Skip to main content

Engineering Soluble Methane Monooxygenase for Biocatalysis

  • Chapter
  • First Online:
Methane Biocatalysis: Paving the Way to Sustainability

Abstract

Soluble methane monooxygenase (sMMO) has more than 100 known substrates in addition to its natural substrate methane. It is one of the most versatile and powerful biological oxidation catalysts, although regioselectivity and enantioselectivity with the wild-type enzyme are generally low. Protein engineering of sMMO has presented a major challenge because attempts to express the active site-containing hydroxylase component of the enzyme in Escherichia coli have to date been unsuccessful. Use of a homologous expression system, in which the enzyme is expressed in a methane-oxidising bacterium where the chromosomal copy of the sMMO genes is deleted, has allowed construction, expression and purification of active mutant enzymes. This work has given the first indications for the roles of specific amino acids in the hydroxylase component of sMMO in substrate oxidation and control of regioselectivity. Most recently, an enzyme with significantly improved activity and regioselectivity with a diaromatic substrate has been prepared. It is hoped that future work will produce recombinant sMMO derivatives developed for the production of high-value fine and bulk chemicals.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Bailey LJ, Elsen NL, Pierce BS, Fox BG (2008) Soluble expression and purification of the oxidoreductase component of toluene 4-monooxygenase. Protein Expr Purif 57:9–16

    Article  CAS  PubMed  Google Scholar 

  • Banerjee R, Proshlyakov Y, Lipscomb JD, Proshlyakov DA (2015) Structure of the key species in the enzymatic oxidation of methane to methanol. Nature 518:431–434

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Blatny JM, Brautaset T, Winther-Larsen HC, Haugan K, Valla S (1997) Construction and use of a versatile set of broad-host-range cloning and expression vectors based on the RK2 replicon. Appl Environ Microbiol 63:370–379

    PubMed  PubMed Central  CAS  Google Scholar 

  • Borodina E, Nichol T, Dumont MG, Smith TJ, Murrell JC (2007) Mutagenesis of the “leucine gate” to explore the basis of catalytic versatility in soluble methane monooxygenase. Appl Environ Microbiol 73:6460–6467

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Brazeau BJ, Lipscomb JD (2003) Key amino acid residues in the regulation of soluble methane monooxygenase catalysis by component B. Biochemistry 42:5618–5631

    Article  CAS  PubMed  Google Scholar 

  • Brazeau BJ, Wallar BJ, Lipscomb JD (2003) Effector proteins from P450cam and methane monooxygenase: lessons in tuning nature’s powerful reagents. Biochem Biophys Res Commun 312:143–148

    Article  CAS  PubMed  Google Scholar 

  • Brusseau GA, Tsien H-C, Hanson RS, Wackett LP (1990) Optimization of trichloroethylene oxidation by methanotrophs and the use of a colorimetric assay to detect soluble methane mono-oxygenase activity. Biodegradation 1:19–29

    Article  CAS  PubMed  Google Scholar 

  • Burrows KJ, Cornish A, Scott D, Higgins IJ (1984) Substrate specificities of the soluble and particulate methane mono-oxygenases of Methylosinus trichosporium OB3b. J Gen Microbiol 130:3327–3333

    CAS  Google Scholar 

  • Callaghan AJ, Smith TJ, Slade SE, Dalton H (2002) Residues near the N-terminus of protein B control autocatalytic proteolysis and the activity of soluble methane monooxygenase. Eur J Biochem 269:1835–1843

    Article  CAS  PubMed  Google Scholar 

  • Chang S-L, Wallar BJ, Lipscomb JD, Mayo KH (1999) Solution structure of component B from methane monooxygenase derived through heteronuclear NMR and molecular modeling. Biochemistry 38:5799–5812

    Article  CAS  PubMed  Google Scholar 

  • Chatwood LL, Müller J, Gross JD, Wagner G, Lippard SJ (2004) NMR Structure of the flavin domain from soluble methane monooxygenase reductase from Methylococcus capsulatus (Bath). Biochemistry 43:11983–11991

    Article  CAS  PubMed  Google Scholar 

  • Colby J, Stirling DI, Dalton H (1977) The soluble methane monooxygenase of Methylococcus capsulatus (Bath): its ability to oxygenate n-alkanes, n-alkenes, ethers, and alicyclic, aromatic and heterocyclic compounds. Biochem J 165:395–402

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Coleman NV, Bui NB, Holmes AJ (2006) Soluble di-iron monooxygenase gene diversity in soils, sediments and ethene enrichments. Environ Microbiol 8:1228–1239

    Article  CAS  PubMed  Google Scholar 

  • Coufal DE, Blazyk JL, Whittington DA, Wu WW, Rosenzweig AC, Lippard SJ (2000) Sequencing and analysis of the Methylococcus capsulatus (Bath) soluble methane monooxygenase genes. Eur J Biochem 267:2174–2185

    Article  CAS  PubMed  Google Scholar 

  • Dedysh SN, Knief C, Dunfield PF (2005) Methylocella species are facultatively methanotrophic. J Bacteriol 187:4665–4670

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • DeWitt JG, Bentsen JG, Rosenzweig AC, Hedman B, Green J, Pilkington S, Papaefthymiou GC, Dalton H, Hodgson KO, Lippard SJ (1991) X-ray absorption, Mössbauer, and EPR studies of the dinuclear iron center in the hydroxylase component of methane monooxygenase. J Am Chem Soc 113:9219–9235

    Article  CAS  Google Scholar 

  • Elango N, Radmakrishnan R, Froland WA, Wallar BJ, Earhart CA, Lipscomb JD, Ohlendorf DH (1997) Crystal structure of the hydroxylase component of methane monooxygenase from Methylosinus trichosporium OB3b. Protein Sci 6:556–568

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fox BG, Liu Y, Dege JE, Lipscomb JD (1991) Complex formation between the protein components of methane monooxygenase from Methylosinus trichosporium OB3b. J Biol Chem 266:540–550

    PubMed  CAS  Google Scholar 

  • George AR, Wilkins PC, Dalton H (1996) A computational investigation of the possible substrate binding sites in the hydroxylase of soluble methane monooxygenase. J Molec Catal B 2:103–113

    Article  CAS  Google Scholar 

  • Green J, Dalton H (1989) Substrate specificity of soluble methane monooxygenase – mechanistic implications. J Biol Chem 264:17698–17703

    PubMed  CAS  Google Scholar 

  • Hakemian AS, Rosenzweig AC (2007) The biochemistry of methane oxidation. Ann Rev Biochem 76:223–241

    Article  CAS  PubMed  Google Scholar 

  • Jahng D, Wood TK (1994) Trichloroethylene and chloroform degradation by a recombinant pseudomonad expressing soluble methane monooxygenase from Methylosinus trichosporium OB3b. Appl Environ Microbiol 60:2473–2482

    PubMed  PubMed Central  CAS  Google Scholar 

  • Jahng D, Kim CS, Hanson RS, Wood TK (1996) Optimization of trichloroethylene degradation using soluble methane monooxygenase of Methylosinus trichosporium OB3b expressed in recombinant bacteria. Biotechnol Bioeng 51:349–359

    Article  CAS  PubMed  Google Scholar 

  • Jiang H, Chen Y, Jiang P, Zhang C, Smith TJ, Murrell JC, Xing X-H (2010) Methanotrophs: multifunctional bacteria with promising applications in environmental bioengineering. Biochem Eng J 49:277–288

    Article  CAS  Google Scholar 

  • Johnson GR, Olsen RH (1995) Nucleotide-sequence analysis of genes encoding a toluene benzene-2-monooxygenase from Pseudomonas sp. strain JS150. Appl Environ Microbiol 61:3336–3346

    PubMed  PubMed Central  CAS  Google Scholar 

  • Leahy JG, Batchelor PJ, Morcomb SM (2003) Evolution of the soluble diiron monooxygenases. FEMS Microbiol Rev 27:449–479

    Article  CAS  PubMed  Google Scholar 

  • Lee SJ, McCormick MS, Lippard SJ, Cho US (2013) Control of substrate access to the active site in methane monooxygenase. Nature 494:380–384

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lewis JC, Coelho PS, Arnold FH (2011) Enzymatic functionalization of carbon–hydrogen bonds. Chem Soc Rev 40:2003–2021

    Article  CAS  PubMed  Google Scholar 

  • Lindner AS, Adriaens P, Semrau JD (2000) Transformation of ortho-substituted biphenyls by Methylosinus trichosporium OB3b: substituent effects on oxidation kinetics and product formation. Arch Microbiol 174:35–41

    Article  CAS  PubMed  Google Scholar 

  • Lipscomb JD (1994) Biochemistry of the soluble methane monooxygenase. Ann Rev Microbiol 48:371–399

    Article  CAS  Google Scholar 

  • Lloyd JS, Bhambra A, Murrell JC, Dalton H (1997) Inactivation of the regulatory protein B of soluble methane monooxygenase from Methylococcus capsulatus (Bath) by proteolysis can be overcome by a Gly to Gln modification. Eur J Biochem 248:72–79

    Article  CAS  PubMed  Google Scholar 

  • Lloyd JS, DeMarco P, Dalton H, Murrell JC (1999a) Heterologous expression of soluble methane monooxygenase genes in methanotrophs containing only particulate methane monooxygenase. Arch Microbiol 171:364–370

    Article  CAS  PubMed  Google Scholar 

  • Lloyd JS, Finch R, Dalton H, Murrell JC (1999b) Homologous expression of soluble methane monooxygenase genes in Methylosinus trichosporium OB3b. Microbiology 145:461–470

    Article  CAS  PubMed  Google Scholar 

  • Lock M, Nichol T, Murrell JC, Smith TJ (2017) Mutagenesis and expression of methane monooxygenase to alter regioselectivity with aromatic substrates. FEMS Microbiol Lett 364. https://doi.org/10.1093/femsle/fnx137

  • Martin H, Murrell JC (1995) Methane monooxygenase mutants of Methylosinus trichosporium constructed by marker-exchange mutagenesis. FEMS Microbiol Lett 127:243–248

    Article  CAS  Google Scholar 

  • Merkx M, Lippard SJ (2002) Why OrfY? Characterization of MmoD, a long overlooked component of the soluble methane monooxygenase from Methylococcus capsulatus (Bath). J Biol Chem 277:5858–5865

    Article  CAS  PubMed  Google Scholar 

  • Nordlund P, Dalton H, Ecklund H (1992) The active-site structure of methane monooxygenase is closely related to the binuclear iron center of ribonucleotide reductase. FEBS Lett 307:257–262

    Article  CAS  PubMed  Google Scholar 

  • Pikus JD, Studts JM, McClay K, Steffan RJ, Fox BG (1997) Changes in the regiospecificity of aromatic hydroxylation produced by active site engineering in the diiron enzyme toluene 4-monooxygenase. Biochemistry 36:9283–9289

    Article  CAS  PubMed  Google Scholar 

  • Richards AO, Stanley SH, Suzuki M, Dalton H (1994) The biotransformation of propylene to propylene oxide by Methylococcus capsulatus (Bath): 3. Reactivation of inactivated whole cells to give a high productivity system. Biocatalysis 8:253–267

    Article  CAS  Google Scholar 

  • Rosenzweig AC, Frederick CA, Lippard SJ, Nordlund P (1993) Crystal structure of a bacterial nonheme iron hydroxylase that catalyzes the biological oxidation of methane. Nature 366:537–543

    Article  CAS  PubMed  Google Scholar 

  • Rosenzweig AC, Nordlund P, Takahara PM, Frederick CA, Lippard SJ (1995) Geometry of the soluble methane monooxygenase catalytic diiron center in two oxidation states. Chem Biol 2:409–418

    Article  CAS  PubMed  Google Scholar 

  • Rosenzweig AC, Brandstetter H, Whittington DA, Nordlund P, Lippard SJ, Frederick CA (1997) Crystal structure of the methane monooxygenase hydroxylase from Methylococcus capsulatus (Bath): implications for substrate gating and component interactions. Proteins 29:141–152

    Article  CAS  PubMed  Google Scholar 

  • Saeki H, Furuhashi K (1994) Cloning and characterisation of the Nocardia corallina B-276 gene cluster encoding alkene monooxygenase. J Ferment Bioeng 78:399–406

    Article  CAS  Google Scholar 

  • Semrau JD, Jagadevan S, DiSpirito AA, Khalifa A, Scanlan J, Bergman BH, Freemeier BC, Baral BS, Bandow NL, Vorobev A, Haft DH, Vuilleumier S, Murrell JC (2013) Methanobactin and MmoD work in concert to act as the ‘copper switch’ in methanotrophs. Environ Microbiol 15:3077–3086

    PubMed  CAS  Google Scholar 

  • Shu L, Nesheim JC, Kauffmann K, Münck E, Lipscomb JD, Que L (1997) An FeIV2O2 diamond core structure for the key intermediate Q of methane monooxygenase. Science 275:515–517

    Article  CAS  PubMed  Google Scholar 

  • Sjöberg B-M (1997) Ribonucleotide reducatases – a group of enzymes with different metallosites and a similar reaction mechanism. Struct Bond 88:139–173

    Article  Google Scholar 

  • Smith TJ, Dalton H (2004) Biocatalysis by methane monooxygenase and its implications for the petroleum industry. Stud Surface Sci Catal 151:177–192

    Article  CAS  Google Scholar 

  • Smith TJ, Murrell JC (2009) Methanotrophy/methane oxidation. In: Schaechter M (ed) Encyclopedia of microbiology, vol 3. Elsevier, San Diego, CA, pp 293–298

    Chapter  Google Scholar 

  • Smith TJ, Murrell JC (2011) Mutagenesis of soluble methane monooxygenase. Methods Enzymol 495:135–147

    Article  CAS  PubMed  Google Scholar 

  • Smith TJ, Slade SE, Burton NP, Murrell JC, Dalton H (2002) Improved system for protein engineering of the hydroxylase component of soluble methane monooxygenase. Appl Environ Microbiol 68:5265–5273

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stafford GP, Scanlan J, McDonald IR, Murrell JC (2003) rpoN, mmoR and mmoG, genes involved in regulating the expression of soluble methane monooxygenase in Methylosinus trichosporium OB3b. Microbiology 149:1771–1784

    Article  CAS  PubMed  Google Scholar 

  • Stanley SH, Prior SD, Leak DJ, Dalton H (1983) Copper stress underlies the fundamental change in intracellular location of methane monooxygenase in methane-oxidizing organisms – studies in batch and continuous cultures. Biotechnol Lett 5:487–492

    Article  CAS  Google Scholar 

  • Wang W, Lippard SJ (2014) Diiron oxidation state control of substrate access to the active site of soluble methane monooxygenase mediated by the regulatory component. J Am Chem Soc 136:2244–2247

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • West CA, Salmond GPC, Dalton H, Murrell JC (1992) Functional expression in Escherichia coli of protein B and protein C from soluble methane monooxygenase of Methylococcus capsulatus (Bath). J Gen Microbiol 138:1301–1307

    Article  CAS  PubMed  Google Scholar 

  • Whittington DA, Rosenzweig AC, Frederick CA, Lippard SJ (2001) Xenon and halogenated alkanes track putative substrate binding cavities in the soluble methane monooxygenase hydroxylase. Biochemistry 40:3476–3482

    Article  CAS  PubMed  Google Scholar 

  • Zhou NY, Jenkins A, Chion CKNCK, Leak DJ (1999) The alkene monooxygenase from Xanthobacter strain Py2 is closely related to aromatic monooxygenases and catalyzes aromatic monohydroxylation of benzene, toluene, and phenol. Appl Environ Microbiol 65:1589–1595

    PubMed  PubMed Central  CAS  Google Scholar 

Download references

Acknowledgements

TJS gratefully acknowledges funding for work on expression and mutagenesis of sMMO from the Biotechnology and Biological Sciences Research Council and the Biomolecular Sciences Research Centre at Sheffield Hallam University.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Thomas J. Smith .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer International Publishing AG, part of Springer Nature

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Smith, T.J., Nichol, T. (2018). Engineering Soluble Methane Monooxygenase for Biocatalysis. In: Kalyuzhnaya, M., Xing, XH. (eds) Methane Biocatalysis: Paving the Way to Sustainability. Springer, Cham. https://doi.org/10.1007/978-3-319-74866-5_10

Download citation

Publish with us

Policies and ethics