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Volume 155, Issue 6

Kinetic characterization of the soluble butane monooxygenase from , formerly ‘’ Free

Abstract

Soluble butane monooxygenase (sBMO), a three-component di-iron monooxygenase complex expressed by the C–C alkane-utilizing bacterium , was kinetically characterized by measuring substrate specificities for C–C alkanes and product inhibition profiles. sBMO has high sequence homology with soluble methane monooxygenase (sMMO) and shares a similar substrate range, including gaseous and liquid alkanes, aromatics, alkenes and halogenated xenobiotics. Results indicated that butane was the preferred substrate (defined by  :  ratios). Relative rates of oxidation for C–C alkanes differed minimally, implying that substrate specificity is heavily influenced by differences in substrate values. The low micromolar for linear C–C alkanes and the millimolar for methane demonstrate that sBMO is two to three orders of magnitude more specific for physiologically relevant substrates of . Methanol, the product of methane oxidation and also a substrate itself, was found to have similar and values to those of methane. This inability to kinetically discriminate between the C alkane and C alcohol is observed as a steady-state concentration of methanol during the two-step oxidation of methane to formaldehyde by sBMO. Unlike methanol, alcohols with chain length C–C do not compete effectively with their respective alkane substrates. Results from product inhibition experiments suggest that the geometry of the active site is optimized for linear molecules four to five carbons in length and is influenced by the regulatory protein component B (butane monooxygenase regulatory component; BMOB). The data suggest that alkane oxidation by sBMO is highly specialized for the turnover of C–C alkanes and the release of their respective alcohol products. Additionally, sBMO is particularly efficient at preventing methane oxidation during growth on linear alkanes ≥C despite its high sequence homology with sMMO. These results represent, to the best of our knowledge, the first kinetic characterization of the closest known homologue of sMMO.

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Keyword(s): BMOB, butane monooxygenase regulatory component , BMOH, butane monooxygenase hydroxylase , BMOR, butane monooxygenase reductase , MMOB, methane monooxygenase regulatory component , MMOH, methane monooxygenase hydroxylase , sBMO, soluble butane monooxygenase , sMMO, soluble methane monooxygenase and WT, wild-type
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2009-06-01
2024-04-26
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References

  1. Arp D. J. 1999; Butane metabolism by butane-grown ‘ Pseudomonas butanovora ’. Microbiology 145:1173–1180
     [Google Scholar]
  2. Ausubel F. M., Brent R., Kingston R. E., Moore D. D., Seidman J. G., Smith J. A., Struhl K. 2003 Current Protocols in Molecular Biology New York: Green Publishing & Wiley Interscience;
  3. Borodina E., Nichol T., Dumont M. G., Smith T. J., Murrell J. C. 2007; Mutagenesis of the “leucine gate” to explore the basis of catalytic versatility in soluble methane monooxygenase. Appl Environ Microbiol 73:6460–6467
     [Google Scholar]
  4. Burton S. G. 2003; Oxidizing enzymes as biocatalysts. Trends Biotechnol 21:543–549
     [Google Scholar]
  5. Colby J., Stirling D. I., Dalton H. 1977; The soluble methane mono-oxygenase of Methylococcus capsulatus (Bath). Its ability to oxygenate n -alkanes, n -alkenes, ethers, and alicyclic, aromatic and heterocyclic compounds. Biochem J 165:395–402
     [Google Scholar]
  6. Cornish-Bowden A. 1995 Fundamentals of Enzyme Kinetics p– 108 London: Portland Press Ltd;
  7. Doughty D. M., Halsey K. H., Vieville C. J., Sayavedra-Soto L. A., Arp D. J., Bottomley P. J. 2007; Propionate inactivation of butane monooxygenase activity in ‘ Pseudomonas butanovora ’: biochemical and physiological implications. Microbiology 153:3722–3729
     [Google Scholar]
  8. Dubbels B. L., Sayavedra-Soto L. A., Arp D. J. 2007; Butane monooxygenase of ‘ Pseudomonas butanovora ’: purification and biochemical characterization of a terminal-alkane hydroxylating diiron monooxygenase. Microbiology 153:1808–1816
     [Google Scholar]
  9. Dubbels B. L., Sayavedra-Soto L. A., Bottomley P. J., Arp D. J. 2009; Thauera butanivorans sp. nov., a C2–C9 alkane oxidizing bacterium previously referred to as ‘ Pseudomonas butanovora ’. Int J Syst Evol Microbiol in press
    [Google Scholar]
  10. Elliott S. J., Zhu M., Tso L., Nguyen H. H. T., Yip J. H. K., Chan S. I. 1997; Regio- and stereoselectivity of particulate methane monooxygenase from Methylococcus capsulatus (Bath. J Am Chem Soc 119:9949–9955
     [Google Scholar]
  11. Enzien M. V., Picardal F., Hazen T. C., Arnold R. G., Fliermans C. B. 1994; Reductive dechlorination of trichloroethylene and tetrachloroethylene under aerobic conditions in a sediment column. Appl Environ Microbiol 60:2200–2204
     [Google Scholar]
  12. Froland W. A., Andersson K. K., Lee S. K., Liu Y., Lipscomb J. D. 1992; Methane monooxygenase component B and reductase alter the regioselectivity of the hydroxylase component-catalyzed reactions. A novel role for protein–protein interactions in an oxygenase mechanism. J Biol Chem 267:17588–17597
     [Google Scholar]
  13. Funhoff E. G., Bauer U., Garcia-Rubio I., Witholt B., van Beilen J. B. 2006; CYP153A6, a soluble P450 oxygenase catalyzing terminal-alkane hydroxylation. J Bacteriol 188:5220–5227
     [Google Scholar]
  14. Green J., Dalton H. 1986; Steady-state kinetic analysis of soluble methane mono-oxygenase from Methylococcus capsulatus (Bath. Biochem J 236:155–162
     [Google Scholar]
  15. Halsey K. H., Sayavedra-Soto L. A., Bottomley P. J., Arp D. J. 2006; Site-directed amino acid substitutions in the hydroxylase α subunit of butane monooxygenase from Pseudomonas butanovora : implications for substrates knocking at the gate. J Bacteriol 188:4962–4969
     [Google Scholar]
  16. Halsey K. H., Doughty D. M., Sayavedra-Soto L. A., Bottomley P. J., Arp D. J. 2007; Evidence for modified mechanisms of chloroethene oxidation in Pseudomonas butanovora mutants containing single amino acid substitutions in the hydroxylase α -subunit of butane monooxygenase. J Bacteriol 189:5068–5074
     [Google Scholar]
  17. Johnson E. L., Hyman M. R. 2006; Propane and n -butane oxidation by Pseudomonas putida GPo1. Appl Environ Microbiol 72:950–952
     [Google Scholar]
  18. Korth H.-G., Sicking W. 1997; Prediction of methyl C–H bond dissociation energies by density functional theory calculations. J Chem Soc, Perkin Trans 2:715–719
     [Google Scholar]
  19. Kotani T., Yamamoto T., Yurimoto H., Sakai Y., Kato N. 2003; Propane monooxygenase and NAD+-dependent secondary alcohol dehydrogenase in propane metabolism by Gordonia sp. strain TY-5. J Bacteriol 185:7120–7128
     [Google Scholar]
  20. Kotani T., Kawashima Y., Yurimoto H., Kato N., Sakai Y. 2006; Gene structure and regulation of alkane monooxygenases in propane-utilizing Mycobacterium sp. TY-6 and Pseudonocardia sp. TY-7. J Biosci Bioeng 102:184–192
     [Google Scholar]
  21. Leahy J. G., Batchelor P. J., Morcomb S. M. 2003; Evolution of the soluble diiron monooxygenases. FEMS Microbiol Rev 27:449–479
     [Google Scholar]
  22. Lee S. K., Nesheim J. C., Lipscomb J. D. 1993; Transient intermediates of the methane monooxygenase catalytic cycle. J Biol Chem 268:21569–21577
     [Google Scholar]
  23. Leskovac V. 2003 Comprehensive Enzyme Kinetics New York: Kluwer Academic/Plenum Publishers;
  24. Li Q., Sritharathikhun P., Motomizu S. 2007; Development of novel reagent for Hantzsch reaction for the determination of formaldehyde by spectrophotometry and fluorometry. Anal Sci 23:413–417
     [Google Scholar]
  25. Lide D. R., Frederikse H. P. R. 1995 CRC Handbook of Chemistry and Physics Boca Raton, FL: CRC Press;
  26. Lopes Ferreira N., Mathis H., Labbe D., Monot F., Greer C. W., Fayolle-Guichard F. 2007; n -Alkane assimilation and tert -butyl alcohol (TBA) oxidation capacity in Mycobacterium austroafricanum strains. Appl Microbiol Biotechnol 75:909–919
     [Google Scholar]
  27. Mitic N., Schwartz J. K., Brazeau B. J., Lipscomb J. D., Solomon E. I. 2008; CD and MCD studies of the effects of component B variant binding on the biferrous active site of methane monooxygenase. Biochemistry 47:8386–8397
     [Google Scholar]
  28. Murray L. J., Naik S. G., Ortillo D. O., Garcia-Serres R., Lee J. K., Huynh B. H., Lippard S. J. 2007; Characterization of the arene-oxidizing intermediate in ToMOH as a diiron(III) species. J Am Chem Soc 129:14500–14510
     [Google Scholar]
  29. Nesheim J. C., Lipscomb J. D. 1996; Large kinetic isotope effects in methane oxidation catalyzed by methane monooxygenase: evidence for C–H bond cleavage in a reaction cycle intermediate. Biochemistry 35:10240–10247
     [Google Scholar]
  30. Pace C. N., Shirley B. A., McNutt M., Gajiwala K. 1996; Forces contributing to the conformational stability of proteins. FASEB J 10:75–83
     [Google Scholar]
  31. Parales R. E., Bruce N. C., Schmid A., Wackett L. P. 2002; Biodegradation, biotransformation, and biocatalysis (B3. Appl Environ Microbiol 68:4699–4709
     [Google Scholar]
  32. Percival M. D. 1991; Human 5-lipoxygenase contains an essential iron. J Biol Chem 266:10058–10061
     [Google Scholar]
  33. Rosenzweig A. C., Brandstetter H., Whittington D. A., Nordlund P., Lippard S. J., Frederick C. A. 1997; Crystal structures of the methane monooxygenase hydroxylase from Methylococcus capsulatus (Bath): implications for substrate gating and component interactions. Proteins 29:141–152
     [Google Scholar]
  34. Sambrook J., Fritsch E. F., Maniatis T. 1989 Molecular Cloning: a Laboratory Manual Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
  35. Sayavedra-Soto L. A., Doughty D. M., Kurth E. G., Bottomley P. J., Arp D. J. 2005; Product and product-independent induction of butane oxidation in Pseudomonas butanovora . FEMS Microbiol Lett 250:111–116
     [Google Scholar]
  36. Sazinsky M. H., Lippard S. J. 2005; Product bound structures of the soluble methane monooxygenase hydroxylase from Methylococcus capsulatus (Bath): protein motion in the α -subunit. J Am Chem Soc 127:5814–5825
     [Google Scholar]
  37. Schwartz J. K., Wei P. P., Mitchell K. H., Fox B. G., Solomon E. I. 2008; Geometric and electronic structure studies of the binuclear nonheme ferrous active site of toluene-4-monooxygenase: parallels with methane monooxygenase and insight into the role of the effector proteins in O2 activation. J Am Chem Soc 130:7098–7109
     [Google Scholar]
  38. Shennan J. L. 2006; Utilisation of C2–C4 gaseous hydrocarbons and isoprene by microorganisms. J Chem Technol Biotechnol 81:237–256
     [Google Scholar]
  39. Shu L., Nesheim J. C., Kauffmann K., Munck E., Lipscomb J. D., Que L. Jr 1997; An Fe2 IVO2 diamond core structure for the key intermediate Q of methane monooxygenase. Science 275:515–518
     [Google Scholar]
  40. Sluis M. K., Sayavedra-Soto L. A., Arp D. J. 2002; Molecular analysis of the soluble butane monooxygenase from ‘ Pseudomonas butanovora ’. Microbiology 148:3617–3629
     [Google Scholar]
  41. Smith T. J., Dalton H. 2004; Biocatalysis by methane monooxygenase and its implications for the petroleum industry. In Petroleum Biotechnology , Developments and Perspectives pp 177–192 Edited by Vazquez-Duhalt R., Qintero-Ramirez R. Amsterdam: Elsevier;
     [Google Scholar]
  42. Smith C. A., O'Reilly K. T., Hyman M. R. 2003; Characterization of the initial reactions during the cometabolic oxidation of methyl tert -butyl ether by propane-grown Mycobacterium vaccae JOB5. Appl Environ Microbiol 69:796–804
     [Google Scholar]
  43. Tabor S., Richardson C. C. 1985; A bacteriophage T7 RNA polymerase/promoter system for controlled exclusive expression of specific genes. Proc Natl Acad Sci U S A 82:1074–1078
     [Google Scholar]
  44. Takahashi J., Ichikawa Y., Sagae H., Komura I., Kanou H., Yamada K. 1980; Isolation and identification of n -butane assimilating bacterium. Agric Biol Chem 44:1835–1840
     [Google Scholar]
  45. van Beilen J. B., Funhoff E. G. 2007; Alkane hydroxylases involved in microbial alkane degradation. Appl Microbiol Biotechnol 74:13–21
     [Google Scholar]
  46. van Beilen J. B., Kingma J., Witholt B. 1994; Substrate specificity of the alkane hydroxylase system of Pseudomonas oleovorans GPo1. Enzyme Microb Technol 16:904–911
     [Google Scholar]
  47. Vangnai A. S., Arp D. J. 2001; An inducible 1-butanol dehydrogenase, a quinohaemoprotein, is involved in the oxidation of butane by ‘ Pseudomonas butanovora ’. Microbiology 147:745–756
     [Google Scholar]
  48. Vangnai A. S., Sayavedra-Soto L. A., Arp D. J. 2002; Roles for the two 1-butanol dehydrogenases of Pseudomonas butanovora in butane and 1-butanol metabolism. J Bacteriol 184:4343–4350
     [Google Scholar]
  49. Wallar B. J., Lipscomb J. D. 1996; Dioxygen activation by enzymes containing binuclear non-heme iron clusters. Chem Rev 96:2625–2658
     [Google Scholar]
  50. Wallar B. J., Lipscomb J. D. 2001; Methane monooxygenase component B mutants alter the kinetics of steps throughout the catalytic cycle. Biochemistry 40:2220–2233
     [Google Scholar]
  51. Werner D. S., Lee T. R., Lawrence D. S. 1996; Is protein kinase substrate efficacy a reliable barometer for successful inhibitor design?. J Biol Chem 271:180–185
     [Google Scholar]
  52. Zheng H., Lipscomb J. D. 2006; Regulation of methane monooxygenase catalysis based on size exclusion and quantum tunneling. Biochemistry 45:1685–1692
     [Google Scholar]
  53. Zhu C. Z., Ouyang B., Wang J. Q., Huang L., Dong W. B., Hou H. Q. 2007; Photochemistry in the mixed aqueous solution of nitrobenzene and nitrous acid as initiated by the 355 nm UV light. Chemosphere 67:855–861
     [Google Scholar]
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Kinetic characterization of the soluble butane monooxygenase from Thauera butanivorans, formerly ‘Pseudomonas butanovora’
Microbiology 155, 2086 (2009); https://doi.org/10.1099/mic.0.028175-0
/content/journal/micro/10.1099/mic.0.028175-0
/content/journal/micro/10.1099/mic.0.028175-0
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