[Fe]-hydrogenase

This entry was last updated at: June 15, 2016, 3:51 a.m.

Properties

Group	[Fe]-hydrogenases
Subgroup	N/A
Function	Directly couples oxidation of H₂ to reduction of 5,10-methenyltetrahydromethanopterin during hydrogenotrophic methanogenesis. Reverse reaction proposed to occur during formatotrophic methanogenesis.
Activity	Bidirectional
Oxygen tolerance	O₂-tolerant
Localisation	Cytosolic

Distribution

Ecosystem distribution	Methanogenic environments such as anoxic soils, marine sediments, and gastrointestinal tracts
Taxonomic distribution	Encoded in multiple methanogenic orders

Genetic Organisation

e.g. Methanothermobacter marburgensis (WP_013296316.1):

Architecture

Structures	3DAG (Methanocaldococcus jannaschii, 1.8 Å resolution) 2B0J (Methanocaldococcus jannaschii, 1.8 Å resolution) 4JJF (Methanothermobacter marburgensis, 2.2 Å resolution) 4JJG (Methanothermobacter marburgensis, 2.5 Å resolution)
Subunits	1
Subunit description	HmdI (catalytic subunit)
Catalytic site	[Fe]-guanylylpyridinol centre
FeS clusters	Absent

Sequences in this class

NCBI Accession	Organism	Hydrogenase Class	Phylum	Order	Activity (Predicted)	Oxygen Tolerance (Predicted)	Subunits (Predicted)	Metal Centres (Predicted)	Accessory Subunits (Predicted)
WP_004030875.1	Methanobacterium formicicum	[Fe]	Euryarchaeota	Methanobacteriales	Bidirectional	Tolerant	1	Fe ion	None
WP_004591226.1	Methanocaldococcus villosus	[Fe]	Euryarchaeota	Methanococcales	Bidirectional	Tolerant	1	Fe ion	None
WP_007044258.1	Methanotorris formicicus	[Fe]	Euryarchaeota	Methanococcales	Bidirectional	Tolerant	1	Fe ion	None
WP_010870290.1	Methanocaldococcus jannaschii	[Fe]	Euryarchaeota	Methanococcales	Bidirectional	Tolerant	1	Fe ion	None
WP_010876766.1	Methanothermobacter thermautotrophicus	[Fe]	Euryarchaeota	Methanobacteriales	Bidirectional	Tolerant	1	Fe ion	None
WP_011018385.1	Methanopyrus kandleri	[Fe]	Euryarchaeota	Methanopyrales	Bidirectional	Tolerant	1	Fe ion	None
WP_011834108.1	Methanocorpusculum labreanum	[Fe]	Euryarchaeota	Methanomicrobiales	Bidirectional	Tolerant	1	Fe ion	None
WP_011869295.1	Methanococcus maripaludis	[Fe]	Euryarchaeota	Methanococcales	Bidirectional	Tolerant	1	Fe ion	None
WP_011973735.1	Methanococcus aeolicus	[Fe]	Euryarchaeota	Methanococcales	Bidirectional	Tolerant	1	Fe ion	None
WP_012065947.1	Methanococcus vannielii	[Fe]	Euryarchaeota	Methanococcales	Bidirectional	Tolerant	1	Fe ion	None
WP_012819445.1	Methanocaldococcus vulcanius	[Fe]	Euryarchaeota	Methanococcales	Bidirectional	Tolerant	1	Fe ion	None
WP_012955328.1	Methanobrevibacter ruminantium	[Fe]	Euryarchaeota	Methanobacteriales	Bidirectional	Tolerant	1	Fe ion	None
WP_012980975.1	Methanocaldococcus sp. FS406-22	[Fe]	Euryarchaeota	Methanococcales	Bidirectional	Tolerant	1	Fe ion	None
WP_013100253.1	Methanocaldococcus infernus	[Fe]	Euryarchaeota	Methanococcales	Bidirectional	Tolerant	1	Fe ion	None
WP_013180733.1	Methanococcus voltae	[Fe]	Euryarchaeota	Methanococcales	Bidirectional	Tolerant	1	Fe ion	None
WP_013296316.1	Methanothermobacter marburgensis	[Fe]	Euryarchaeota	Methanobacteriales	Bidirectional	Tolerant	1	Fe ion	None
WP_013329929.1	Methanoplanus petrolearius	[Fe]	Euryarchaeota	Methanomicrobiales	Bidirectional	Tolerant	1	Fe ion	None
WP_013413799.1	Methanothermus fervidus	[Fe]	Euryarchaeota	Methanobacteriales	Bidirectional	Tolerant	1	Fe ion	None
WP_013799270.1	Methanotorris igneus	[Fe]	Euryarchaeota	Methanococcales	Bidirectional	Tolerant	1	Fe ion	None
WP_013866724.1	Methanothermococcus okinawensis	[Fe]	Euryarchaeota	Methanococcales	Bidirectional	Tolerant	1	Fe ion	None
WP_015284887.1	Methanoregula formicica	[Fe]	Euryarchaeota	Methanomicrobiales	Bidirectional	Tolerant	1	Fe ion	None
WP_015791545.1	Methanocaldococcus fervens	[Fe]	Euryarchaeota	Methanococcales	Bidirectional	Tolerant	1	Fe ion	None
WP_016357634.1	Methanobrevibacter sp. AbM4	[Fe]	Euryarchaeota	Methanobacteriales	Bidirectional	Tolerant	1	Fe ion	None
WP_018153721.1	Methanothermococcus thermolithotrophicus	[Fe]	Euryarchaeota	Methanococcales	Bidirectional	Tolerant	1	Fe ion	None
WP_019263574.1	Methanobrevibacter smithii	[Fe]	Euryarchaeota	Methanobacteriales	Bidirectional	Tolerant	1	Fe ion	None

Literature

Genetics:

Afting, C., Kremmer, E., Brucker, C., Hochheimer, A., and Thauer, R.K. (2000) Regulation of the synthesis of H₂-forming methylenetetrahydromethanopterin dehydrogenase (Hmd) and of HmdII and HmdIII in Methanothermobacter marburgensis. Arch. Microbiol. 174: 225-232.
Bünau, R., Zirngibl, C., Thauer, R.K., and Klein, A. (1991) Hydrogen-forming and coenzyme-F₄₂₀-reducing methylene tetrahydromethanopterin dehydrogenase are genetically distinct enzymes in Methanobacterium thermoautotrophicum (Marburg). Eur. J. Biochem. 202: 1205-1208.

Physiology:

Afting, C., Hochheimer, A., and Thauer, R.K. (1998) Function of H₂-forming methylenetetrahydromethanopterin dehydrogenase from Methanobacterium thermoautotrophicum in coenzyme F₄₂₀ reduction with H₂. Arch. Microbiol. 169: 206-210.
Hartmann, G.C., Klein, A.R., Linder, M. and Thauer, R.K., 1996. Purification, properties and primary structure of H₂-forming N⁵, N¹⁰-methylenetetrahydromethanopterin dehydrogenase from Methanococcus thermolithotrophicus. Arch. Microbiol. 165: 187-193.
Hendrickson, E.L. and Leigh, J. (2008) Roles of coenzyme F₄₂₀-reducing hydrogenases and hydrogen- and F₄₂₀-dependent methylenetetrahydromethanopterin dehydrogenases in reduction of F₄₂₀ and production of hydrogen during methanogenesis. J. Bacteriol. 190: 4818-4821.
Lie, T.J., Costa, K.C., Pak, D., Sakesan, V., and Leigh, J.A. (2013) Phenotypic evidence that the function of the [Fe]-hydrogenase Hmd in Methanococcus maripaludis requires seven hcg (hmd co-occurring genes) but not hmdII. FEMS Microbiol. Lett. 343: 156-160.

Biochemistry:

Afting, C., Hochheimer, A., and Thauer, R.K. (1998) Function of H₂-forming methylenetetrahydromethanopterin dehydrogenase from Methanobacterium thermoautotrophicum in coenzyme F₄₂₀ reduction with H₂. Arch. Microbiol. 169: 206-210.
Buurman, G., Shima, S., and Thauer, R.K. (2000) The metal-free hydrogenase from methanogenic archaea: evidence for a bound cofactor. FEBS Lett. 485: 200-204.
Fujishiro, T., Ataka, K., Ermler, U., and Shima, S. (2015) Towards a functional identification of catalytically inactive [Fe]-hydrogenase paralogs. FEBS J. 282: 3412-3423.
Hartmann, G.C., Klein, A.R., Linder, M., and Thauer, R.K. (1996) Purification, properties and primary structure of H₂-forming N⁵, N¹⁰-methylenetetrahydromethanopterin dehydrogenase from Methanococcus thermolithotrophicus. Arch. Microbiol. 165: 187-193.
Hiromoto, T., Ataka, K., Pilak, O., Vogt, S., Stagni, M.S., Meyer-Klaucke, W., Warkentin, E., Thauer, R.K., Shima, S., and 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.
Hiromoto, T., Warkentin, E., Moll, J., Ermler, U., and Shima, S. (2009) The crystal structure of an [Fe]-hydrogenase-substrate complex reveals the framework for H₂ activation. Angewandte Chemie 48: 6457-6460.
Korbas, M., Vogt, S., Meyer-Klaucke, W., Bill, E., Lyon, E.J., Thauer, R.K., and 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.
Ma, K., Zirngibl, C., Linder, D., Stetter, K.O., and Thauer, R.K. (1991) N⁵, N¹⁰-methylenetetrahydromethanopterin dehydrogenase (H₂-forming) from the extreme thermophile Methanopyrus kandleri. Arch. Microbiol. 156: 43-48.
Ma, K. and Thauer, R.K. (1990) Purification and properties of N⁵, N¹⁰-methylenetetrahydromethanopterin reductase from Methanobacterium thermoautotrophicum (strain Marburg). Eur. J. Biochem. 191: 187-193.
Pilak, O., Mamat, B., Vogt, S., Hagemeier, C.H., Thauer, R.K., Shima, S., Vonrhein, C., Warkentin, E., and Ermler, U. (2006) The crystal structure of the apoenzyme of the iron-sulphur cluster-free hydrogenase. J. Mol. Biol. 358: 798-809.
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. 134: 3271-3280.
Schwörer, B., Fernández, V.M., Zirngibl, C., and Thauer, R.K. (1993) H₂-forming N⁵, N¹⁰-methylenetetrahydromethanopterin dehydrogenase from Methanobacterium thermoautotrophicum. Eur. J. Biochem. 212: 255-261.
Shima, S. and Ermler, U. (2011) Structure and function of [Fe]-hydrogenase and its iron-guanylylpyridinol (FeGP) cofactor. Eur. J. Inorg. Chem. 2011: 963-972.
Shima, S., Pilak, O., Vogt, S., Schick, M., Stagni, M.S., Meyer-Klaucke, W., Warkentin, E., Thauer, R.K., and Ermler, U. (2008) The crystal structure of [Fe]-hydrogenase reveals the geometry of the active site. Science 321: 572-575.
Shima, S. and Thauer, R.K. (2007) A third type of hydrogenase catalyzing H₂ activation. Chem. Rec. 7: 37-46.
Zirngibl, C., Dongen, W., Schwörer, B., Bünau, R., Richter, M., Klein, A., and Thauer, R.K. (1992) H₂-forming methylenetetrahydromethanopterin dehydrogenase, a novel type of hydrogenase without iron-sulfur clusters in methanogenic archaea. Eur. J. Biochem. 208: 511-520.
Zirngibl, C., Hedderich, R., and Thauer, R.K. (1990) N⁵, N¹⁰-methylenetetrahydromethanopterin dehydrogenase from Methanobacterium thermoautotrophicum has hydrogenase activity. FEBS Lett. 261: 112-116.

Chemistry:

Dey, A. (2010) Density functional theory calculations on the mononuclear non-heme iron active site of Hmd hydrogenase: role of the internal Ligands in tuning external ligand binding and driving H₂ heterolysis. J. Am. Chem. Soc. 132: 13892-13901.
Geierstanger, B.H., Prasch, T., Griesinger, C., Hartmann, G., Buurman, G., and Thauer, R.K. (1998) Catalytic mechanism of the metal-free hydrogenase from methanogenic archaea: reversed stereospecificity of the catalytic and noncatalytic reaction. Angewandte Chemie 37: 3300-3303.
Guo, Y., Wang, H., Xiao, Y., Vogt, S., Thauer, R.K., Shima, S., Volkers, P.I., Rauchfuss, T.B., Pelmenschikov, V., Case, D.A., and Alp, E.E. (2008) Characterization of the Fe site in iron-sulfur cluster-free hydrogenase (Hmd) and of a model compound via nuclear resonance vibrational spectroscopy (NRVS). Inorg. Chem. 47: 3969-3977.
Hartmann, G.C., Santamaria, E., Fernández, V.M., and Thauer, R.K. (1996) Studies on the catalytic mechanism of H₂-forming methylenetetrahydromethanopterin dehydrogenase: Para-ortho H₂ conversion rates in H₂O and D₂O. J. Biol. Inorg. Chem. 1: 446-450.
Klein, A.R., Fernández, V.M., and Thauer, R.K., 1995. H₂-forming N⁵, N¹⁰-methylenetetrahydromethanopterin dehydrogenase: mechanism of H₂ formation analyzed using hydrogen isotopes. FEBS Lett. 368: 203-206.
Klein, A.R., Hartmann, G.C., and Thauer, R.K. (1995) Hydrogen isotope effects in the reactions catalyzed by H₂-forming N⁵, N¹⁰-methylenetetrahydromethanopterin dehydrogenase from methanogenic archaea. Eur. J. Biochem. 233: 372-376.
Lyon, E.J., Shima, S., Boecher, R., Thauer, R.K., Grevels, F.W., Bill, E., Roseboom, W., and Albracht, S.P. (2004) Carbon monoxide as an intrinsic ligand to iron in the active site of the iron-sulfur-cluster-free hydrogenase H₂-forming methylenetetrahydromethanopterin dehydrogenase as revealed by infrared spectroscopy. J. Am. Chem. Soc. 126: 14239-14248.
Lyon, E.J., Shima, S., Buurman, G., Chowdhuri, S., Batschauer, A., Steinbach, K., and Thauer, R.K. (2004) UV-A/blue-light inactivation of the 'metal-free' hydrogenase (Hmd) from methanogenic archaea. Eur. J. Biochem. 271: 195-204.
Nakatani, N., Nakao, Y., Sato, H., and Sakaki, S. (2009) Theoretical study of the iron sulfur cluster-free hydrogenase (Hmd): what is the active center of Hmd? Chem. Lett. 38: 958-959.
Salomone-Stagni, M., Stellato, F., Whaley, C.M., Vogt, S., Morante, 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.
Shima, S. and Ataka, K. (2011) Isocyanides inhibit [Fe]-hydrogenase with very high affinity. FEBS Lett. 585: 353-356.
Shima, S., Lyon, E.J., Sordel-Klippert, M., Kauß, M., Kahnt, J., Thauer, R.K., Steinbach, K., Xie, X., Verdier, L., and Griesinger, C. (2004) The cofactor of the iron-sulfur cluster free hydrogenase Hmd: structure of the light-inactivation product. Angewandte Chemie 116: 2601-2605.
Shima, S., Lyon, E.J., Thauer, R.K., Mienert, B., and 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.
Shima, S., Schick, M., Kahnt, J., Ataka, K., Steinbach, K., and 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., Vogt, S., Göbels, A., and Bill, E. (2010) Iron-chromophore circular dichroism of [Fe]-hydrogenase: the conformational change required for H₂ activation. Angewandte Chemie 49: 9917-9921.
Stiebritz, M.T., Finkelmann, A.R., and Reiher, M. (2011) Oxygen coordination to the active site of Hmd in relation to [FeFe] hydrogenase. Eur. J. Inorg. Chem. 2011: 1163-1171.
Stiebritz, M.T. and Reiher, M. (2010) A unifying structural and electronic concept for Hmd and [FeFe] hydrogenase active sites. Inorg. Chem. 49: 5818-5823.
Vogt, S., Lyon, E.J., Shima, S., and Thauer, R.K. (2008) The exchange activities of [Fe] hydrogenase (iron-sulfur-cluster-free hydrogenase) from methanogenic archaea in comparison with the exchange activities of [FeFe] and [NiFe] hydrogenases. J. Biol. Inorg. Chem. 13: 97-106.
Wang, X., Li, Z., Zeng, X., Luo, Q., Evans, D.J., Pickett, C.J., and Liu, X. (2008) The iron centre of the cluster-free hydrogenase (Hmd): low-spin Fe(II) or low-spin Fe(0)? Chem. Commun. 30: 3555-3557.
Yang, X. and Hall, M.B. (2008) Trigger mechanism for the catalytic hydrogen activation by monoiron (iron-sulfur cluster-free) hydrogenase. J. Am. Chem. Soc. 130: 14036-14037.