  13.Liu PP, Zhang JJ, Zhou NY (2010) Characterization of mutagenesis of a two-component monooxygenase involved in para-nitrophenol degradation by an Arthrobacter strain. Int Biodeterior Biodegrad 64:293-99CrossRef
  14.Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search algorithms. Nucleic Acids Res 50:3389-402CrossRef
  15.Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-10CrossRef PubMed
  16.Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The protein data bank. Nucl Acids Res 28:235-42PubMed Central CrossRef PubMed
  17.Chenna R, Sugawana H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD (2003) Multiple sequence alignment with the clustal series of programs. Nucl Acid Res 31:3497-500CrossRef
  18.Sali AL, Overington JP (1994) Derivation of rules for comparative protein modeling from a database of protein structure alignments. Protein Sci 3:1582-596PubMed Central CrossRef PubMed
  19.Sali AL, Potterton F, van Vlijmen H, Karplus M (1995) Evaluation of comparative protein modeling by MODELLER. Proteins 23:318-26CrossRef PubMed
  20.Umamaheswari A, Pradhan D, Hemanthkumar M (2010) Virtual screening for potential inhibitors of homology modeled Leptospira interrogans MurD ligase. J Chem Biol 3:175-87PubMed Central CrossRef PubMed
  21.Laskowski RA, Rullmann JA, MacArthur MW, Kaptein R, Thrornton JM (1996) AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR 8:477-86CrossRef PubMed
  22.Hooft R, Vriend WWG, Sander C, Abola EE (1996) Errors in protein structure. Nature 38:272CrossRef
  23.Colovos C, Yeates TO (1993) Verification of protein crystal structures: patterns of non-bonded atomic interactions. Protein Sci 2:1511-519PubMed Central CrossRef PubMed
  24.Tomii K, Hirokawa T, Motono C (2005) Protein structure prediction using a variety of profile libraries and 3D verification. Proteins 61:114-21CrossRef PubMed
  25.Maestro v9.0 (2009) Schrodinger, LLC, Portland, OR
  26.Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ (2004) Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 47:1739-749CrossRef PubMed
  27.Friesner RA, Murphy RB, Repasky MP, Frye LL, Greenwood JR (2006) Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. J Med Chem 49:6177-196CrossRef PubMed
  28.Priyadarshini V, Pradhan D, Munikumar M, Umamaheswari A, Rajasekhar D Srinivasa, Rao PV
• 作者单位：Monika Kallubai (1)
  Umamaheswari Amineni (2)
  Megharaj Mallavarapu (3)
  Venkateswarlu Kadiyala (1)
  
  1. Department of Microbiology, Sri Krishnadevaraya University, Anantapur, 515055, India
  2. Department of Bioinformatics, Sri Venkateswara Institute for Medical Sciences, Tirupati, 517507, India
  3. Centre for Environmental Risk Assessment and Remediation, and CRC for Contamination Assessment and Remediation of the Environment, University of South Australia, Adelaide, SA, 5095, Australia
  
• 刊物主题：Computer Appl. in Life Sciences; Computational Biology/Bioinformatics; Statistics for Life Sciences, Medicine, Health Sciences; Theoretical and Computational Chemistry; Theoretical, Mathematical and Computational Physics; Computational Science and Engineering;
• 出版者：International Association of Scientists in the Interdisciplinary Areas
• ISSN：1867-1462

文摘

p-Nitrophenol (PNP), used primarily for manufacturing pesticides and dyes, has been recognized as a priority environmental pollutant. It is therefore important to reduce the input of this toxicant into the environment and to establish approaches for its removal from the contaminated sites. PNP monooxygenase, a novel enzyme from Gram-positive bacteria like Arthrobacter sp. and Bacillus sp., that comprises two components, a flavoprotein reductase and an oxygenase, catalyzes the initial two sequential monooxygenations to convert PNP to trihydroxybenzene. Accurate and reliable prediction of this enzyme–substrate interactions and binding affinity are of vital importance in understanding these catalytic mechanisms of the two sequential reactions. As crystal structure of the enzyme has not yet been published, we built a homology model for PNP monooxygenase using crystallized chlorophenol 4-monooxygenase from Burkholderia cepacia AC1100 (3HWC) as the template. The model was assessed for its reliability using PROCHECK, ERRAT and ProSA. Molecular docking of the physiological substrates, PNP and 4-nitrocatechol (4-NC), was carried out using Glide v5.7 implemented in Maestro v9.2, and the binding energies were calculated to substantiate the prediction. Docking complexes formed by molecular level interactions of PNP monooxygenase-PNP/4-NC without or with the cofactors, FAD and NADH, showed good correlation with the established experimental evidence that the two-component PNP monooxygenase catalyzes both the hydroxylation of PNP and the oxidative release of nitrite from 4-NC in B. sphaericus JS905. Furthermore, molecular dynamics simulations performed for docking complexes using Desmond v3.0 showed stable nature of the interactions as well. Keywords PNP monooxygenase Arthrobacter sp. strain JS443 Bacillus sphaericus JS905 Homology modeling Molecular docking Molecular dynamics simulations