[FeFe] Group C3-hydrogenase Putative

This entry was last updated at: Feb. 9, 2018, 6:15 a.m.

Properties

Group	[FeFe]-hydrogenases
Subgroup	[FeFe] Group C3: Phosphatase-linked
Function	Unconfirmed role. May serve as H₂-sensors in regulatory cascades. Enzyme predicted to transfer H₂-liberated electrons to PAS domain. Associated redox change may modulate activity of associated serine/threonine phosphatase or AAA-type ATPase domains. Members of this class are co-transcribed with fermentative hydrogenases and appear to regulate their transcription.
Activity	H₂-sensing?
Oxygen tolerance	O₂-labile
Localisation	Cytosolic

Distribution

Ecosystem distribution	Gastrointestinal tracts, anoxic soils and sediments
Taxonomic distribution	Widespread in anaerobic bacteria, including Firmicutes, Deltaproteobacteria, and Spirochaete

Genetic Organisation

Organisation 1: Ruminococcus albus (WP_002849014.1):

Organisation 2: Geobacter sulfurreducens (WP_014552161.1):

Architecture

Structures	None
Subunits	1 or 3
Subunit description	Organisation 1: HydS (catalytic subunit with PAS domain), HydP (serine/threonine phosphatase), HydT (thioredoxin) Organisation 2: HydS fusion (catalytic subunit with PAS domain fused to AAA-type ATPase domain)
Catalytic site	[FeFe]-centre
FeS clusters	2 [4Fe4S] clusters

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_005659983.1	Dethiosulfovibrio peptidovorans	[FeFe] Group C3	Synergistetes	Synergistales	Sensory	Labile	3	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase, thioredoxin
WP_012547917.1	Dictyoglomus thermophilum	[FeFe] Group C3	Dictyoglomi	Dictyoglomales	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
WP_012582931.1	Dictyoglomus turgidum	[FeFe] Group C3	Dictyoglomi	Dictyoglomales	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
WP_012414922.1	Elusimicrobium minutum	[FeFe] Group C3	Elusimicrobia	Elusimicrobiales	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
WP_013484024.1	Ethanoligenens harbinense	[FeFe] Group C3	Firmicutes	Clostridiales	Sensory	Labile	1	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Fusion with transcriptional activator
WP_013379523.1	Eubacterium limosum	[FeFe] Group C3	Firmicutes	Clostridiales	Sensory	Labile	3	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase, thioredoxin
WP_011993504.1	Fervidobacterium nodosum	[FeFe] Group C3	Thermotogae	Thermotogales	Sensory	Labile	3	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase, thioredoxin
WP_014451413.1	Fervidobacterium pennivorans	[FeFe] Group C3	Thermotogae	Thermotogales	Sensory	Labile	3	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase, thioredoxin
WP_012532230.1	Geobacter bemidjiensis	[FeFe] Group C3	Deltaproteobacteria	Desulfuromonadales	Sensory	Labile	1	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Fusion with transcriptional activator
WP_026841112.1	Geobacter bremensis	[FeFe] Group C3	Deltaproteobacteria	Desulfuromonadales	Sensory	Labile	1	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Fusion with transcriptional activator
WP_012645645.1	Geobacter daltonii	[FeFe] Group C3	Deltaproteobacteria	Desulfuromonadales	Sensory	Labile	1	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Fusion with transcriptional activator
WP_004514179.1	Geobacter metallireducens	[FeFe] Group C3	Deltaproteobacteria	Desulfuromonadales	Sensory	Labile	1	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Fusion with transcriptional activator
WP_015722465.1	Geobacter sp. M18	[FeFe] Group C3	Deltaproteobacteria	Desulfuromonadales	Sensory	Labile	1	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Fusion with transcriptional activator
WP_015839082.1	Geobacter sp. M21	[FeFe] Group C3	Deltaproteobacteria	Desulfuromonadales	Sensory	Labile	1	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Fusion with transcriptional activator
WP_015839082.1	Geobacter sp. M21	[FeFe] Group C3	Deltaproteobacteria	Desulfuromonadales	Sensory	Labile	1	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Fusion with transcriptional activator
WP_014552161.1	Geobacter sulfurreducens	[FeFe] Group C3	Deltaproteobacteria	Desulfuromonadales	Sensory	Labile	1	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Fusion with transcriptional activator
WP_011940950.1	Geobacter uraniireducens	[FeFe] Group C3	Deltaproteobacteria	Desulfuromonadales	Sensory	Labile	1	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Fusion with transcriptional activator
WP_020675965.1	Geopsychrobacter electrodiphilus	[FeFe] Group C3	Deltaproteobacteria	Desulfuromonadales	Sensory	Labile	1	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Fusion with transcriptional activator
WP_013406267.1	Halanaerobium hydrogeniformans	[FeFe] Group C3	Firmicutes	Halanaerobiales	Sensory	Labile	1	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Fusion with transcriptional activator
WP_014553745.1	Halanaerobium praevalens	[FeFe] Group C3	Firmicutes	Halanaerobiales	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
WP_005487145.1	Halanaerobium saccharolyticum	[FeFe] Group C3	Firmicutes	Halanaerobiales	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
WP_015325786.1	Halobacteroides halobius	[FeFe] Group C3	Firmicutes	Halanaerobiales	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
WP_008825904.1	Haloplasma contractile	[FeFe] Group C3	Tenericutes	Haloplasmatales	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
WP_012635137.1	Halothermothrix orenii	[FeFe] Group C3	Firmicutes	Halanaerobiales	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
WP_012635165.1	Halothermothrix orenii	[FeFe] Group C3	Firmicutes	Halanaerobiales	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
WP_012635244.1	Halothermothrix orenii	[FeFe] Group C3	Firmicutes	Halanaerobiales	Sensory	Labile	1	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Fusion with transcriptional activator
WP_006059864.1	Holdemania filiformis	[FeFe] Group C3	Firmicutes	Erysipelotrichales	Sensory	Labile	3	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase, thioredoxin
WP_005037180.1	Holophaga foetida	[FeFe] Group C3	Acidobacteria	Holophagales	Sensory	Labile	3	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase, thioredoxin
WP_014559402.1	Ignavibacterium album	[FeFe] Group C3	Ignavibacteriae	Ignavibacteriales	Sensory	Labile	1	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Fusion with histidine kinase
WP_013387666.1	Ilyobacter polytropus	[FeFe] Group C3	Fusobacteria	Fusobacteriales	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
WP_007287482.1	Intestinibacter bartlettii	[FeFe] Group C3	Firmicutes	Clostridiales	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
WP_007287485.1	Intestinibacter bartlettii	[FeFe] Group C3	Firmicutes	Clostridiales	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
WP_026892185.1	Lachnoclostridium aerotolerans	[FeFe] Group C3	Firmicutes	Clostridiales	Sensory	Labile	3	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase, thioredoxin
WP_007715934.1	Lachnoclostridium asparagiforme	[FeFe] Group C3	Firmicutes	Clostridiales	Sensory	Labile	3	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase, thioredoxin
WP_002568890.1	Lachnoclostridium bolteae	[FeFe] Group C3	Firmicutes	Clostridiales	Sensory	Labile	3	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase, thioredoxin
WP_007863168.1	Lachnoclostridium citroniae	[FeFe] Group C3	Firmicutes	Clostridiales	Sensory	Labile	3	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase, thioredoxin
WP_027640429.1	Lachnoclostridium clostridioforme	[FeFe] Group C3	Firmicutes	Clostridiales	Sensory	Labile	3	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase, thioredoxin
WP_006778911.1	Lachnoclostridium hathewayi	[FeFe] Group C3	Firmicutes	Clostridiales	Sensory	Labile	3	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase, thioredoxin
WP_006442325.1	Lachnoclostridium hylemonae	[FeFe] Group C3	Firmicutes	Clostridiales	Sensory	Labile	3	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase, thioredoxin
WP_029502581.1	Lachnoclostridium phytofermentans	[FeFe] Group C3	Firmicutes	Clostridiales	Sensory	Labile	3	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase, thioredoxin
WP_013273994.1	Lachnoclostridium saccharolyticum	[FeFe] Group C3	Firmicutes	Clostridiales	Sensory	Labile	3	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase, thioredoxin
WP_004608289.1	Lachnoclostridium scindens	[FeFe] Group C3	Firmicutes	Clostridiales	Sensory	Labile	3	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase, thioredoxin
WP_003499089.1	Lachnoclostridium symbiosum	[FeFe] Group C3	Firmicutes	Clostridiales	Sensory	Labile	3	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase, thioredoxin
WP_003507891.1	Lachnoclostridium symbiosum	[FeFe] Group C3	Firmicutes	Clostridiales	Sensory	Labile	3	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase, thioredoxin
WP_013781007.1	Mahella australiensis	[FeFe] Group C3	Firmicutes	Thermoanaerobacterales	Sensory	Labile	1	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Fusion with transcriptional activator
WP_010663847.1	Marinilabilia salmonicolor	[FeFe] Group C3	Bacteroidetes	Bacteroidales	Sensory	Labile	1	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Fusion with transcriptional activator
WP_014296384.1	Marinitoga piezophila	[FeFe] Group C3	Thermotogae	Thermotogales	Sensory	Labile	1	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Fusion with methyl-accepting chemotaxis protein
WP_014855313.1	Melioribacter roseus	[FeFe] Group C3	Ignavibacteriae	Ignavibacteriales	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
AIO18481.1	Mollicutes bacterium HR1	[FeFe] Group C3	Tenericutes	Mollicutes	Sensory	Labile	3	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase, thioredoxin
WP_011393215.1	Moorella thermoacetica	[FeFe] Group C3	Firmicutes	Thermoanaerobacterales	Sensory	Labile	1	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Fusion with transcriptional activator

Literature

Genetics:

Calusinska, M., Happe, T., Joris, B., and Wilmotte, A. (2010) The surprising diversity of clostridial hydrogenases: a comparative genomic perspective. Microbiol. 156: 1575-1588.
Greening, C., Biswas, A., Carere, C.R., Jackson, C.J., Taylor, M.C., Stott, M.B., Cook, G.M., and Morales, S.E. (2016) Genomic and metagenomic surveys of hydrogenase distribution indicate H₂ is a widely utilised energy source for microbial growth and survival. ISME J. 10: 761-777.
Poudel, S., Tokmina-Lukaszewska, M., Colman, D.R., Refai, M., Schut, G.J., King, P.W., Maness, P.C., Adams, M.W., Peters, J.W., Bothner, B., and Boyd, E.S. (2016) Unification of [FeFe]-hydrogenases into three structural and functional groups. BBA Gen. Subj. 1860: 1910-1921.
Wolf, P.G., Biswas, A., Morales, S.E., Greening, C., and Gaskins, H.R. (2016) H₂ metabolism is widespread and diverse among human colonic microbes. Gut Microb. 7: 235-245.
Søndergaard, D., Petersen, C.N.S., and Greening, C. (2017) HydDB: a web tool for hydrogenase classification and analysis. Sci. Rep. 6: 34212.
Zheng, Y., Kahnt, J., Kwon, I.H., Mackie, R.I., and Thauer, R.K. (2014) Hydrogen formation and its regulation in Ruminococcus albus: involvement of an electron-bifurcating [FeFe]-hydrogenase, of a non-electron-bifurcating [FeFe]-hydrogenase, and of a putative hydrogen-sensing [FeFe]-hydrogenase. J. Bacteriol. 196: 3840-3852.

Physiology:

Shaw, A.J., Hogsett, D.A., and Lynd, L.R. (2009) Identification of the [FeFe]-hydrogenase responsible for hydrogen generation in Thermoanaerobacterium saccharolyticum and demonstration of increased ethanol yield via hydrogenase knockout. J. Bacteriol. 191: 6457-6464.

Biochemistry:

Chongdar, N., Birrell, J.A., Pawlak, K., Sommer, C., Reijerse, E.J., Rüdiger, O., Lubitz, W., and Ogata, H. (2018). Unique spectroscopic properties of the H-cluster in a putative sensory [FeFe] hydrogenase. J. Am. Chem. Soc. 140: 1057-1068.