A four-helix bundle stores copper for methane oxidation

Article metrics

Abstract

Methane-oxidizing bacteria (methanotrophs) require large quantities of copper for the membrane-bound (particulate) methane monooxygenase1,2. Certain methanotrophs are also able to switch to using the iron-containing soluble methane monooxygenase to catalyse methane oxidation, with this switchover regulated by copper3,4. Methane monooxygenases are nature’s primary biological mechanism for suppressing atmospheric levels of methane, a potent greenhouse gas. Furthermore, methanotrophs and methane monooxygenases have enormous potential in bioremediation and for biotransformations producing bulk and fine chemicals, and in bioenergy, particularly considering increased methane availability from renewable sources and hydraulic fracturing of shale rock5,6. Here we discover and characterize a novel copper storage protein (Csp1) from the methanotroph Methylosinus trichosporium OB3b that is exported from the cytosol, and stores copper for particulate methane monooxygenase. Csp1 is a tetramer of four-helix bundles with each monomer binding up to 13 Cu(I) ions in a previously unseen manner via mainly Cys residues that point into the core of the bundle. Csp1 is the first example of a protein that stores a metal within an established protein-folding motif. This work provides a detailed insight into how methanotrophs accumulate copper for the oxidation of methane. Understanding this process is essential if the wide-ranging biotechnological applications of methanotrophs are to be realized. Cytosolic homologues of Csp1 are present in diverse bacteria, thus challenging the dogma that such organisms do not use copper in this location.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Figure 1: Identification and purification of Csp1 from M. trichosporium OB3b.
Figure 2: The structure of apo-Csp1.
Figure 3: Cu(I)-binding by Csp1.
Figure 4: Cu(I) affinity of Csp1 and Cu(I) release.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates have been deposited in the Protein Data Bank under accession numbers 5AJE and 5AJF for apo- and Cu(I)-Csp1 respectively.

References

  1. 1

    Hanson, R. S. & Hanson, T. E. Methanotrophic bacteria. Microbiol. Rev. 60, 439–471 (1996)

  2. 2

    Balasubramanian, R. et al. Oxidation of methane by a biological dicopper centre. Nature 465, 115–119 (2010)

  3. 3

    Murrell, J. C., McDonald, I. R. & Gilbert, B. Regulation of expression of methane monooxygenases by copper ions. Trends Microbiol. 8, 221–225 (2000)

  4. 4

    Hakemian, A. S. & Rosenzweig, A. C. The biochemistry of methane oxidation. Annu. Rev. Biochem. 76, 223–241 (2007)

  5. 5

    Jiang, H. et al. Methanotrophs: multifunctional bacteria with promising applications in environmental bioengineering. Biochem. Eng. J. 49, 277–288 (2010)

  6. 6

    Haynes, C. A. & Gonzalez, R. Rethinking biological activation of methane and conversion to liquid fuels. Nature Chem. Biol. 10, 331–339 (2014)

  7. 7

    Ma, Z., Jacobsen, F. E. & Giedroc, D. P. Coordination chemistry of bacterial metal transport and sensing. Chem. Rev. 109, 4644–4681 (2009)

  8. 8

    Festa, R. A. & Thiele, D. J. Copper: an essential metal in biology. Curr. Biol. 21, R877–R883 (2011)

  9. 9

    Argüello, J. M., Raimunda, D. & Padilla-Benavides, T. Mechanisms of copper homeostasis in bacteria. Front. Cell. Infect. Microbiol. 3, 73 (2013)

  10. 10

    Poutney, D. L., Schauwecker, I., Zarn, J. & Vašák, M. Formation of mammalian Cu8-metallothionein in vitro: evidence for the existence of two Cu(I)4-thiolate clusters. Biochemistry 33, 9699–9705 (1994)

  11. 11

    Calderone, V. et al. The crystal structure of yeast copper thionein: the solution of a long-lasting enigma. Proc. Natl Acad. Sci. USA 102, 51–56 (2005)

  12. 12

    Sutherland, D. E. K. & Stillman, M. J. The “magic numbers” of metallothionein. Metallomics 3, 444–463 (2011)

  13. 13

    Gold, B. et al. Identification of a copper-binding metallothionein in pathogenic bacteria. Nature Chem. Biol. 4, 609–616 (2008)

  14. 14

    Davies, S. L. & Whittenbury, R. Fine structure of methane and other hydrocarbon-utilising bacteria. J. Gen. Microbiol. 61, 227–232 (1970)

  15. 15

    Reed, W. M., Titus, J. A., Dugan, P. R. & Pfister, R. M. Structure of Methylosinus trichosporium exospores. J. Bacteriol. 141, 908–913 (1980)

  16. 16

    Kim, H. J. et al. Methanobactin, a copper-acquisition compound from methane-oxidizing bacteria. Science 305, 1612–1615 (2004)

  17. 17

    El Ghazouani, A. et al. Copper-binding properties and structures of methanobactins from Methylosinus trichosporium OB3b. Inorg. Chem. 50, 1378–1391 (2011)

  18. 18

    El Ghazouani, A. et al. Variations in methanobactin structure influence copper utilization by methane-oxidizing bacteria. Proc. Natl Acad. Sci. USA 109, 8400–8404 (2012)

  19. 19

    Balasubramanian, R., Kenney, G. E. & Rosenzweig, A. C. Dual pathways for copper uptake by methanotrophic bacteria. J. Biol. Chem. 286, 37313–37319 (2011)

  20. 20

    Semrau, J. D. et al. Methanobactin and MmoD work in concert to act as the ‘copper-switch’ in methanotrophs. Environ. Microbiol. 15, 3077–3086 (2013)

  21. 21

    Stein, L. Y. et al. Genome sequence of the obligate methanotroph Methylocystis trichosporium strain OB3b. J. Bacteriol. 192, 6497–6498 (2010)

  22. 22

    Barrow, C. J., Yasuda, A., Kenny, P. T. M. & Zagorski, M. G. Solution conformations and aggregational properties of synthetic amyloid β-peptides of Alzheimer’s disease. Analysis of circular dichroism spectra. J. Mol. Biol. 225, 1075–1093 (1992)

  23. 23

    Cobine, P. A. et al. Copper transfer from the Cu(I) chaperone, CopZ, to the repressor, Zn(II)CopY: metal coordination environments and protein interactions. Biochemistry 41, 5822–5829 (2002)

  24. 24

    Badarau, A., Firbank, S. J., McCarthy, A. A., Banfield, M. J. & Dennison, C. Visualizing the metal-binding versatility of copper trafficking sites. Biochemistry 49, 7798–7810 (2010)

  25. 25

    Bagchi, P., Morgan, M. T., Bacsa, J. & Fahrni, C. J. Robust affinity standards for Cu(I) biochemistry. J. Am. Chem. Soc. 135, 18549–18559 (2013)

  26. 26

    Kau, L. S., Spira-Solomon, D. J., Penner-Han, J. E., Hodgson, K. O. & Solomon, E. I. X-ray absorption edge determination of the oxidation state and coordination number of copper: applications to the type 3 site in Rhus vernicifera laccase and its reaction with oxygen. J. Am. Chem. Soc. 109, 6433–6442 (1987)

  27. 27

    Theil, E. C. Ferritin protein nanocages use ion channels, catalytic sites, and nucleation channels to manage iron/oxygen chemistry. Curr. Opin. Chem. Biol. 15, 304–311 (2011)

  28. 28

    Kharenko, O. A., Kennedy, D. C., Demeler, B., Maroney, M. J. & Ogawa, M. Y. Cu(I) luminescence from the tetranuclear Cu4S4 cofactor of a synthetic 4-helix bundle. J. Am. Chem. Soc. 127, 7678–7679 (2005)

  29. 29

    Palmer, T. & Berks, B. C. Moving folded proteins across the bacterial cell membrane. Microbiology 149, 547–556 (2003)

  30. 30

    Tottey, S. et al. Protein-folding location can regulate manganese-binding versus copper- or zinc-binding. Nature 455, 1138–1142 (2008)

  31. 31

    Hellman, U., Wernstedt, C., Gonez, J. & Heldin, C. H. Improvement of an “In-Gel” digestion procedure for the micropreparation of internal protein fragments for amino acid sequencing. Anal. Biochem. 224, 451–455 (1995)

  32. 32

    Bendtsen, J. D., Nielsen, H., Widdick, D., Palmer, T. & Brunak, S. Prediction of twin-arginine signal peptides. BMC Bioinform. 6, 167 (2005)

  33. 33

    Riddles, P. W., Blakeley, R. L. & Zerner, B. Ellman’s reagent: 5,5′-dithiobis(2-nitrobenzoic acid)—a re-examination. Anal. Biochem. 94, 75–81 (1979)

  34. 34

    Riener, C. K., Kada, G. H. & Gruber, J. Quick measurement of protein sulfhydryls with Ellman’s reagent and with 4,4′-dithiodipyridine. Anal. Bioanal. Chem. 373, 266–276 (2002)

  35. 35

    Allen, S., Badarau, A. & Dennison, C. Cu(I) affinities of the domain 1 and 3 sites in the human metallochaperone for Cu,Zn-superoxide dismutase. Biochemistry 51, 1439–1448 (2012)

  36. 36

    Badarau, A. & Dennison, C. Thermodynamics of copper and zinc distribution in the cyanobacterium Synechocystis PCC 6803. Proc. Natl Acad. Sci. USA 108, 13007–13012 (2011)

  37. 37

    Badarau, A. & Dennison, C. Copper trafficking mechanism of CXXC-containing domains: insight from the pH-dependence of their Cu(I) affinities. J. Am. Chem. Soc. 133, 2983–2988 (2011)

  38. 38

    Xiao, Z., Donnelly, P. S., Zimmerman, M. & Wedd, A. G. Transfer of copper between bis(thiosemicarbazone) ligands and intracellular copper-binding proteins. Insights into mechanisms of copper uptake and hypoxia selectivity. Inorg. Chem. 47, 4338–4347 (2008)

  39. 39

    Xiao, Z., Loughlin, F., George, G. N., Howlett, G. J. & Wedd, A. G. C-terminal domain of the membrane copper transporter Ctr1 from Saccharomyces cerevisiae binds four Cu(I) ions as a cuprous-thiolate polynuclear cluster: sub-femtomolar Cu(I) affinity of three proteins involved in copper trafficking. J. Am. Chem. Soc. 126, 3081–3090 (2004)

  40. 40

    Banci, L. et al. Affinity gradients drive copper to cellular destinations. Nature 465, 645–648 (2010)

  41. 41

    Allen, S., Badarau, A. & Dennison, C. The influence of protein folding on the copper affinities of trafficking and target sites. Dalton Trans. 42, 3233–3239 (2013)

  42. 42

    Kabsch, W. XDS. Acta Crystallogr. D 66, 125–132 (2010)

  43. 43

    Evans, P. R. & Murshudov, G. N. How good are my data and what is the resolution? Acta Crystallogr. D 69, 1204–1214 (2013)

  44. 44

    Evans, P. R. Scaling and assessment of data quality. Acta Crystallogr. D 62, 72–82 (2006)

  45. 45

    McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Cryst. 40, 658–674 (2007)

  46. 46

    Winn, M. D. et al. Overview of the CCP4 suite and current developments. Acta Crystallogr. D 67, 235–242 (2011)

  47. 47

    Sheldrick, G. M. Experimental phasing with SHELXC/D/E: combining chain tracing with density modification. Acta Crystallogr. D 66, 479–485 (2010)

  48. 48

    Cowtan, K. Recent developments in classical density modification. Acta Crystallogr. D 66, 470–478 (2010)

  49. 49

    Cowtan, K. The Buccaneer software for automated model building. Acta Crystallogr. D 62, 1002–1011 (2006)

  50. 50

    Vagin, A. & Teplyakov, A. MOLREP: an automated program for molecular replacement. J. Appl. Cryst. 30, 1022–1025 (1997)

  51. 51

    Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D 66, 12–21 (2010)

  52. 52

    Schäfer, A. et al. Small mobilizable multi-purpose cloning vectors derived from the Escherichia coli plasmids pK18 and pK19: selection of defined deletions in the chromosome of Corynebacterium glutamicum . Gene 145, 69–73 (1994)

  53. 53

    Simon, R., Priefer, U. & Puhler, A. A broad host range mobilization system for in vivo genetic engineering: transposon mutagenesis in Gram negative bacteria. Nature Biotechnol. 1, 784–791 (1983)

  54. 54

    Stafford, G. P., Scanlan, J., McDonald, I. R. & Murrell, J. C. rpoN, mmoR and mmoG, genes involved in regulating the expression of soluble methane monooxygenase in Methylosinus trichosporium OB3b. Microbiology 149, 1771–1784 (2003)

  55. 55

    Brusseau, G. A., Tsien, H.-C., Hanson, R. S. & Wackett, L. P. Optimization of trichloroethylene oxidation by methanotrophs and the use of a colorimetric assay to detect soluble methane monooxygenase activity. Biodegradation 1, 19–29 (1990)

  56. 56

    Xie, F., Sutherland, D. E. K., Stillman, N. J. & Ogawa, M. Y. Cu(I) binding properties of a designed metalloprotein. J. Inorg. Biochem. 104, 261–267 (2010)

  57. 57

    Notredame, C., Higgins, D. G. & Heringa, J. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302, 205–217 (2000)

Download references

Acknowledgements

We thank staff of the Diamond Light Source for help with diffraction data collection, J. Gray for performing mass spectrometry studies, the School of Civil Engineering and Geosciences and D. Graham for access to facilities at the very start of this work, A. Badarau for discussions about determining Cu(I) affinities and S. J. Firbank for structural modelling at the initial stages of this project. This work was supported by Biotechnology and Biological Sciences Research Council (grant BB/K008439/1 to C.D. and K.J.W.) and Newcastle University (part funding of a PhD studentship for S.P.). K.J.W. was supported by a Sir Henry Dale Fellowship funded by the Wellcome Trust and the Royal Society (098375/Z/12/Z).

Author information

C.D. and K.J.W. designed the research, N.V. and S.J.A. performed in vitro characterization of Csp1 and Cu(I) binding, S.P. isolated Csp1 from M. trichosporium OB3b and crystallized the protein, A.B. and N.G.P. solved the crystal structures, and A.T.C. and J.C.M. constructed and characterized the Δcsp1csp2 M. trichosporium OB3b strain. C.D. wrote the paper with help from all authors.

Correspondence to Christopher Dennison.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Extended data figures and tables

Extended Data Figure 1 Purification of proteins from M. trichosporium OB3b and the amino-acid sequence of Csp1.

a, The copper content of anion-exchange fractions (NaCl gradient shown as a dashed line) and the SDS–PAGE analysis of selected fractions (1 ml) from the purification of soluble extract from M. trichosporium OB3b cells. The band just below the 14.4 kDa marker, indicated with an arrow, is present. Fraction 32 was judged to have the lowest level of contaminating proteins and was further purified by gel-filtration chromatography on a Superdex 75 column (b). Csp1 is present in the peak that elutes at 11 ml and contains considerable copper (see Fig. 1c). c, The amino-acid sequence of Csp1 showing the predicted Tat leader peptide (the first 24 residues of the pre-protein) in italics. The 13 Cys residues are highlighted in yellow, and His36 (cyan), Met40, Met43 and Met48 (magenta) are also indicated (the numbering of these residues refers to the mature protein). The CXXXC and CXXC motifs are underlined. The region in bold corresponds to the single tryptic fragment identified on two separate occasions in MS analysis, representing 11% sequence coverage of the mature protein (Mascot search of peptide mass fingerprint, expectation value = 1.9 × 10−5). The sequence of this fragment was confirmed by liquid chromatography/MS/MS (data not shown). This is the only tryptic peptide from the mature protein that would be anticipated to be readily detected by MS (owing to either small mass or presence of Cys residues in all other theoretical tryptic fragments) and is unique to this protein among all proteobacterial protein sequences in the NCBInr database.

Extended Data Figure 2 Cu(I) binding to Csp1.

a, UV–vis difference spectra upon the addition of Cu(I) to apo-Csp1 (5.32 μM) showing the appearance of S(Cys)→Cu(I) LMCT bands10,23,24. b, Plots of absorbance at 250 nm (filled squares), 275 nm (filled circles) and 310 nm (open circles) against [Cu(I)]/[Csp1] ratio taken from the spectra in a. The absorbance rises steeply until 11–15 Cu(I) equivalents but continues to rise, particularly at lower wavelengths, making binding stoichiometry difficult to determine precisely with this approach. Systems that bind multiple Cu(I) ions in clusters such as those found in metallothioneins, typically give rise to luminescence at around 600 nm (refs 10, 13). However, limited luminescence is observed at 600 nm during the titration of Cu(I) into Csp1 (data not shown). c, X-ray absorption near-edge spectrum of a fresh crystal of Cu(I)-Csp1 at 100 K. d, Plots of [Cu(BCS)2]3− formation against time after the addition of Cu(I)-Csp1 (0.93 μM) loaded with 11.8 equivalents of Cu(I) to 2,510 μM BCS either in the absence (dashed line) or presence (solid line) of 7.9 M urea. Cu(I) is removed faster in urea and is limited by the rate of Cu(I)-Csp1 unfolding (Extended Data Fig. 5i). The presence of urea has little effect on the end point for this reaction. Experiments in a, b and d were all performed in 20 mM HEPES pH 7.5 containing 200 mM NaCl.

Extended Data Figure 3 Sequence comparison of Csp1 homologues in M. trichosporium OB3b.

The M. trichosporium OB3b genome possesses two genes that code for Csp1 homologues, Csp2 and Csp3, having 58 and 19% sequence identity to Csp1, respectively. The predicted Tat leader peptides of Csp1 (MERRDFVTAFGALAAAAAASSAFA) and Csp2 (MERRQFVAAIGAAAAAASASRAFA) are omitted. The Cys residues (13 in Csp1 and Csp2 and 18 in Csp3) are highlighted in yellow with CXXXC and CXXC motifs underlined. A CXXXC motif in an α-helix allows both of the Cys residues to coordinate the same Cu(I) ion (Fig. 3d, e), which is not the case for a CXXC motif. This is consistent with the observation that a synthetic peptide containing a CXXC motif binds a Cu4S4 cluster via a four-helix bundle made from four peptides, with coordination involving only one Cys per peptide28,56. The alignment was produced using the T-coffee alignment tool57. Asterisks indicate fully conserved sequence positions; the ‘:’ and ‘.’ symbols indicate strongly and weakly similar sequence positions respectively.

Extended Data Figure 4 sMMO activity of wild-type M. trichosporium OB3b and the Δcsp1/csp2 strain.

Purple colour, indicating sMMO activity, is evident at 19.25 h in the Δcsp1/csp2 strain (tubes 4–6), but not until 24.5 h in the wild type (WT, tubes 1–3) when using a qualitative assay. When quantified spectrophotometrically at 27.75 h, the average sMMO activity in the Δcsp1/csp2 strain (grey) is 1.8-fold greater (P = 0.04, one-tailed t-test) than that of the wild type (WT, white), as shown in the bar chart (mean ± s.d. of three replicates).

Extended Data Figure 5 The dependence on pH of competition between Csp1 and BCA for Cu(I), and far-UV circular dichroism spectra showing pH stability and unfolding of Csp1 in urea.

a, Plots of [Cu(BCA)2]3− concentration against [Cu(I)]/[Csp1] ratio for the addition of Cu(I) to apo-Csp1 (2.38–2.56 μM) in the presence of 103 μM BCA in 20 mM buffer (see Methods) at pH 5.5 (filled squares), 6.5 (filled circles), 7.5 (filled triangles), 8.5 (open circles) and 9.5 (open squares) plus 200 mM NaCl. Equilibration is fast (<20 min) at pH 6.5 and higher and the data shown are from titrations of Cu(I) into apo-Csp1. At pH 5.5 equilibration is slower and the data are for mixtures incubated for 21 h. Also shown are results for mixtures of Cu(I) with apo-Csp1 (3.31–3.67 µM) at pH 6.5 (b) and 9.5 (c) in the presence of 120 µM (filled squares), 300 µM (open circles), 450 µM (stars), 600 µM (filled triangles) and 900 µM (open squares) BCA, all after incubation for 15 h. At lower BCA concentrations, Csp1 is able to compete effectively for Cu(I) in the pH range 6.5–9.5, giving Cu(I) binding stoichiometries of 12–14 (see also Figs 3a and 4a). At pH 5.5, Csp1 competes less effectively with BCA for Cu(I), most probably because of the protonation of Cys ligands37. This is consistent with greater competition by 600 μM BCA at pH 6.5 (b) compared with pH 7.5 (Fig. 4a). The stability of apo-Csp1 over the pH and time ranges used for experiments with BCA (and BCS) was determined using far-UV circular dichroism spectroscopy. The spectra of apo-Csp1 (solid lines) at pH (d) 5.5 (34.1 μM, 0.43 mg ml−1), (e) 7.5 (36.5 μM, 0.46 mg ml−1) and (f) 9.5 (32.6 μM, 0.41 mg ml−1) are compared with those for samples incubated for 43 h (dashed lines), and for 3 h (dotted line) and 17 h (dashed/dotted lines) at pH 9.5. At pH 9.5 and in the presence of higher BCA concentrations (c), Csp1 binds approximately one less equivalent of Cu(I), which must be because of changes in structure that are observed at this pH value (no change after 3 h but there is a decrease of 15–20% α-helical content at longer incubation times, see f). However, the remaining sites bind Cu(I) more tightly (c) than at pH 7.5 (Fig. 4a) because of deprotonation of the Cys ligands37. g, Far-UV circular dichroism spectra of apo-Csp1 (19.9 μM, 0.25 mg ml−1) in 20 mM HEPES pH 7.5 containing 200 mM NaCl at 0, 30, 60, 120 and 240 min (solid lines) after the addition of urea (7 M) compared with the spectrum for apo-Csp1 in the same buffer but with no urea (dashed line). h, Far-UV circular dichroism spectra of apo-Csp1 (7.94 μM, 0.10 mg ml−1) as in g except that spectra were acquired at 0, 15, 30, 45 and 60 min (solid lines) after addition of urea (7 M); unfolding is significantly faster at lower protein concentrations and is consistent with the reaction with DTNB in urea being complete in 20 min at Csp1 concentrations <4 μM. i, Far-UV circular dichroism spectra of Csp1 incubated with 14.0 equivalents of Cu(I) (19.9 μM, 0.25 mg ml−1) as in g but at 0, 60, 240, 360 and 480 min and 24 h (solid lines) after addition of urea (7 M) compared with the spectrum for Cu(I)-Csp1 in buffer with no urea (dashed line). The arrow in g to i indicates how the spectrum changes with time.

Extended Data Figure 6 Competition for Cu(I) between Csp1 and chromophoric ligands and the determination of the apparent average Cu(I) dissociation constant for Csp1 using BCS.

a, Plots of [Cu(L)2]3− concentration against [L] (BCA or BCS) after the incubation of Cu(I)-Csp1 (2.59 μM) loaded with 10.4 equivalents of Cu(I) with different concentrations of BCA (filled circles) and BCS (filled squares) for 17 h. b, Plots of [Cu(BCS)2]3− concentration against [Cu(I)] for apo-Csp1 (2.71 μM) in the presence of 99.2 μM (open squares) and 248 μM (filled squares) BCS incubated with increasing concentrations of Cu(I) (0, 4.38, 11.0, 15.3 and 21.9 equivalents; data shown after 17 h incubation). BCS competes much more effectively with Csp1 for Cu(I) than BCA, and [Cu(BCS)2]3− is stoichiometrically formed at 248 μM BCS. c, Plot of [Cu(BCS)2]3− concentration against the [Cu(I)]/[Csp1] ratio for mixtures of Cu(I) plus apo-Csp1 (2.70 μM) in the presence of 101 μM BCS (open squares) for 19 h. For comparison, the data from b (2.71 μM Csp1 in the presence of 99.2 μM BCS for 17 h) are also shown (filled squares). The data in ac were all acquired in 20 mM HEPES plus 200 mM NaCl at pH 7.5. d, Fractional occupancy of Cu(I)-binding sites in Csp1 (maximum value is 11.3 equivalents in this experiment) at different concentrations of free Cu(I) for the experiment shown in c. The solid line shows the fit of the data to the nonlinear Hill equation giving KCu = (1.3 ± 0.1) × 10−17 M (n = 2.7 ± 0.2). Hill coefficients larger than 1 indicate positive cooperativity for Cu(I) binding by Csp1. Confirmation, and the cause, of this effect will be the subject of further studies.

Extended Data Figure 7 Cu(I) exchange between Csp1 and mbtin.

UV–vis spectra of apo-mbtin (dashed lines) and at various times up to 360 min (thick lines) after the addition of either Cu(I)-Csp1 or Cu(I). Cu(I)-Csp1 (1.02 μM) loaded with 13.0 equivalents of Cu(I) was added to either 13.4 μM (a) or 27.4 μM (c) apo-mbtin. Cu(I) alone (13.3 μM) was added to 13.4 μM (b) or 27.1 μM (d) apo-mbtin. Plots of absorbance at 394 nm against time for ad are shown in Fig. 4d. Mbtin from M. trichosporium OB3b has a Cu(I) affinity of (6–7) × 1020 M−1 at pH 7.5 (determined17 using a logβ2 value of 19.8 for [Cu(BCS)2]3−, but is an order of magnitude tighter if the more recent logβ2 value of 20.8 (ref. 25) is used) and stoichiometrically removes Cu(I) from Csp1 within 1 h. e, UV–vis spectra of Cu(I)-mbtin (2.71 μM, black line) immediately after mixing with apo-Csp1 (234 μM, green line) and after incubation under anaerobic conditions for 1 h (blue line) and 20 h (red line). Small increases in absorbance are observed because of the absorbance of apo-Csp1 at these wavelengths and precipitation. The latter was more of a problem at longer incubation times and the sample at 20 h required filtering before running the spectrum shown. The small changes observed are not consistent with the formation of apo-mbtin17. All experiments were performed in 20 mM HEPES pH 7.5 plus 200 mM NaCl.

Extended Data Figure 8 Sequence comparison of Csp homologues from diverse bacteria.

Homology searches show that Csp homologues are encoded in the genomes of diverse bacteria. Multiple sequence alignment of the three M. trichosporium OB3b proteins (OB3b Csp1, OB3b Csp2 and OB3b Csp3) with a selection of these proteins, including one member (from Neisseria gonorrhoeae) that also possesses a putative Tat signal sequence (underlined), shows that the Cys residues (highlighted in yellow) are highly conserved. The alignment was produced using the T-coffee alignment tool57. Asterisks indicate fully conserved sequence positions; the ‘:’ and ‘.’ symbols indicate strongly and weakly similar sequence positions respectively. N. gonorrhoeae sequence: open reading frame (ORF) NGAG_01502, UniProt accession C1I025; P. aeruginosa sequence: ORF PA96_2930, UniProt accession X5E748 (PDB accession number 3KAW); Streptomyces coelicolor sequence: ORF SCO3281, UniProt accession Q9X8F4; N. multiformis sequence: ORF NmuI_A1745, UniProt accession Q2Y879 (PDB accession number 3LMF); Rhizobium leguminosarum sequence: ORF RLEG_20420, UniProt accession W0IHZ3; Ralstonia metallidurans sequence: ORF Rmet_5753, UniProt accession Q1LB64; Salmonella enterica sv. Typhimurium sequence: ORF STM14_1521, UniProt accession D0ZVJ6; Bacillus subtilis sequence: ORF BSU10600, UniProt accession O07571; Legionella pneumophila sequence: ORF LPE509_p00081, UniProt accession M4SK87.

Extended Data Table 1 Data collection and refinement statistics
Extended Data Table 2 Primers used for cloning Csp1 and making the Δcsp1/csp2 M. trichosporium OB3b strain

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Vita, N., Platsaki, S., Baslé, A. et al. A four-helix bundle stores copper for methane oxidation. Nature 525, 140–143 (2015) doi:10.1038/nature14854

Download citation

Further reading

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.