Cloning, Expression, and Characterization of a cis-3-Chloroacrylic Acid Dehalogenase: Insights into the Mechanistic, Structural, and Evolutionary Relationship between Isomer-Specific 3-Chloroacrylic Acid Dehalogenases

Biochemistry

Volumn 43, Issue 3, 2004, Pages 759-772

  Poelarends, Gerrit J ^a   Serrano, Hector ^a   Person, Maria D ^a   Johnson Jr , William H ^a   Murzin, Alexey G ^b   Whitman, Christian P ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^b MRC CENTRE FOR PROTEIN ENGINEERING   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ACETYLENE; BACTERIA; CATALYSIS; CLONING; ENZYMES; FILTRATION; GEL PERMEATION CHROMATOGRAPHY; GENES; HYDRATION; MUTAGENESIS; ORGANIC ACIDS; REACTION KINETICS;

GENE ENCODING;

BIOCHEMISTRY;

2 OXO 3 PENTYNOATE; 3 CHLOROACRYLIC ACID DEHALOGENASE; 3 HOLOACRYLATE; 4 OXALOCROTONATE TAUTOMERASE; ACETYLENE DERIVATIVE; ACRYLIC ACID; BACTERIAL ENZYME; PYRUVIC ACID DERIVATIVE; UNCLASSIFIED DRUG;

ACTINOMYCETALES; ARTICLE; BACTERIAL STRAIN; CATALYSIS; CHEMICAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME KINETICS; ENZYME STRUCTURE; EVOLUTION; GENE OVEREXPRESSION; GENETIC CODE; HYDRATION; ISOMERIZATION; MOLECULAR CLONING; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN QUATERNARY STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; SITE DIRECTED MUTAGENESIS;

AMINO ACID SEQUENCE; ARGININE; CLONING, MOLECULAR; CORYNEBACTERIUM; ENZYME INHIBITORS; EVOLUTION, MOLECULAR; GLUTAMIC ACID; HYDROLASES; ISOMERASES; KINETICS; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; MUTAGENESIS, SITE-DIRECTED; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PEPTIDE FRAGMENTS; PROLINE; PROTEIN STRUCTURE, SECONDARY; PROTONS; SEQUENCE HOMOLOGY, AMINO ACID; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION; SUBSTRATE SPECIFICITY;

BACTERIA (MICROORGANISMS); CORYNEFORM BACTERIUM; HOMO;

EID: 1642576243     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi0355948     Document Type: Article

References (30)

1. Poelarends, G. J., Wilkens, M., Larkin, M. J., van Elsas, J. D., and Janssen, D. B. (1998) Degradation of 1,3-dichloropropene by Pseudomonas pavonaceae 170. Appl. Environ. Microbiol. 64, 2931-2936.
2. Poelarends, G. J., van Hylckama Vlieg, J. E. T., Bosma, T., and Janssen, D. B. (2002) The haloalkane dehalogenase genes dhlA and dhaA are globally distributed and highly conserved, in Biotechnology for the Environment: Strategy and Fundamentals (Agathos, S. N., and Reineke, W., Eds.) pp 59-66, Kluwer Academic Publishers, Dordrecht, The Netherlands.
3. van Hylckama Vlieg, J. E. T., and Janssen, D. B. (1992) Bacterial degradation of 3-chloroacrylic acid and the characterization of cis- and trans-specific dehalogenases. Biodegradation 2, 139-150.
4. Hartmans, S., Jansen, M. W., van der Werf, M. J., and de Bont, J. A. M. (1991) Bacterial metabolism of 3-chloroacrylic acid. J. Gen. Microbiol. 137, 2025-2032.
5. Poelarends, G. J., Saunier, R., and Janssen, D. B. (2001) trans-3-Chloroacrylic acid dehalogenase from Pseudomonas pavonaceae 170 shares structural and mechanistic similarities with 4-oxalocrotonate tautomerase. J. Bacteriol. 183, 4269-4277.
6. Wang, S. C., Person, M. D., Johnson, W. H., Jr., and Whitman, C. P. (2003) Reactions of trans-3-chloroacrylic acid dehalogenase with acetylene substrates: consequences of and evidence for a hydration reaction. Biochemistry 42, 8762-8773.
7. Murzin, A. G. (1996) Structural classification of proteins: new superfamilies. Curr. Opin. Struct. Biol. 6, 386-394.
8. Whitman, C. P. (2002) The 4-oxalocrotonate tautomerase family of enzymes: how nature makes new enzymes using a β-α-β structural motif. Arch. Biochem. Biophys. 402, 1-13.
9. Poelarends, G. J., Johnson Jr., W. H., Murzin, A. G., and Whitman, C. P. (2003) Mechanistic characterization of a bacterial malonate semialdehyde decarboxylase: identification of a new activity in the tautomerase superfamily. J. Biol. Chem. 278, 48674-48683.
10. Janssen, D. B., Oppentocht, J. E., and Poelarends, G. J. (2003) Bacterial growth on halogenated aliphatic hydrocarbons: genetics and biochemistry, in Dehalogenation: Microbial Processes and Environmental Applications (Häggblom, M. M., and Bossert, I. D., Eds.) pp 207-226, Kluwer Academic Publishers, Dordrecht, The Netherlands.
11. Copley, S. D. (2003) Aromatic dehalogenases: insights into structures, mechanisms, and evolutionary origins in Dehalogenation: Microbial Processes and Environmental Applications (Häggblom, M. M., and Bossert, I. D., Eds.) pp 227-259, Kluwer Academic Publishers, Dordrecht, The Netherlands.
12. Johnson, Jr., W. H., Czerwinski, R. M., Fitzgerald, M. C., and Whitman, C. P. (1997) Inactivation of 4-oxalocrotonate tautomerase by 2-oxo-3-pentynoate. Biochemistry, 36, 15724-15732.
13. Strauss, F., Kollek, L., and Heyn, W. (1930) Uber den ersatz positiven wasserstoffs durch halogen. Chem. Ber. 63, 1868-1899.
14. Andersson, K. (1972) Additions to propiolic and halogen substituted propiolic acids. Chem. Scr. 2, 117-120.
15. Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual, 2nd ed, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
16. Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
17. Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680.
18. Ho, S. N., Hunt, H. D., Horton, R. M., Pullen, J. K., and Pease. L. R. (1989) Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene 77, 51-59.
19. Guthrie, J. P. (1972) Acetopyruvic acid. Rate and equilibrium constants for hydration and enolization. J. Am. Chem. Soc. 94, 7020-7024.
20. Taylor, A. B., Czerwinski, R. M., Johnson, W. H., Whitman, C. P., and Hackert M. L. (1998) Crystal structure of 4-oxalocrotonate tautomerase inactivated by 2-oxo-3-pentynoate at 2.4 A resolution: analysis and implications for the mechanism of inactivation and catalysis. Biochemistry 37, 14692-14700.
21. Chen L. H., Kenyon G. L., Curtin F., Harayama S., Bembenck M. E., Hajipour G., and Whitman C. P. (1992) 4-Oxalocrotonate tautomerase, an enzyme composed of 62 amino acid residues per monomer. J. Biol. Chem. 267, 17716-17721.
22. de Jong, R. M., and Dijkstra, B. W. (2003) Structure and mechanism of bacterial dehalogenases: different ways to cleave a carbon-halogen bond. Curr. Opin. Struct. Biol. 13, 722-730.
23. Sorensen, S. B., Sørenson, T. L., and Breddam, K. (1991) Fragmentation of proteins by S. aureus strain V8 protease. Ammonium bicarbonate strongly inhibits the enzyme but does not improve the selectivity for glutamic acid. FEBS 294, 195-197.
24. Houmard, J., and Drapeau, G. R. (1972) Staphylococcal protease: a proteolytic enzyme specific for glutamoyl bonds. Proc. Natl. Acad. Sci. U.S.A. 69, 3506-3509.
25. Person, M. D., Monks, T. J., and Lau, S. S. (2003) An integrated approach to identifying chemically induced posttranslational modifications using comparative MALDI-MS and targeted HPLC-ESI-MS/MS. Chem. Res. Toxicol. 16, 598-608.
26. Azurmendi, H. F., Wang, S. C., Whitman, C. P., and Mildvan, A. S. (2003) New role for the amino-terminal proline in the tautomerase superfamily: trans-3-chloroacrylic acid dehalogenase. Biochemistry 42, 8619, Abstr. No. 113.
27. Harayama, S., Rekik, M., Ngai, K.-L., and Ornston, L. N. (1989) Physically associated enzymes produce and metabolize 2-hydroxy-2.4-dienoate, a chemically unstable intermediate formed in catechol metabolism via meta cleavage in Pseudomonas putida. J. Bacteriol. 171, 6251-6258.
28. Sparnins, V. L., Chapman, P. J., and Dagley, S. (1974) Bacterial degradation of 4-hydroxyphenylacetic acid and homoprotocatechuic acid. J. Bacteriol. 120, 159-167.
29. Subramanya, H. S., Roper, D. I., Dauter, Z., Dodson, E. J., Davies, G. J., Wilson, K. S., and Wigley, D. B. (1996) Enzymatic ketonization of 2-hydroxymuconate: specificity and mechanism investigated by the crystal structures of two isomerases. Biochemistry, 35, 792-802.
30. Taylor, A. B., Johnson, W. H., Jr., Czerwinski, R. M., Li, H.-S., Hackert, M. L., and Whitman, C. P. (1999) Crystal structure of macrophage migration inhibitory factor complexed with (E)-2-fluoro-p-hydroxycinnamate at 1.8 Å resolution: implications for enzymatic catalysis and inhibition. Biochemistry 38, 7444-7452.