Characterization of a novel meta-fission product hydrolase from Dyella ginsengisoli LA-4

Process Biochemistry

Volumn 45, Issue 1, 2010, Pages 94-100

  Li, Ang ^a,b   Qu, Yuanyuan ^a   Zhou, Jiti ^a   Ma, Fang ^b   Zhou, Hao ^a   Shi, Shengnan ^a  

^a MOE   (China)

^b HARBIN INSTITUTE OF TECHNOLOGY   (China)

Author keywords

hydrolase; bph gene cluster; Dyella ginsengisoli; meta fission product

Indexed keywords

AMINO ACID SEQUENCE; APPARENT KINETIC PARAMETERS; BIODEGRADATION PROCESS; BPH GENE CLUSTER; GENE CLUSTERS; HIS-TAG; HYDROLASE FAMILY; HYDROLASE GENE; HYDROLASES; LOW TEMPERATURES; MONOCYCLIC COMPOUNDS; PSEUDOMONAS PUTIDA; SDS-PAGE ANALYSIS;

AMINES; AMINO ACIDS; BIODEGRADATION; DIFFUSERS (OPTICAL); ORGANIC ACIDS;

FISSION PRODUCTS;

DYELLA; PSEUDOMONAS PUTIDA;

EID: 70449686035     PISSN: 13595113     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.procbio.2009.08.011     Document Type: Article

References (46)

1. Dagley S. Biochemistry of aromatic hydrocarbon degradation in Pseudomonads. In: Sokatch J., and Ornston L.N. (Eds). The bacteria (1986), Academic Press, Orlando 527-555
2. Diaz E., Ferrandez A., Prieto M.A., and Garcia J.L. Biodegradation of aromatic compounds by Escherichia coli. Microbiol Mol Biol Rev 65 (2001) 523-569
3. Saravanan P., Pakshirajan K., and Saha P. Biodegradation of phenol and m-cresol in a batch and fed batch operated internal loop airlift bioreactor by indigenous mixed microbial culture predominantly Pseudomonas sp. Bioresour Technol 99 (2008) 8553-8558
4. Diaz E. Bacterial degradation of aromatic pollutants: a paradigm of metabolic versatility. Int Microbiol 7 (2004) 173-180
5. Zylstra G.J., and Gibson D.T. Aromatic hydrocarbon degradation: a molecular approach. In: Setlow J.K. (Ed). Genetic engineering (1991), Plenum Press, New York 183-203
6. van der Meer J.R., de Vos W.M., Harayama S., and Zehnder A.J. Molecular mechanisms of genetic adaptationto xenobiotic compounds. Microbial Rev 56 (1992) 677-694
7. Ollis D.L., Cheah E., Cygler M., Dijkstra B., Frolow F., Franken S.M., et al. The α/β hydrolase fold. Protein Eng 5 (1992) 197-211
8. Heikinheimo P., Goldman A., Jeffries C., and Ollis D.L. Of barn owls and bankers: a lush variety of α/β hydrolases. Structure 7 (1999) 141-146
9. Nardini M., and Dijkstra B.W. α/β-Hydrolase fold enzymes: the family keeps growing. Curr Opin Struct Biol 9 (1999) 732-733
10. Dunn G., Montgomery M.G., Mohammed F., Coker A., Cooper J.B., Robertson T., et al. The structure of the C-C bond hydrolase MhpC provides insights into its catalytic mechanism. J Mol Biol 346 (2005) 253-265
11. Fushinobu S., Jun S.Y., Hidaka M., Nojiri H., Yamane H., Shoun H., et al. A series of crystal structures of a meta-cleavage product hydrolase from Pseudomonas fluorescens IP01 (CumD) complexed with various cleavage products. Biosci Biotechnol Biochem 69 (2005) 491-498
12. Horsman G.P., Ke J., Dai S., Seah S.Y., Bolin J.T., and Eltis L.D. Kinetic and structural insight into the mechanism of BphD, a C-C bond hydrolase from the biphenyl degradation pathway. Biochemistry 45 (2006) 11071-11086
13. Horn J.M., Harayama S., and Timmis K.N. DNA sequence determination of the TOL plasmid (pWWO) xylGFJ genes of Pseudomonas putida: implications for the evolution of aromatic catabolism. Mol Microbiol 5 (1991) 2459-2474
14. Bayly R.C., and Di Berardino D. Purification and properties of 2-hydroxy-6-oxo-2,4-heptadienoate hydrolase from two strains of Pseudomonas putida. J Bacteriol 134 (1978) 30-37
15. Mishra V., Lal R., and Srinivasan. Enzymes and operons mediating xenobiotic degradation in bacteria. Crit Rev Microbiol 27 (2001) 133-166
16. Siddavattam D., Khajamohiddin S., Manavathi B., Pakala S.B., and Merrick M. Transposon-like organization of the plasmid-borne organophosphate degradation (opd) gene cluster found in Flavobacterium sp. Appl Environ Microbiol 69 (2003) 2533-2539
17. Diaz E., and Timmis K.N. Identification of functional residues in a 2-hydroxymuconic semialdehyde hydrolase: a new member of the α/β hydrolase-fold family of enzymes which cleaves carbon-carbon bonds. J Biol Chem 270 (1995) 6403-6411
18. Furukawa K., Hirose J., Suyama A., Zaiki T., and Hayashida S. Gene components responsible for discrete substrate specificity in the metabolism of biphenyl (bph operon) and toluene (tod operon). J Bacteriol 175 (1993) 5224-5232
19. Cho M.C., Kang D.O., Yoon B.D., and Lee K. Toluene degradation pathway from Pseudomonas putida F1: substrate specificity and gene induction by 1-substituted benzenes. J Ind Microbiol Biotechnol 25 (2000) 163-170
20. Harayama S., Mermod N., Rekik M., Lehrbach P.R., and Timmis K.N. Roles of the divergent branches of the meta-cleavage pathway in the degradation of benzoate and substituted benzoates. J Bacteriol 169 (1987) 558-564
21. Khajamohiddin S., Repalle E.R., and Pinjari A.B. Biodegradation of aromatic compounds: an overview of meta-fission product hydrolases. Crit Rev Microbiol 34 (2008) 13-31
22. Khajamohiddin S., Babu P.S., Chakka D., Merrick M., Bhaduri A., Sowdhamini R., et al. A novel meta-cleavage product hydrolase from Flavobacterium sp. ATCC27551. Biochem Biophys Res Commun 351 (2006) 675-681
23. Li A., Qu Y.Y., Zhou J.T., and Gou M. Isolation and characteristics of a novel biphenyl-degrading bacterial strain, Dyella ginsengisoli LA-4. J Environ Sci 21 (2009) 211-217
24. Li A., Qu Y.Y., Zhou J.T., and Ma F. Enzyme-substrate interaction and characterization of a 2,3-dihydroxybiphenyl 1,2-dioxygenase from Dyella ginsengisoli LA-4. FEMS Microbiol Lett 292 (2009) 231-239
25. Qu Y.Y., Wang J., Zhou J.T., and Xing L.L. Decolorization of bromoamine acid by a newly isolated strain of Sphingomonas xenophaga QYY and its resting cells. Biochem Eng J 27 (2005) 104-109
26. Ausubel F.M., Brent R., Kingston R.E., Moore D.D., Seidman J.G., Smith J.A., et al. Current protocols in molecular biology (2000), J. Wiley and Sons Inc., New York
27. Saitou N., and Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4 (1987) 406-425
28. Schwede T., Kopp J., Guex N., and Peitsch M.C. SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res 31 (2003) 3381-3385
29. Laemmli U.K. Cleavage of structural proteins during assembly of the head of bacteriophage T4. Nature 227 (1970) 680-685
30. Bradford M.M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72 (1976) 248-254
31. Eltis L.D., Hofmann B., Hecht H., Lunsdorf H., and Timmis K.N. Purification and crystallization of 2,3-dihydroxybiphenyl 1,2-dioxygenase. J Biol Chem 268 (1993) 2727-2732
32. Hatta T., Mukerjee-Dhar G.M., Damborsky J., Kiyohara H., and Kimbara K. Characterization of a novel thermostable Mn (II)-dependent 2,3-dihydroxybiphenyl 1,2-dioxygenase from a polychlorinated biphenyl- and naphthalene-degrading Bacillus sp. JF8. J Biol Chem 278 (2003) 21483-21492
33. Seah S.Y.K., Terracina G., Bolin J., Riebel P., Snieckus V., and Eltis L.D. Purification and preliminary characterization of a serine hydrolase involved in the microbial degradation of polychlorinated biphenyls. J Biol Chem 273 (1998) 22943-22949
34. Hatta T., Shimada T., Yoshihara T., Yamada A., Masi E., Fukuda M., et al. meta-Fission product hydrolases from a strong PCB degrader Rhodococcus sp. RHA1. J Ferment Bioeng 85 (1998) 174-179
35. Nandhagopal N., Yamada A., Hatta T., Masai E., Furuda M., Mitsui Y., et al. Crystal structure of 2-hydroxyl-6-oxo-6-phenylhexa-2,4-dienoic acid (HPDA) hydrolase (BphD enzyme) from the Rhodococcus sp. strain RHA1 of the PCB degradation pathway. J Mol Biol 309 (2001) 1139-1151
36. Fushinobu S., Saku T., Hidaka M., Jun S.Y., Nojiri H., Yamane H., et al. Crystal structures of a meta-cleavage product hydrolase from Pseudomonas fluorescens IP01 (CumD) complexed with cleavage products. Protein Science 11 (2002) 2184-2195
37. Li C., Li J.J., Montgomery M.G., Wood S.P., and Bugg T.D. Catalytic role for arginine 188 in the C-C hydrolase catalytic mechanism for Escherichia coli MhpC and Burkholderia xenovorans LB400 BphD. Biochemistry 45 (2006) 12470-12479
38. Li C., Montgomery M.G., Mohammed F., Li J.J., Wood S.P., and Bugg T.D. Catalytic mechanism of C-C hydrolase MhpC from Escherichia coli: kinetic analysis of His263 and Ser110 site-directed mutants. J Mol Biol 346 (2005) 241-251
39. Horsman G.P., Bhowmik S., Seah S.Y., Kumar P., Bolin J.T., and Eltis L.D. The tautomeric half-reaction of BphD, a C-C bond hydrolase: kinetic and structural evidence supporting a key role for histidine 265 of the catalytic triad. J Biol Chem 282 (2007) 19894-19904
40. Duggleby C.J., and Williams P.A. Purification and some properties of 2-hydroxy-6-oxo-2,4-heptadienoate hydrolase from two strains of Pseudomonas putida. J Gen Microbiol 132 (1986) 717-726
41. Riddle R.R., Gibbs P.R., Willson R.C., and Benedik M.J. Purification and properties of 2-hydroxy-6-oxo-6-(2′-aminophenyl)hexa-2,4-dienoic acid hydrolase involved in microbial degradation of carbazole. Protein Exp Purif 28 (2003) 182-189
42. Nojiri H., Taira H., Iwata K., Morii K., Nam J.W., Yoshida T., et al. Purification and characterization of meta-cleavage compound hydrolase from a carbazole degrader Pseudomonas resinovorans strain CA10. Biosci Biotechnol Biochem 67 (2003) 36-45
43. Pokorny D., Steiner W., and Ribbons D.M. β-Ketolases forgotten hydrolytic enzymes?. Trends Biotechnol 15 (1997) 291-296
44. Saku T., Fushinobu S., Jun S.Y., Ikeda N., Nojiri H., Yamane H., et al. Purification, characterization, and steady-state kinetics of a meta-cleavage compound hydrolase from Pseudomonas fluorescens IPO1. J Biosci Bioeng 93 (2002) 568-574
45. Powers J.C., and Harper J.W. In: Barrett A.J., and Salvesen G. (Eds). Proteinase inhibitors (1986), Elsevier Science Publishers BV, Amsterdam
46. Miles E.W. Modification of histidyl residues in proteins by diethylpyrocarbonate. Methods Enzymol 47 (1977) 431-442