Crystal structures of the methane monooxygenase hydroxylase from Methylococcus capsulatus (Bath): Implications for substrate gating and component interactions

Proteins: Structure, Function and Genetics

Volumn 29, Issue 2, 1997, Pages 141-152

  Rosenzweig, Amy C ^a,c,d   Brandstetter, Hans ^a,c   Whittington, Douglas A ^c   Nordlund, Pär ^b   Lippard, Stephen J ^c   Frederick, Christin A ^a,e  

^a DANA FARBER CANCER INSTITUTE   (United States)

^b STOCKHOLM UNIVERSITY   (Sweden)

^c MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^d NORTHWESTERN UNIVERSITY   (United States)

^e HARVARD MEDICAL SCHOOL   (United States)

Author keywords

Dinuclear iron center; Leucine gate; Nonheme iron enzyme; Protein crystallography; Reductase binding site

Indexed keywords

BACTERIAL ENZYME; GLUTAMIC ACID; HISTIDINE; LEUCINE; METHANE; UNSPECIFIC MONOOXYGENASE;

ARTICLE; BINDING SITE; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; ENZYME ACTIVE SITE; ENZYME STRUCTURE; METHANOTROPHIC BACTERIUM; NONHUMAN; PRIORITY JOURNAL; STRUCTURE ANALYSIS;

CRYSTALLOGRAPHY, X-RAY; LEUCINE; METHYLOCOCCACEAE; OXYGENASES; SUBSTRATE SPECIFICITY;

BACTERIA (MICROORGANISMS); METHYLOCOCCUS CAPSULATUS;

EID: 0030885887     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(199710)29:2<141::AID-PROT2>3.0.CO;2-G     Document Type: Article

References (48)

1. Higgins, I.J., Best, D.J., Hammond, R.C. New findings in methane-utilizing bacteria highlight their importance in the biosphere and their commercial potential. Nature 286:561-564, 1980.
2. Starr, C., Searl, M.F., Alpert, S. Energy sources: A realistic outlook. Science 256:981-987, 1992.
3. Periana, R.A., Taube, D.J., Evitt, E.R., Löffler, D.G., Wentrcek, P.R., Voss, G., Masuda, T. A mercury-catalyzed, high-yield system for the oxidation of methane to methanol. Science 259:340-343, 1993.
4. Colby, J., Stirling, D.I., Dalton, H. The soluble methane monooxygenase of Methylococcus capsulatus (Bath). Biochem. J. 165:395-402, 1977.
5. Green, J., Dalton, H. Substrate specificity of soluble methane monooxygenase. J. Biol. Chem. 264:17698-17703, 1989.
6. Fox, B.G., Borneman, J.G., Wackett, L.P., Lipscomb, J.D. Haloalkene oxidation by the soluble methane monooxygenase from Methylosinus trichosporium OB3b: Mechanistic and environmental implications. Biochemistry 29:6419-6427, 1990.
7. Ensley, B.D. Biochemical diversity of trichloroethylene metabolism. Annu. Rev. Microbiol. 45:283-299, 1991.
8. Chappellaz, J., Barnola, J.M., Raynaud, D., Korotkevich, Y.S., Lorius, C. Ice-core record of atmospheric methane over the past 160,000 years. Nature 345:127-131, 1990.
9. Colby, J., Dalton, H. Resolution of the methane monooxygenase of Methylococcus capsulatus (Bath) into three components. Biochem. J. 171:461-468, 1978.
10. Liu, K.E., Valentine, A.M., Wang, D., Huynh, B.H., Edmondson, D.E., Salifoglou, A., Lippard, S.J. Kinetic and spectroscopic characterization of intermediates and component interactions in reactions of methane monooxygenase from Methylococcus capsulatus (Bath). J. Am. Chem. Soc. 117: 10174-10185, 1995.
11. Froland, W.A., Andersson, K.K., Lee, S.-K., Liu, Y., Lipscomb, J.D. Methane monooxygenase component B and reductase alter the regioselectivity of the hydroxylase component-catalyzed reaction. J. Biol. Chem. 267:17588-17597, 1992.
12. Que Jr., L., True, A.E. Dinuclear iron-and manganese oxo sites in biology. Prog. Inorg. Chem. 38:97-200, 1990.
13. Vincent, J.B., Olivier-Lilley, G.L., Averill, B.A. Proteins containing oxo-bridged dinuclear iron centers: A bioinorganic perspective. Chem. Rev. 90:1447-1467, 1990.
14. Nordlund, P., Eklund, H. Di-iron-carboxylate proteins. Curr. Opin. Struct. Biol. 5:758-766, 1995.
15. 4 and ferritin-like diiron domains. Nature Struct. Biol. 3:539-546, 1996.
16. Fox, B.G., Shanklin, J., Somerville, C., Münck, E. Stearoylacyl carrier protein Δ9 desaturase from Ricinus communis is a diiron-oxo protein. Proc. Natl. Acad. Sci. U.S.A. 90:2486-2490, 1993.
17. Rosenzweig, A.C., Frederick, C.A., Lippard, S.J., Nordlund, P. Crystal structure of a bacterial non-haem iron hydroxylase that catalyses the biological oxidation of methane. Nature 366:537-543, 1993.
18. Rosenzweig, A.C., Nordlund, P., Takahara, P.M., Frederick, C.A., Lippard, S.J. Geometry of the soluble methane monooxygenase catalytic diiron center in two oxidation states. Chem. Biol. 2:409-418, 1995.
19. Elango, N., Radhakrishnan, R., Froland, W.A., Wallar, B.J., Earhart, C.A., Lipscomb, J.D., Ohlendorf, D.H. Crystal structure of the hydroxylase component of methane monooxygenase from Methylosinus trichosporium OB3b. Protein Sci. 6:556-568, 1997.
20. Sheriff, S., Hendrickson, W.A., Smith, J.L. Structure of myohemerythrin in the azidomet state at 1.7/1.3 Å resolution. J. Mol. Biol. 197:273-296, 1987.
21. DeWitt, J.G., Bentsen, J.G., Rosenzweig, A.C., Hedman, B., Green, J., Pilkington, S., Papaefthymiou, G.C., Dalton, H., Hodgson, K.O., Lippard, S.J. 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, 1991.
22. DeRose, V., Liu, K.E., Lippard, S.J., Hoffman, B. Proton ENDOR identification of bridging hydroxide ligands in mixed-valent diiron centers of proteins: methane monooxygenase and semimet azidohemerythrin. J. Am. Chem. Soc. 115:6440-6441, 1993.
23. 1 Compounds: Proceedings of the Eighth International Symposium." Lidstrom, M.E., Tabita, F.R. (eds.). Dordrecht: Kluwer Academic Publishers, 1996: 141-149.
24. Yamashita, M.M., Wesson, L., Eisenman, G., Eisenberg, D. Where metal ions bind in proteins. Proc. Natl. Acad. Sci. U.S.A. 87:5648-5652, 1990.
25. Liu, K.E., Johnson, C.C., Newcomb, M., Lippard, S.J. Radical clock studies and kinetic isotope effect studies of the hydroxylation of hydrocarbons by methane monooxygenase. J. Am. Chem. Soc. 115:939-947, 1993.
26. Kleywegt, G.J., Jones, T.A. Detection, delineation, measurement and display of cavities in macromolecular structures. Acta Crystallogr. D50:178-185, 1994.
27. Liu, K.E., Lippard, S.J. Redox properties of the hydroxylase component of methane monooxygenase from Methylococcus capsulatus (Bath). J. Biol. Chem. 266:12836-12839, 24859, 1991.
28. Fox, E.G., Liu, Y., Dege, J.E., Lipscomb, J.D. Complex formation between the protein components of methane monooxygenase from Methylosinus trichosporium OB3b. J. Biol. Chem. 266:540-550, 1991.
29. Paulsen, K.E., Liu, Y., Fox, E.G., Lipscomb, J.D., Münck, E., Stankovich, M.T. Oxidation-reduction potentials of the methane monooxygenase hydroxylase component from Methylosinus trichosporium OB3b. Biochemistry 33:713-722, 1994.
30. Liu, K.E., Feig, A.L., Goldberg, D.P., Watton, S.P., Lippard, S.J. Methane monooxygenase: models and mechanism. In: "The Activation of Dioxygen and Homogeneous Catalytic Oxidation." Barton, D.H.R., Martell, A.E., Sawyer, D., (eds.). New York: Plenum, 1993:301-320.
31. Wallar, B.J., Lipscomb, J.D. Dioxygen activation by enzymes containing binuclear non-heme iron clusters. Chem. Rev. 96:2625-2657, 1996.
32. Rosenzweig, A.C., Frederick, C.A., Lippard, S.J. Crystallization and preliminary X-ray analysis of the methane monooxygenase hydroxylase protein from Methylococcus capsulatus (Bath). J. Mol. Biol. 227:283-285, 1992.
33. Otwinowski, Z. Data collection and processing. In: "Proceedings of the CCP4 Study Weekend." Warrington, UK: Daresbury Laboratory, 1993:56-62.
34. Collaborative Computational Project, Number 4. The CCP4 suite: Programs for protein crystallography. Acta Crystallogr. D50:760-763, 1994.
35. Higashi, T. The processing of diffraction data taken on a screenless Weissenberg camera for macromolecular crystallography. J. Appl. Crystallogr. 22:9-18, 1989.
36. Terwillinger, T.C., Eisenberg, D. Unbiased three-dimensional refinement of heavy-atom parameters by correlation of origin-removed Patterson functions. Acta Crystallogr. A39:813-817, 1983.
37. Otwinowski, Z. MLPHARE, CCP4 Proc. 80-88. Warrington, UK: Daresbury Laboratory, 1991.
38. Jones, T.A. a, yaap, asap, @#*? A set of averaging programs. In: "Molecular Replacement." Dodson, E.J., Glover, S., Wolf, W. (eds.). Warrington, UK: SERC Daresbury Laboratory, 1992:91-105.
39. Kleywegt, G.J., Jones, T.A. Halloween . . . masks and bones. In: "From First Map to Final Model." Bailey, S., Hubbard, R., Waller, D. (eds.). Warrington, UK: SERC Daresbury Laboratory, 1994:59-66.
40. Jones, T.A., Zou, J.-Y., Cowan, S.W., Kjeldgaard, M. Improved methods for building protein models in electron density maps and location of errors in these models. Acta Crystallogr. A47:110-119, 1991.
41. Barton, G.J. Protein multiple sequence alignment and flexible pattern matching. Methods Enzymol. 183:403-428, 1990.
42. Rost, B., Sander, C. Prediction of protein structure at better than 70% accuracy. J. Mol. Biol. 232:584-599, 1993.
43. Rost, B. PHD: Predicting one-dimensional protein structure by profile based neural networks. Methods Enzymol. 266:525-539, 1996.
44. Green, J., Dalton, H. Steady-state kinetic analysis of soluble methane monooxygenase from Methylococcus capsulatus (Bath). Biochem. J. 236:155-162, 1986.
45. Kraulis, P.J. MOLSCRIPT: A program to produce detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24:946-950, 1991.
46. Merritt, E.A., Murphy, M.E.P. Raster3d Version 2.0: A program for photorealistic molecular graphics. Acta Crystallogr. D50:869-873, 1994.
47. Nicholls, A., Sharp, K.A., Honig, B. Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11:281-296, 1991.
48. Turk, D. Weiterentwicklung eines Programmes für Molekulgraphik und Elektronendichte-Manipulation und seine Anwendung auf verschiedene Protein Strukturaufklarungen. Ph.D. thesis, Technische Universität München. 1992.