Active site residues controlling substrate specificity in 2-nitrotoluene dioxygenase from Acidovorax sp. strain JS42

Journal of Industrial Microbiology and Biotechnology

Volumn 32, Issue 10, 2005, Pages 465-473

  Lee, Kyung Seon ^a   Parales, Juanito V ^a   Friemann, Rosmarie ^b   Parales, Rebecca E ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

Author keywords

2 Nitrotoluene dioxygenase; Biodegradation; Enantiospecificity; Rieske non heme iron oxygenase; Substrate specificity

Indexed keywords

2 NITROTOLUENE; GUAIACOL; NAPHTHALENE; PHENYLALANINE;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; BACTERIAL STRAIN; ENANTIOSELECTIVITY; ENERGY RESOURCE; ENZYME ACTIVE SITE; ENZYME SPECIFICITY; HYDROGEN BOND; NONHUMAN; PSEUDOMONAS; STRAIN DIFFERENCE; WILD TYPE;

AMINO ACID SUBSTITUTION; BINDING SITES; COMAMONADACEAE; MODELS, MOLECULAR; MUTAGENESIS, SITE-DIRECTED; NAPHTHALENES; OXYGENASES; PHENYLALANINE; SUBSTRATE SPECIFICITY;

ACIDOVORAX; BACTERIA (MICROORGANISMS); COMAMONAS SP.; PSEUDOMONAS;

EID: 27444439187     PISSN: 13675435     EISSN: 14765535     Source Type: Journal    
DOI: 10.1007/s10295-005-0021-z     Document Type: Article

References (41)

1. An D, Gibson DT, Spain JC (1994) Oxidative release of nitrite from 2-nitrotoluene by a three-component enzyme system from Pseudomonas sp. strain JS42. J Bacteriol 176:7462-7467
2. Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K (1993) Current protocols in molecular biology. John Wiley, New York
3. Bradford MM (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72:248-254
4. Davis RW, Botstein D, Roth JR (1980) Advanced bacterial genetics. Cold Spring Harbor Laboratory, Cold Spring Harbor
5. DeLano WL (2002) The PyMOL molecular graphics system. http://www.pymol.org
6. Friemann R, Ivkovic-Jensen MM, Lessner DJ, Yu C-L, Gibson DT, Parales RE, Eklund H, Ramaswamy S (2005) Structural insights into the dioxygenation of nitroarene compounds: the crystal structure of the nitrobenzene dioxygenase. J Mol Biol 348:1139-1151
7. Fuenmayor SL, Wild M, Boyles AL, Williams PA (1998) A gene cluster encoding steps in the conversion of naphthalene to gentisate in Pseudomonas sp. strain U2. J Bacteriol 180:2522-2530
8. Gibson DT, Parales RE (2000) Aromatic hydrocarbon dioxygenases in environmental biotechnology. Curr Opin Biotechnol 11:236-243
9. Haigler BE, Wallace WH, Spain JC (1994) Biodegradation of 2-nitrotoluene by Pseudomonas sp. strain JS42. Appl Environ Microbiol 60:3466-3469
10. Haigler BE, Spain JC (1993) Biodegradation of 4-nitrotoluene by Pseudomonas sp. strain 4NT. Appl Environ Microbiol 59:2239-2243
11. Hartter DR (1985) The use and importance of nitroaromatic chemicals in the chemical industry. In: Rickert DE (ed) Toxicity of nitroaromatic compounds Chemical Industry Institute of Toxicology Series. Hemisphere, Washington DC, pp 1-14
12. van den Heuvel RH, van den Berg WA, Rovida S, van Berkel WJ (2004) Laboratory-evolved vanillyl-alcohol oxidase produces natural vanillin. J Biol Chem 279:33492-33500
13. Jeffrey AM, Yeh HJC, Jerina DM, Patel TR, Davey JF, Gibson DT (1975) Initial reactions in the oxidation of naphthalene by Pseudomonas putida. Biochemistry 14:575-583
14. Jones TA, Zou JY, Cowan SW, Kjeldgaard M (1991) Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Cryst 47:110-119
15. Kauppi B, Lee K, Carredano E, Parales RE, Gibson DT, Eklund H, Ramaswamy S (1998) Structure of an aromatic ring-hydroxylating dioxygenase- naphthalene 1,2-dioxygenase. Structure 6:571-586
16. Keenan BG, Leungsakul T, Smets BF, Wood TK (2004) Saturation mutagenesis of Burkholderia cepacia R34 2,4-dinitrotoluene dioxygenase at DntAc valine 350 for synthesizing nitrohydroquinone, methylhydroquinone, and methoxyhydroquinone. Appl Environ Microbiol 70:3222-3231
17. Keenan BG, Leungsakul T, Smets BF, Mori MA, Henderson DE, Wood TK (2005) Protein engineering of the archetypal nitroarene dioxygenase of Ralstonia sp. strain U2 for activity on aminonitrotoluenes and dinitrotoluenes through alpha-subunit residues leucine 225, phenylalanine 350, and glycine 407. J Bacteriol 187:3302-3310
18. Klecka GM, Gibson DT (1979) Metabolism of dibenzo[1,4]dioxan by a Pseudomonas species. Biochem J 180:639-645
19. Lessner DJ, Johnson GR, Parales RE, Spain JC, Gibson DT (2002) Molecular characterization and substrate specificity of nitrobenzene dioxygenase from Comamonas sp. strain JS765. Appl Environ Microbiol 68:634-641
20. Lessner DJ, Parales RE, Narayan S, Gibson DT (2003) Expression of nitroarene dioxygenase genes in Comamonas sp. strain JS765 and Acidovorax sp. strain JS42 is induced by multiple aromatic compounds. J Bacteriol 185:3895-3904
21. Meyer A, Schmid A, Held M, Westphal AH, Rothlisberger M, Kohler HP, van Berke WJ, Witholt B (2002) Changing the substrate reactivity of 2-hydroxybiphenyl 3-monooxygenase from Pseudomonas azelaica HBP1 by directed evolution. J Biol Chem 277:5575-5582
22. Nishino SF, Paoli GC, Spain JC (2000) Aerobic degradation of dinitrotoluenes and the pathway for bacterial degradation of 2,6-dinitrotoluene. Appl Environ Microbiol 66:2139-2147
23. Nishino SF, Spain JC (1993) Degradation of nitrobenzene by a Pseudomonas pseudoalcaligenes. Appl Environ Microbiol 59:2520-2525
24. Nishino SF, Spain JC (1995) Oxidative pathway for the biodegradation of nitrobenzene by Comamonas sp. strain JS765. Appl Environ Microbiol 61:2308-2313
25. Oue S, Okamoto A, Yano T, Kagamiyama H (1999) Redesigning the substrates specificity of an enzyme by cumulative effects of the mutations of non-active site residues. J Biol Chem 274:2344-2349
26. Parales JV, Kumar A, Parales RE, Gibson DT (1996) Cloning and sequencing of the genes encoding 2-nitrotoluene dioxygenase from Pseudomonas sp. JS42. Gene 181:57-61
27. Parales JV, Parales RE, Resnick SM, Gibson DT (1998) Enzyme specificity of 2-nitrotoluene 2,3-dioxygenase from Pseudomonas sp. strain JS42 is determined by the C-terminal region of the α subunit of the oxygenase component. J Bacteriol 180:1194-1199
28. Parales RE, Emig MD, Lynch NA, Gibson DT (1998) Substrate specificities of hybrid naphthalene and 2,4-dinitrotoluene dioxygenase enzyme systems. J Bacteriol 180:2337-2344
29. Parales RE, Resnick SM, Yu CL, Boyd DR, Sharma ND, Gibson DT (2000) Regioselectivity and enantioselectivity of naphthalene dioxygenase during arene cis-dihydroxylation: control by phenylalanine 352 in the α subunit. J Bacteriol 182:5495-5504
30. Parales RE, Huang R, Yu CL, Parales JV, Lee FKN, Ivkovic-Jensen MM, Liu W, Lessner DJ, Friemann R, Ramaswamy S, Gibson DT (2005) Purification, characterization, and crystallization of the components of the nitrobenzene and 2-nitrotoluene dioxygenase enzyme systems. Appl Environ Microbiol 71:3806-3814
31. Parales RE, Lee K, Resnick SM, JiangH, Lessner DJ, Gibson DT (2000) Substrate specificity of naphthalene dioxygenase: effect of specific amino acids at the active site of the enzyme. J Bacteriol 182:1641-1649
32. Pollmann K, Wray V, Hecht H-J, Pieper DH (2003) Rational engineering of the regioselectivity of TecA tetrachlorobenzene dioxygenase for the transformation of chlorinated toluenes. Microbiology 149:903-913
33. Resnick SM, Torok DS, Lee K, Brand JM, Gibson DT (1994) Regiospecific and stereoselective hydroxylation of 1-indanone and 2-indanone by naphthalene dioxygenase and toluene dioxygenase. Appl Environ Microbiol 60:3323-3328
34. Robertson JB, Spain JC, Haddock JD, Gibson DT (1992) Oxidation of nitrotoluene by toluene dioxygenase: evidence for a monooxygenase reaction. Appl Environ Microbiol 58:2643-2648
35. Simon MJ, Osslund TD, Saunders R, Ensley BD, Suggs S, Harcourt A, Suen W-C, Cruden DL, Gibson DT, Zylstra GJ (1993) Sequences of genes encoding naphthalene dioxygenase in Pseudomonas putida strains G7 and NCIB 9816-4. Gene 127:31-37
36. Spanggord RJ, Spain JC, Nishino SF, Mortelmans KE (1991) Biodegradation of 2,4-dinitrotoluene by a Pseudomonas sp. Appl Environ Microbiol 57:3200-3205
37. Stanier RY, Palleroni NJ, Doudoroff M (1966) The aerobic pseudomonads: a taxonomic study. J Gen Microbiol 43:159-271
38. Suen W-C, Haigler BE, Spain JC (1996) 2,4-Dinitrotoluene dioxygenase from Burkholderia sp. strain DNT: similarity to naphthalene dioxygenase. J Bacteriol 178:4926-4934
39. Yanisch-Perron C, Vieira J, Messing J (1985) Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 33:103-119
40. Yu C-L, Parales RE, Gibson DT (2001) Multiple mutations at the active site of naphthalene dioxygenase affect regioselectivity and enantioselectivity. J Ind Microbiol Biotechnol 27:94-103
41. Zielinski M, Kahl S, Hecht HJ, Hofer B (2003) Pinpointing biphenyl dioxygenase residues that are crucial for substrate interaction. J Bacteriol 185:6976-6980