Quinoprotein ethanol dehydrogenase of Pseudomonas aeruginosa is a homodimer: Sequence of the gene and deduced structural properties of the enzyme

European Journal of Biochemistry

Volumn 257, Issue 2, 1998, Pages 409-419

  Diehl, Annette ^a   Wintzingerode, Friedrich V ^b   Görisch, Helmut ^a  

^a TECHNISCHE UNIVERSITÄT BERLIN   (Germany)

^b HUMBOLDT UNIVERSITY   (Germany)

Author keywords

Ethanol dehydrogenase; Nucleotide sequence; Primary structure; Pseudomonas aeruginosa; Quinoprotein

Indexed keywords

ALCOHOL; BACTERIAL ENZYME; CALCIUM; DIMER; GLUCOSE; GLYCINE; PYRROLOQUINOLINEQUINONE; QUININE SULFATE; QUINOPROTEIN ETHANOL DEHYDROGENASE; QUINOPROTEIN METHANOL DEHYDROGENASE; SHIKIMIC ACID; TRYPTOPHAN; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; ENZYME STRUCTURE; ESCHERICHIA COLI; GENE SEQUENCE; METHYLOBACTERIUM; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PSEUDOMONAS AERUGINOSA; SEQUENCE HOMOLOGY;

BACTERIA (MICROORGANISMS); CINCHONA PUBESCENS; ESCHERICHIA COLI; METHYLOBACTERIUM EXTORQUENS; PROKARYOTA; PSEUDOMONAS; PSEUDOMONAS AERUGINOSA;

EID: 0032532793     PISSN: 00142956     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1432-1327.1998.2570409.x     Document Type: Article

References (64)

1. Anthony, C. (1996) Quinoprotein-catalysed reactions, Biochem. J. 320, 697-711.
2. Duine, J. A., Frank Jzn., J. & Verwiel, P. E. (1980) Structure and activity of the prosthetic group of methanol dehydrogenase, Eur. J. Biochem. 108, 187-192.
3. Matsushita, K. & Adachi, O. (1993) Bacterial quinoproteins glucose dehydrogenase and alcohol dehydrogenase, in Principles and application of quinoproteins (Davidson, V. L., ed.) pp. 47-63, Marcel Dekker, New York.
4. Arfman, N., Watling, E. M., Clement, W., van Oosterwijk, R. J., de Vries, G. B., Harder, W., Attwood, M. M. & Dijkhuizen, L. (1989) Methanol metabolism in thermotolerant methylotrophic Bacillus strains involving a novel catabolic NAD-dependent methanol dehydrogenase as a key enzyme, Arch. Microbiol. 152, 280-288.
5. Anthony, C. (1993) Methanol dehydrogenase in gram-negative bacteria, in Principles and applications of quinoproteins (Davidson, V. L., ed.) pp. 17-45, Marcel Dekker, New York.
6. Anderson, D. J., Morris, C. J., Nunn, D. N., Anthony, C. & Lidstrom, M. E. (1990) Nucleotide sequence of the Methylobacterium extorquens AM1 moxF and moxJ genes involved in methanol oxidation, Gene (Amst.) 90, 173-176.
7. Machlin, S. M. & Hanson, R. S. (1988) Nucleotide sequence and transcriptional start site of the Methylobacterium organophilum XX methanol dehydrogenase structural gene, J. Bacteriol. 170, 4739-4747.
8. Tanaka, Y., Yoshida, T., Watanabe, K., Izumi, Y. & Mitsunaga, T. (1997) Cloning and analysis of methanol oxidation genes in the methylotroph Hyphomicrobium methylovorium GM2, FEMS Microbiol. Lett. 154, 397-401.
9. Harms, N., de Vries, G. E., Maurer, K., Hoogendijk, J. & Stouthamer, A. H. (1987) Isolation and nucleotide sequence of methanol dehydrogenase structural gene from Paracoccus denitrificans, J. Bacteriol. 169, 3969-3975.
10. Xia, Z.-x., Dai, W.-w., Zhang, Y.-f., White, S., Boyd, G. D. & Mathews, F. S. (1996) Determination of the gene sequence and the three-dimensional structure at 2.4 angstrom resolution of methanol dehydrogenase from Methylophilus W3A1, J. Mol. Biol. 259, 480-501.
11. Ghosh, M., Anthony, C., Harlos, K., Goodwin, M. G. & Blake, C. (1995) The refined structure of the quinoprotein methanol dehydrogenase from Methylobacterium extorquens at 1.94 Å, Structure 3, 177-187.
12. Tamaki, T., Fukaya, M., Takemura, H., Tayama, K., Okumura, H., Kawamura, Y., Nishiyama, M., Horinouchi, S. & Beppu, T. (1991) Cloning and sequencing of the gene cluster encoding two subunits of membrane-bound alcohol dehydrogenase from Acetobacter polyoxogenes, Biochim. Biophys. Acta 1088, 292-300.
13. Kondo, K. & Horinouchi, S. (1997) Characterization of the genes encoding the three-component membrane-bound alcohol dehydrogenase from Gluconobacter suboxydans and their expression in Acetobacter pasteurianus, Appl. Environ. Microbiol. 63, 1131-1138.
14. Takemura, H., Kondo, K., Horinouchi, S. & Beppu, T. (1993) Induction by ethanol of alcohol dehydrogenase activity in Acetobacter pasteurianus, J. Bacteriol. 175, 6857-6866.
15. Inoue, T., Sunagawa, M., Mori, A., Imai, Ch., Fukuda, M., Takagi, M. & Yano, K. (1989) Cloning and sequencing of the gene encoding the 72-kilodalton dehydrogenase subunit of alcohol dehydrogenase from Acetobacter aceti, J. Bacteriol. 171, 3115-3122.
16. De Jong, G. A. H., Geerlof, A., Stoorvogel, J., Jongejan, J. A., De Vries, S. & Duine, J. A. (1995) Quinohaemoprotein ethanol dehydrogenase from Comamonas testosteroni: Purification, characterization, and reconstitution of the apoenzyme with pyrroloquinoline quinone analogous, Eur. J. Biochem. 230, 899-905.
17. Stoorvogel, J., Kraayveld, D. E., Van Sluis, C. A., Jongejan, J. A., De Vries, S. & Duine, J. A. (1996) Characterization of the gene encoding quinohaemo-protein ethanol dehydrogenase of Comamonas testosteroni, Eur. J. Biochem. 235, 690-698.
18. Rupp, M. & Görisch, H. (1988) Purification, crystallization and characterization of quinoprotein ethanol dehydrogenase from Pseudomonas aeruginosa, Biol. Chem. Hoppe-Seyler 369, 431-439.
19. Görisch, H. & Rupp, M. (1989) Quinoprotein ethanol dehydrogenase from Pseudomonas, Antonia Leeuvenhoek 56, 35-45.
20. Toyama, H., Fujii, A., Matsushita, K., Shinagawa, E., Ameyama, M. & Adachi, O. (1995) Three distinct quinoprotein alcohol dehydrogenases are expressed when Pseudomonas putida is grown on different alcohols, J. Bacteriol. 177, 2442-2450.
21. Schrover, J. M. J., Frank, J., van Wielink, J. F. & Duine, J. A. (1993) Quaternary structure of quinoprotein ethanol dehydrogenase from Pseudomonas aeruginosa and its reoxidation with a novel cytochrome c from this organism, Biochem. J. 290, 123-127.
22. Yanish-Perron, C., Vieira, J. & Messing, J. (1985) Improved M13 phage cloning vectors and host strains: nucleotid sequence of the M13mp18 and pUC19 vectors, Gene 33, 103-119.
23. 550 from Thiobacillus versutus: cloning, expression in E. coli, and purification of the heterologous holoprotein, J. Bacteriol. 174, 3704-3714.
24. Sambrook, J., Fritsch, E. F. & Maniatis, T. (1989) Maleculur cloning: a labaratory manual, 2nd edn, Cold Spring Habour Laboratory, Cold Spring Harbour NY.
25. Brown, T. (1993) Southern Blotting: Alternate Protocol, in Current protocols in molecular biology (Ausubel, I. & Frederick, M., eds) pp. 2.9.7.-2.9.15, John Wiley & Sons Inc., New York.
26. Laemmli, U. K. (1970) Cleavage of structural proteins during the assembly of the head of Bacteriophage T4, Nature 277, 680-685.
27. Okajima, T., Tanabe, T. & Yasuda, T. (1993) Nonurea sodium dodecyl sulfate-polyacrylamide gel electrophoresis with high-molarity buffers for the separation of proteins and peptides, Anal. Biochem. 211, 293-300.
28. Nesterenko, M. V., Tilley, M. & Upton, S. J. (1994) A simple modification of Blum's silver stain method allows for 30 minute detection of proteins in polyacrylamide gels, J. Biochem. Biophys. Methods 28, 239-242.
29. Schagger, H. & von Jagow, G. (1987) Tricin-sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the separation of proteins in the range from 1 to 100 kDa, Anal. Biochem. 166, 368-379.
30. Gallagher, S., Winston, S. E., Fuller, S. A. & Hurrell, J. G. R. (1997) Immunoblotting and Immunodetection, in Current protocols in molecular biology (Ausubel, 1. & Frederick, M., eds) pp. 10.8.1-10.8.21, John Wiley & Sons Inc., New York.
31. Mutzel, A. (1992) Untersuchungen an der Quinoprotein-Ethanolde-hydrogenase aus Pseudomonas aeruginosa ATCC 17933 and der Quinoprotein-Methanoldehydrogenase aus Methylobacterium OG1, Ph.D. Thesis, Universität Hohenheim, Stuttgart-Hohenheim, Germany.
32. Groves, W. E., Davis, F. C. & Sells, B. H. (1968) Spectrophotometric determination of microgram quantities of protein without nucleic acid interference, Anal. Biochem. 22, 195-210.
33. Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25, 3389-3402.
34. Bairoch, A. & Bucher, P. (1994) Prosite: recent developments, Nucleic Acids Res. 22, 3583-3589.
35. Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994) ClustalW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice, Nucleic Acids Res. 22, 4673-4680.
36. Nielsen, H., Engelbrecht, J., Brunak, S. & von Heijne, G. (1997) Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites, Protein Eng. 10, 1-6.
37. Shine, J. & Dalgarno, L. (1975) Terminal-sequence analysis of bacterial ribosomal RNA. Correlation between the 3′-terminal-polypyrimidin sequence of 16-S RNA and translation specificity of the ribosome, Eur. J. Biochem. 57, 221-230.
38. 550 from Pseudomonas aeruginosa, Biochem. J. 289, 173-178.
39. West, S. E. & Iglewski, B. H. (1988) Codon usage in Pseudomonas aeruginosa, Nucleic Acid Res. 16, 9323-9335.
40. Geiger, O. & Görisch, H. (1986) Crystalline quinoprotein glucose dehydrogenase from Acinetobacter calcoaceticus, Biochemistry 25, 6043-6048.
41. Cleton-Jansen, A.-M., Goosen, N., Vink, K. & van de Putte, P. (1989) Cloning, characterization and DNA sequencing of the gene encoding the Mr 50000 quinoprotein glucose dehydrogenase from Acinetobacter calcoaceticus, Mol. Gen. Genet. 217, 430-436.
42. 553i of Paracoccus denitrificans and characterization of the mutant strain, J. Bacteriol. 173, 6971-6979.
43. Chistoserdova, L. & Lidstrom, M. E. (1997) Molecular and mutational analysis of a DNA region separating two methylotrophy gene clusters in Methylobacterium extorquens AM1, Microbiology 143, 1729-1736.
44. Elsemore, D. A. & Ornston, L. N. (1994) The pca-pob supraoperonic cluster of Acinetobacter calcoaceticus contains quiA, the structural gene for quinate shikimate dehydrogenase, J. Bacteriol. 176, 7659-7666.
45. Cleton-Jansen, A.-M., Goosen, N., Fayet, O. & van de Putte, P. (1990) Cloning, mapping and sequencing of the gene encoding Excherichia coli quinoprotein glucose dehydrogenase, J. Bacteriol. 172, 6308-6315.
46. Cleton-Jansen, A.-M., Goosen, N., Odle, G. & van de Putte, P. (1988) Nucleotide sequence of the gene coding for quinoprotein glucose dehydrogenase from Acinetobacter calcoaceticus, Nucleic. Acids Res. 16, 6228.
47. Cleton-Jansen, A.-M., Dekker, S., van de Putte, P. & Goosen, N. (1991) A single amino acid substitution changes the substrate specificity of quinoprotein glucose dehydrogenase in Gluconobacter oxydans, Mol. Gen. Genet 229, 206-212.
48. Shimao, M., Tamogami, T., Nishi, K. & Harayama, S. (1996) Cloning and characterization of the gene encoding pyrroloquinoline quinone-dependent poly(vinyl alcohol) dehydrogenase of Pseudonionas sp. strain VM15C, Biosci. Biotech. Biochem. 60, 1056-1062.
49. Cha, J. S., Pujol, C. & Kado, C. I. (1997) Identification and characterization of a Pantoea citrea gene encoding glucose dehydrogenase that is essential tor causing pink disease of pineapple, Appl. Environ. Microbiol. 63, 71-76.
50. Matsushita, K., Arents, J. C., Bader, R., Yamada, M., Adachi, O. & Postma, P. W. (1997) Escherichia coli is unable to produce pyrroloquinoline quinone (PQQ), Microbiology 143, 3149-3156.
51. Goodwin, P. M. & Anthony, C. (1995) The biosynthesis of periplasmic electron transport proteins in methylotrophic bacteria, Microbiology 141, 1051-1064.
52. Nunn, D. N., Day, D. & Anthony, C. (1989) The second subunit of methanol dehydrogenase of Methylobacterium extorquens AM1, Biochem. J. 260, 857-862.
53. Anderson, D. J. & Lidstrom, M. E. (1988) The moxFG region encodes four polypeptides in the methanol-oxidizing bacterium Metpylobacterium sp. Strain AM1, J. Bacteriol. 170, 2254-2262.
54. van Spanning, R. J. M., Wansell, C. W., Deboer, T., Hazelaar, M. J. Amazawa, H., Harms, N., Oltmann, L. F. & Stouthammer, A. H. (1991) Isolation and characterization of the moxJ, moxG, moxI, and moxR genes of Paracoccus denitrificans - inactivation of moxJ, moxG, and moxR and the resultant effect on methylotrophic growth, J. Bacteriol. 173, 6948-6961.
55. Lidstrom, M. E. (1995) Genetics of bacterial quinoproteins, Methods Enzymol. 258, 217-227.
56. Springer, A. L., Aumann, A. J. & Lidstrom, M. E. (1998) Sequence and characterization of mxaB, a response regulator involved in regulation of methanol oxidation, and mxaW, a methanol-regulated gene in Methylobacterium extorquens AM1, FEMS Microbiol. Lett. 160, 119-124.
57. Lidstrom, M. E., Anthony, C., Biville, F., Gasser, F. Goodwin, P., Hanson, R. S. & Harms, N. (1994) New unified nomenclature for genes involved in the oxidation of methanol in Gram-negative bacteria, FEMS Microbiol. Lett. 117, 103-106.
58. White, S., Boyd, G., Mathews, S., Xia, Z.-x., Dai, W.-w., Zhang, Y.-f. & Davidson, V. L. (1993) The active site structure of the Ca-containing quinoprotein methanol dehydrogenase, Biochemistry 32, 12455-12958.
59. Blake, C. C. F. Ghosh, M., Harlos, K., Avezoux, A. & Anthony, C. (1994) The active site of methanol dehydrogenase contains a disulphide bridge between adjacent cysteine residues. Nature Struct. Biol. 1, 102-105.
60. Creighton, T. E. (1980) Counting integral numbers of amino acid residues per polypeptide chain, Nature 284, 487-489.
61. Avezoux, A., Goodwin, M. G. & Anthony, C. (1995) The role of the novel disulphide ring in the active site of the quinoprotein methanol dehydrogenase from Methylobacterium extorquens, Biochem. J. 307, 735-741.
62. Matsushita, K., Shinagawa, E., Adachi, O. & Ameyama, M. (1989) Reactivity with ubiquinone of quinoprotein D-glucose dehydrogenase from Gluconobacter suboxydans, J. Biochem. 105, 633-637.
63. Xia, Z.-x., Dai, W.-w., Xiong, J.-p., Hao, Z.-p., Davidson, V. L., White, S. & Mathews, F. S. (1992) The three-dimensional structures of methanol dehydrogenase from two methylotrophic bacteria at 2.6-Å resolution, J. Biol. Chem. 267, 22289-22297.
64. Anthony, C., Ghosh, M. & Blake, C. C. F. (1994) The structure and function of methanol dehydrogenase and related proteins containing pyrroloquinoline quinone, Biochem. J. (Tokyo) 304, 665-674.