Publications

2012-2006

Schick, M., Xie, X., Ataka, K., Kahnt, J., Linne, U. and Shima, S. (2012)
Biosynthesis of the iron-guanylylpyridinol cofactor of [Fe]-hydrogenase in methanogenic archaea as elucidated by stable-isotope labeling. J. Am. Chem. Soc. In press.
Shima, S., Schick, M., Kahnt, J., Ataka, K., Steinbach, K. & Linne, U. (2012)
Evidence for acyl-iron ligation in the active site of [Fe]-hydrogenase provided by mass spectrometry and infrared spectroscopy. Dalton Trans. 41, 767-771.
Shima, S., Krueger, M., Weinert, T. Demmer, U., Kahnt, J., Thauer, R.K. & Ermler, U. (2012)
Structure of a methyl-coenzyme M reductase from Black Sea mats that oxidize methane anaerobically. Nature 481, 98-101.
Basen, M., Krüger, M., Milucka, J., Kuever, J., Kahnt, J., Grundmann, O., Meyerdierks, A., Widdel, F. & Shima, S. (2011)
Bacterial enzymes for dissimilatory sulfate reduction in a marine microbial mat (Black Sea) mediating anaerobic oxidation of methane. Environ. Microbiol. 13, 1370-1379
Shima, S., Schick, M. & Tamura, H. (2011)
Preparation of [Fe]-hydrogenase from methanogenic archaea. Methods Enzymol. 494, 119-137.
Shima, S. & Ermler U. (2011)
Structure and function of [Fe]-hydrogenase and its iron-guanylylpyridinol (FeGP) cofactor. Eur. J. Inorg. Chem. 2011, 963-972.
Shima, S. & Ataka, K. (2011)
Isocyanides inhibit [Fe]-hydrogenase with very high affinity. FEBS Lett. 585, 353-356.
Shima, S., Vogt, S., Göbels, A. & Bill E. (2010)
Iron-chromophore circular dichroism of [Fe]-hydrogenase: the conformational change required for H2 activation. Angew. Chem. Int. Ed. 49, 9917-9921.
Thauer, R.K., Kaster, A.-K., Goenrich, M., Schick, M., Hiromoto, T. & Shima, S. (2010)
Hydrogenases from methanogenic archaea, nickel, a novel cofactor and H2-storage. Ann. Rev. Biochem. 79: 507-536.
Salomone-Stagni, M., Stellato, F., Whaley, C.M., Vogt, S., Shima, S., Rauchfuss, T.B., and Meyer-Klaucke, W. (2010) )
The iron-site structure of [Fe]-hydrogenase and model systems: an X-ray absorption near edge spectroscopy study. Dalton Trans. 39, 3057-3064.
Ceh, K., Demmer, U., Warkentin, E., Moll, J., Thauer, R.K., Shima, S. & Ermler, U. (2009) )
Structural basis of the hydride transfer mechanism in F420 dependent methylene-tetrahydromethanopterin dehydrogenase. Biochemistry 48, 10098-10105.
Hiromoto, T., Warkentin, E., Moll, J., Ermler, U. & Shima, S. (2009) )
The crystal structure of an [Fe]-hydrogenase substrate complex reveals the framework for H2-activation. Angew. Chem. Int. Ed. Engl. 48, 6457-6460.
Hiromoto, T., Ataka, K., Pilak O., Vogt, S., Stagni, M.S., Meyer-Klaucke, W., Warkentin, E., Thauer, R.K., Shima, S., &Ermler, U. (2009)
The crystal structure of C176A mutated [Fe]-hydrogenase suggests an acyl-iron ligation in the active site iron complex. FEBS Lett. 583, 585-590.
Shima, S., Thauer, R.K. and Ermler, U. (2009)
Carbon monoxide as intrinsic ligands to iron in the active site of [Fe]-hydrogenase. In Metal-carbon bonds in enzymes and cofactors, Vol. 6 of Metal Ions in Life Sciences (Sigel, A., Sigel, H., Sigel, R.K.O., eds). John Wiley &Sons, Ltd, Chichester, UK, in press.
Shima, S (2008)
Functions of methyl-coenzyme M reductase in production and degradation of methane, pp. 182-183. In Applied Microbiology (Kumagai, H., Kato, N., Murata, K. &Sakai, Y., eds) Asakura Shoten, Tokyo, Japan.
Ettwig, K.F., Shima, S., van de Pas-Schoonen, K.T., Kahnt, J., Medema, M., op den Camp, H.J.M. Jetten, M.S.M. &Strous, M (2008)
Denitrifying bacteria oxidize methane in the absence of archaea. Env. Microbiol. 10. 3164-3173.
Shima, S (2008)
The structure of the [Fe]-hydrogenase and the convergent evolution of the active site of hydrogenases. Seikagaku, 80, 846-849.
Shima, S., Pilak O., Vogt, S., Schick, M., Stagni, M.S., Meyer-Klaucke, W., Warkentin, E., Thauer, R.K., &Ermler, U. (2008)
The crystal structure of [Fe]-hydrogenase reveals the geometry of the active site. Science, 321, 572-575.
Mayr, S., Latkoczy C., Krüger, M., Günther, D., Shima, S., Thauer, R.K., Widdel, F. and Jaun, B. (2008)
The structure of a F430 variant from archaea associated with anaerobic oxidation of methane. J. Am. Chem. Soc., 130, 10758-10767.
Thauer, R.K. &Shima, S. (2008)
Methane as fuel for anaerobic microorganisms. Ann. NY Acad. Sci. 1125: 158-170.
Guo, Y., Wang, H., Xiao, Y., Vogt, S., Thauer, R.K., Shima, S., Volkers, P.I., Rauchfuss, T.B., Pelmentschikov, V., Case, D.A., Alp, E.E., Sturhahn, W., Yoda, Y. &Cramer, S.P. (2008)
Characterization of the Fe site in the iron-sulfur-cluster-free hydrogenase (Hmd) and of a model compound via nuclear resonance vibrational spectroscopy (NRVS). Inorg. Chem., 47, 3969-3977.
Vogt, S., Lyon, E.J., Shima, S. &Thauer, R.K. (2008)
The exchange activities of [Fe]- hydrogenase (iron-sulfurcluster-free hydrogenase) from methanogenic archaea in comparison with the exchange activities of [FeFe] and [NiFe] hydrogenases. J. Biol. Inorg. Chem. 13, 97-106.
Seedorf, H., Hagemeier, C.H., Shima, S., Thauer, R.K., Warkentin, E. &Ermler, U. (2007)
Structure of coenzyme F420H2 oxidase (FprA), a di-iron flavoprotein from methanogenic archaea catalyzing the reduction of O2 to H2O. FEBS J. 274, 1588-1599.
Kahnt, J, Buchenau, B., Mahlert, F., Krüger, M., Shima, S. &Thauer, R.K. (2007)
Post-translational modifications in the active site region of methyl-coenzyme M reductase from methanogenic and methanotrophic archaea. FEBS J. 274, 4913-4921.
Thauer R.K. &Shima, S. (2007)
Methyl-coenzyme M reductase in methanogenic and methanotrophic archaea. In Archaea (Garrett, R. &Klenk, H.-P., eds) Blackwell Publishing, Inc. Malden, USA, pp 275-283.
Shima, S. &Thauer, R.K. (2007)
A third type of hydrogenase catalyzing H2 activaton. Chem. Rec. 7, 37-46.
Korbas, M., Vogt, S., Meyer-Klaucke, W., Bill, E., Lyon, E.J., Thauer, R.K. &Shima, S. (2006)
The iron-sulfur-cluster-free hydrogenase (Hmd) is a metalloenzyme with a novel iron binding motif. J. Biol. Chem. 281, 30804-30813.
Thauer R.K. &Shima, S. (2006)
Methane and microbes. Nature (News and Views) 440: 878-879.
Shima, S. &Thauer, R.K. (2006)
Anaerobic methane oxidation by archaea: a biochemical approach. Bioscience and Industry, 64:23-26.
Acharya, P., Warkentin, E., Ermler, U., Thauer, R.K. &Shima, S. (2006)
The structure of formylmethanofuran:tetrahydromethanopterin formyltransferase in complex with its coenzymes. J. Mol. Biol. 357:870-879.
Thauer R.K. &Shima, S. (2006)
Methyl-coenzyme M reductase in methanogenic and methanotrophic archaea. In Archaea Biology (Garrett, R. &Klenk, H.-P., eds) Blackwell Publishing, Inc. Malden, USA

2005-2003

Pilak, O., Mamat, B., Vogt, S., Hagemeier, C.H., Thauer, R.K., Shima, S., Vonrhein, C., Warkentin, E. &Ermler, U. (2006)
The crystal structure of the apoenzyme of the iron-sulfur-cluster-free hydrogenase (Hmd). J. Mol. Biol. 358: 798-809.
Shima, S. &Thauer, R.K. (2005)
Methyl-coenzyme M reductase (MCR) and the anaerobic oxidation of methane (AOM) in methanotrophic archaea. Curr. Opin. Microbiol. 8, 643-648.
Shima, S., Lyon, E.J., Thauer, R.K. Mienert, B. &Bill, E (2005)
Mössbauer studies of the iron-sulfur-cluster-free hydrogenase: the electronic state of the mononuclear Fe active site. J. Am. Chem. Soc. 127, 10430-10435.
Aufhammer, S.W., Warkentin, E., Ermler, U., Hagemeier, C.H., Thauer, R.K. &Shima, S. (2005)
Crystal structure of methylenetetrahydromethanopterin reductase (Mer) in complex with coenzyme F420: architecture of the F420/FMN binding site of enzymes within the non-prolyl cis-peptide containing bacterial luciferase family. Protein Sci. 14, 1840-1849.
Warkentin, E., Hagemeier, C.H., Shima, S., Thauer R.K. &Ermler, U. (2005)
The structure of F420-dependent methylenetetrahydromethanopterin dehydrogenase: a crystallographic superstructure of the selenomethionine-labelled protein crystal structure. Acta Crystallog. Sect. D. 61, 198-202.
Shima, S., Thauer, R.K. &Ermler, U. (2004)
Hyperthermophilic and salt-dependent formyltransferase from Methanopyrus kandleri. Biochem. Soc. Trans. 32, 269-272.
Sakasegawa, S., Hagemeier, C.H., Thauer R.K. Essen, L.-O. &Shima, S. (2004)
Structural and functional analysis of the gpsA gene product of Archaeoglobus fulgidus: a glycerol-3-phosphate dehydrogenase with unusual NADP+ preference. Protein Sci. 13, 3162-3171.
Lyon, E.J., Shima, S., Boecher, R., Thauer, R.K., Grevels, F.-W., Bill, E., Roseboom, W. &Albracht, S.P.J. (2004)
Carbon monoxide as an intrinsic ligand to iron in the active site of the iron-sulfur cluster free hydrogenase (Hmd) as revealed by infrared spectroscopy. J. Am. Chem. Soc. 126, 14239-14248.
Seedorf, H., Dreisbach, A., Hedderich, R., Shima, S. &Thauer, R.K. (2004)
F420H2-oxidase (FprA) from Methanobrevibacter arboriphilus, a novel coenzyme F420 dependent enzyme involved in O2 detoxification. Arch. Microbiol. 182, 126-137.
Shima, S., Lyon, E.J., Sordel-Klippert, Kauß, M., Kahnt, J., Thauer, R.K., Steinbach, K., Xie, X., Verdier, L. &Griesinger, C. (2004)
The cofactor of the iron-sulfur cluster free hydrogenase Hmd: structure of the light-inactivation product. Angew. Chem. Int. Ed. 43, 2547-2551.
Aufhammer, S.W., Warkentin, E., Berk, H., Shima, S., Thauer, R.K. &Ermler, U. (2004)
Coenzyme binding in F420-dependent alcohol dehydrogenase, a member of the bacterial luciferase family. Structure, 12, 361-370.
Lyon, E.J., Shima, S., Buurman, G., Chowdhuri, S., Batschauer, A., Steinbach, K. &Thauer, R.K. (2004)
UV-A/blue light inactivation of the "metal-free" hydrogenase (Hmd) from methanogenic archaea: the enzyme appears to contain functional iron after all. Eur. J. Biochem., 271, 195-204.
Krüger, M., Meyerdierks, A., Frank Oliver Glöckner, F.O., Amann, R., Widdel, F., Kube, M., Reinhardt, R., Kahnt, J., Böcher, R., Thauer, R.K. &Shima, S. (2003)
An conspicuous nickel protein in microbial mats that oxidize methane anaerobically. Nature 426, 878-881.
Hagemeier, C.H., Shima, S., Thauer, R.K., Bourenkov, G., Bartunik, H.D. &Ermler, U. (2003)
Coenzyme F420-dependent methylenetetrahydromethanopterin dehydrogenase (Mtd) from Methanopyrus kandleri: A methanogenic enzyme with an unusual quarternary structure. J. Mol. Biol. 332, 1047-1057.
Hagemeier, C.H., Shima, S., Warkentin, E., Thauer, R.K. &Ermler, U. (2003)
Coenzyme F-420-dependent methylenetetrahydromethanopterin dehydrogenase from Methanopyrus kandleri: the selenomethionine-labelled and non-labelled enzyme crystallized in two different forms. Acta Crystallog. Sect. D 59, 1635-1655.