[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_011928108.1	Pelotomaculum thermopropionicum	[FeFe] Group C3	Firmicutes	Clostridiales	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
WP_012065100.1	Alkaliphilus metalliredigens	[FeFe] Group C3	Firmicutes	Clostridiales	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
WP_012268929.1	Thermoanaerobacter pseudethanolicus	[FeFe] Group C3	Firmicutes	Thermoanaerobacterales	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_012447302.1	Natranaerobius thermophilus	[FeFe] Group C3	Firmicutes	Natranaerobiales	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
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_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_012862884.1	Sebaldella termitidis	[FeFe] Group C3	Fusobacteria	Fusobacteriales	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
WP_012996079.1	Thermoanaerobacter italicus	[FeFe] Group C3	Firmicutes	Thermoanaerobacterales	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
WP_013150921.1	Thermoanaerobacter mathranii	[FeFe] Group C3	Firmicutes	Thermoanaerobacterales	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
WP_013387666.1	Ilyobacter polytropus	[FeFe] Group C3	Fusobacteria	Fusobacteriales	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
WP_013570771.1	Thermoanaerobacter brockii	[FeFe] Group C3	Firmicutes	Thermoanaerobacterales	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
WP_013657393.1	Cellulosilyticum lentocellum	[FeFe] Group C3	Firmicutes	Clostridiales	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
WP_013809975.1	Desulfotomaculum carboxydivorans	[FeFe] Group C3	Firmicutes	Clostridiales	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
WP_013823945.1	Desulfotomaculum kuznetsovii	[FeFe] Group C3	Firmicutes	Clostridiales	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
WP_013824003.1	Desulfotomaculum kuznetsovii	[FeFe] Group C3	Firmicutes	Clostridiales	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
WP_013842496.1	Desulfotomaculum ruminis	[FeFe] Group C3	Firmicutes	Clostridiales	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
WP_014553745.1	Halanaerobium praevalens	[FeFe] Group C3	Firmicutes	Halanaerobiales	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
WP_014855313.1	Melioribacter roseus	[FeFe] Group C3	Ignavibacteriae	Ignavibacteriales	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_015518172.1	Ruminiclostridium siraeum	[FeFe] Group C3	Firmicutes	Clostridiales	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
WP_016777698.1	Anaerophaga thermohalophila	[FeFe] Group C3	Bacteroidetes	Bacteroidales	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
WP_017416084.1	Clostridium tunisiense	[FeFe] Group C3	Firmicutes	Clostridiales	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
WP_017873317.1	Caldatribacterium californiense	[FeFe] Group C3	Atribacteria	Unclassified	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
WP_017890116.1	Caldatribacterium saccharofermentans	[FeFe] Group C3	Atribacteria	Unclassified	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
WP_018085928.1	Desulfurispora thermophila	[FeFe] Group C3	Firmicutes	Clostridiales	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
WP_018592801.1	Terrisporobacter glycolicus	[FeFe] Group C3	Firmicutes	Clostridiales	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
WP_019880479.1	Succinispira mobilis	[FeFe] Group C3	Firmicutes	Selenomonadales	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
WP_023383391.1	Youngiibacter fragilis	[FeFe] Group C3	Firmicutes	Clostridiales	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
WP_026475064.1	Alkaliflexus imshenetskii	[FeFe] Group C3	Bacteroidetes	Bacteroidales	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
WP_026894719.1	Clostridiisalibacter paucivorans	[FeFe] Group C3	Firmicutes	Clostridiales	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
WP_027356645.1	Desulfotomaculum thermocisternum	[FeFe] Group C3	Firmicutes	Clostridiales	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
WP_027625074.1	Clostridium lundense	[FeFe] Group C3	Firmicutes	Clostridiales	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
WP_027637671.1	Clostridium cadaveris	[FeFe] Group C3	Firmicutes	Clostridiales	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
WP_027718651.1	Desulfovirgula thermocuniculi	[FeFe] Group C3	Firmicutes	Thermoanaerobacterales	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
WP_028992244.1	Thermoanaerobacter thermocopriae	[FeFe] Group C3	Firmicutes	Thermoanaerobacterales	Sensory	Labile	2	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase
WP_004081666.1	Thermotoga maritima	[FeFe] Group C3	Thermotogae	Thermotogales	Sensory	Sensitive	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_002568890.1	Lachnoclostridium bolteae	[FeFe] Group C3	Firmicutes	Clostridiales	Sensory	Labile	3	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase, thioredoxin
WP_002849014.1	Ruminococcus albus	[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_004608289.1	Lachnoclostridium scindens	[FeFe] Group C3	Firmicutes	Clostridiales	Sensory	Labile	3	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase, thioredoxin
WP_004614045.1	Tyzzerella nexilis	[FeFe] Group C3	Firmicutes	Clostridiales	Sensory	Labile	3	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase, thioredoxin
WP_004629692.1	Ruminiclostridium termitidis	[FeFe] Group C3	Firmicutes	Clostridiales	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_005659983.1	Dethiosulfovibrio peptidovorans	[FeFe] Group C3	Synergistetes	Synergistales	Sensory	Labile	3	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase, thioredoxin
WP_005996231.1	Desulfovibrio fructosivorans	[FeFe] Group C3	Deltaproteobacteria	Desulfovibrionales	Sensory	Labile	3	[FeFe]-centre, 2 x [4Fe4S] clusters, PAS domain	Phosphatase, thioredoxin

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.