Active-site engineering of biphenyl dioxygenase: Effect of substituted amino acids on substrate specificity and regiospecificity

Applied Microbiology and Biotechnology

Volumn 71, Issue 2, 2006, Pages 168-176

  Suenaga, Hikaru ^a   Goto, Masatoshi ^b   Furukawa, Kensuke ^b  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^b KYUSHU UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BIODEGRADATION; CATALYSIS; ENZYME KINETICS; ESCHERICHIA COLI; METABOLISM; MUTAGENS; POLYCHLORINATED BIPHENYLS; SUBSTRATES;

BIPHENYL DIOXYGENASE; DIBENZOFURAN; KF707 BPH DOX; PSEUDOMONAS PSEUDOALCALIGENES KF707;

AMINO ACIDS;

2,4',5 TRICHLOROBIPHENYL; AMINO ACID DERIVATIVE; ASPARTIC ACID; BIPHENYL DERIVATIVE; BIPHENYL DIOXYGENASE; DIBENZOFURAN; DICHLOROBIPHENYL; DIOXYGENASE; GLYCINE; LYSINE; OXYGEN; PHENYLALANINE; SERINE; THREONINE; UNCLASSIFIED DRUG; VALINE;

AMINO ACID; CATALYSIS; ENZYME; FECAL COLIFORM; METABOLISM; PCB;

AMINO ACID SUBSTITUTION; ARTICLE; BURKHOLDERIA XENOVORANS; CONTROLLED STUDY; DECHLORINATION; ENZYME ENGINEERING; ENZYME SPECIFICITY; ESCHERICHIA COLI; NONHUMAN; PROTEIN EXPRESSION; PSEUDOMONAS PSEUDOALCALIGENES; SITE DIRECTED MUTAGENESIS; SUBSTITUTION REACTION;

AMINO ACID SUBSTITUTION; AMINO ACIDS; BINDING SITES; BIODEGRADATION, ENVIRONMENTAL; DNA, BACTERIAL; ESCHERICHIA COLI; IRON-SULFUR PROTEINS; MODELS, MOLECULAR; MUTAGENESIS, SITE-DIRECTED; OXYGENASES; POLYCHLORINATED BIPHENYLS; PROTEIN CONFORMATION; PROTEIN ENGINEERING; PSEUDOMONAS PSEUDOALCALIGENES; RECOMBINANT PROTEINS; STRUCTURE-ACTIVITY RELATIONSHIP; SUBSTRATE SPECIFICITY;

BURKHOLDERIA XENOVORANS; ESCHERICHIA COLI; PSEUDOMONAS PSEUDOALCALIGENES;

EID: 33745028427     PISSN: 01757598     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00253-005-0135-2     Document Type: Article

References (31)

1. Abraham WR, Nogales B, Golyshin PN, Pieper DH, Timmis KN (2002) Polychlorinated biphenyl-degrading microbial communities in soils and sediments. Curr Opin Microbiol 5:246-253
2. Bak-Jensen KS, Andre G, Gottschalk TE, Paes G, Tran V, Svensson B (2004) Tyrosine 105 and threonine 212 at outermost substrate binding subsites -6 and +4 control substrate specificity, oligosaccharide cleavage patterns, and multiple binding modes of barley alpha-amylase 1. J Biol Chem 279:10093-10102
3. Barriault D, Plante M-M, Sylvestre M (2002) Family shuffling of a target bphA region to engineer biphenyl dioxygenase. J Bacteriol 184:3794-3800
4. Carredano E, Karlsson A, Kauppi B, Choudhury D, Parales RE, Parales JV, Lee K, Gibson DT, Eklund H, Ramaswamy S (2000) Substrate binding site of naphthalene 1,2-dioxygenase: functional implications of indole binding. J Mol Biol 296:701-712
5. Erickson BD, Mondello FJ (1992) Nucleotide sequencing and transcriptional mapping of the genes encoding biphenyl dioxygenase, a multicomponent polychlorinated-biphenyl-degrading enzyme in Pseudomonas strain LB400. J Bacteriol 174:2903-2912
6. Erickson BD, Mondello FJ (1993) Enhanced biodegradation of polychlorinated biphenyls after site-directed mutagenesis of a biphenyl dioxygenase gene. Appl Environ Microbiol 59:3858-3862
7. Fedi S, Carnevail M, Fava F, Andracchio A, Zappoli S, Zannoni D (2001) Polychlorinated biphenyl degradation activities and hybridization analyses of fifteen aerobic strains isolated from a PCB-contaminated site. Res Microbiol 152:583-592
8. Furukawa K (1982) Microbial degradation of polychlorinated biphenyls. In: Chakrabarty AM (ed) Biodegradation and detoxification of environmental pollutants. CRC Press, Boca Raton, pp 33-57
9. Furukawa K (1994) Molecular genetics and evolutionary relationship of PCB-degrading bacteria. Biodegradation 5:289-300
10. Furukawa K, Suenaga H, Goto M (2004) Biphenyl dioxygenases: functional versatilities and directed evolution. J Bacteriol 186:5189-5196
11. Gibson DT, Cruden DL, Haddock JD, Zylstra GJ, Brand JM (1993) Oxidation of polychlorinated biphenyls by Pseudomonas sp. strain LB400 and Pseudomonas pseudalcaligenes KF707. J Bacteriol 175:4561-4564
12. Goris J, Vos PD, Caballero-Mellado J, Park J, Falsen E, Quensen JF III, Tiedje JM, Vandamme P (2004) Classification of the biphenyl- and polychlorinated biphenyl-degrading strain LB400T and relatives as Burkholderia xenovorans sp. nov. Int J Syst Evol Microbiol 54:1677-1681
13. Haddock JD, Horton JR, Gibson DT (1995) Dihydroxylation and dechlorination of chlorinated biphenyls by purified biphenyl 2,3-dioxygenase from Pseudomonas sp. strain LB400. J Bacteriol 177:20-26
14. Hegg EL, Que L Jr (1997) The 2-His-1-carboxylate facial triad-an emerging structural motif in mononuclear non-heme iron(II) enzymes. Eur J Biochem 250:625-629
15. Hernandez BS, Arensdorf JJ, Focht DD (1995) Catabolic characteristics of biphenyl-utilizing isolates which cometabolize PCBs. Biodegradation 6:75-82
16. Jiang H, Parales RE, Lynch NA, Gibson DT (1996) Site-directed mutagenesis of conserved amino acids in the α subunit of toluene dioxygenase: potential mononuclear non-heme iron coordination sites. J Bacteriol 178:3133-3139
17. 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
18. 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
19. Kimura N, Nishi A, Goto M, Furukawa K (1997) Functional analyses of a variety of chimeric dioxygenases constructed from two biphenyl dioxygenases that are similar structurally but different functionally. J Bacteriol 179:3936-3943
20. Kumamaru T, Suenaga H, Mitsuoka M, Watanabe T, Furukawa K (1998) Enhanced degradation of polychlorinated biphenyls by directed evolution of biphenyl dioxygenase. Nat Biotechnol 16:663-666
21. Maeda T, Takahashi Y, Suenaga H, Suyama A, Goto M, Furukawa K (2001) Functional analyses of Bph-Tod hybrid dioxygenase, which exhibits high degradation activity toward trichloroethylene. J Biol Chem 276:29833-29838
22. Mondello FJ, Turcich MP, Lobos JH, Erickson BD (1997) Identification and modification of biphenyl dioxygenase sequence that determine the specificity of polychlorinated biphenyl degradation. Appl Environ Microbiol 63:3096-3103
23. Parales RE, Resnick SM, Yu C-L, 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
24. Pollmann K, Wray V, Hecht H-J, Pieper DH (2003) Rational engineering of the regiospecificity of TecA tetrachlorobenzene dioxygenase for the transformation of chlorinated toluenes. Microbiology 149:903-913
25. Seeger M, Timmis KN, Hofer B (1999) Regiospecificity of dioxygenation of di- to pentachlorobiphenyls and their degradation to chlorobenzoates by bph-encoded catabolic pathway of Burkholdena sp. strain LB400. Appl Environ Microbiol 61:761-768
26. Suenaga H, Nishi A, Watanabe T, Sakai M, Furukawa K (1999) Engineering a hybrid Pseudomonad to acquire 3,4-dioxygenase activity for polychlorinated biphenyls. J Biosci Bioeng 87:430-435
27. Suenaga H, Goto M, Furukawa K (2001) Emergence of multifunctional oxygenase activities by random priming recombination. J Biol Chem 276:22500-22506
28. Suenaga H, Watanabe T, Sato M, Ngadiman, Furukawa K (2002) Alteration of regiospecificity in biphenyl dioxygenase by active-site engineering. J Bacteriol 184:3682-3688
29. Taira K, Hirose J, Hayashida S, Furukawa K (1992) Analysis of bph operon from the polychlorinated biphenyl-degrading strain of Pseudomonas pseudoalcaligenes KF707. J Biol Chem 267:4844-4853
30. Xu D, Enroth C, Lindqvist Y, Ballou DP, Massey V (2002) Studies of the mechanism of phenol hydroxylase: effect of mutation of proline 364 to serine. Biochemistry 41:13627-13636
31. Zielinski M, Kahl S, Hecht H-J, Hofer B (2003) Pinpointing biphenyl dioxygenase residue that are crucial for substrate interaction. J Bacteriol 185:6976-6980