[NiFe] Group 3b-hydrogenase

This entry was last updated at: Feb. 9, 2018, 7:34 a.m.

Properties
Group [NiFe] Group 3: Cofactor-coupled bidirectional [NiFe] hydrogenases
Subgroup [NiFe] Group 3b: NADP-coupled
Function Directly couples oxidation of NADPH to fermentative evolution of H2. Reverse reaction may also occur. Some complexes controversially proposed to harbour sulfhydrogenase activity.
Activity Bidirectional
Oxygen tolerance O2-tolerant
Localisation Cytosolic
Distribution
Ecosystem distribution Diverse soil and aquatic environments
Taxonomic distribution Encoded in multiple diverse bacterial and archaeal phyla
Genetic Organisation

e.g. Pyrococcus furiosus (WP_011012029.1):

Architecture
Structures
  • 5ODC (Methanothermococcus thermolithotrophicus, 2.3 Å resolution)
  • 5ODH (Methanothermococcus thermolithotrophicus, 2.2 Å resolution, bound with heterodisulfide)
  • 5ODI (Methanothermococcus thermolithotrophicus, 2.4 Å resolution, bound with coenzyme M)
Subunits 4
Subunit description HyhL (hydrogenase large subunit)
HyhS (hydrogenase small subunit)
HyhG (diaphorase catalytic subunit)
HyhB (diaphorase electron transfer subunit)
Catalytic site [NiFe]-centre
FeS clusters Proximal: 4Cys[4Fe4S]
Medial: 4Cys[4Fe4S]
Distal: 4Cys[4Fe4S]
Important Notes
Despite the ubiquitous nature of this hydrogenase, the enzyme has only been purified from Pyrococcus furiosus. It remains unclear whether bacterial enzymes are also NADP+-specific.
Sequences in this class
NCBI AccessionOrganismHydrogenase ClassPhylumOrderActivity (Predicted)Oxygen Tolerance (Predicted)Subunits (Predicted)Metal Centres (Predicted)Accessory Subunits (Predicted)
WP_008939163.1Marinobacter santoriniensis[NiFe] Group 3bGammaproteobacteriaAlteromonadalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_027854910.1Marinobacterium litorale[NiFe] Group 3bGammaproteobacteriaAlteromonadalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_020680743.1Marinobacterium rhizophilum[NiFe] Group 3bGammaproteobacteriaAlteromonadalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_010321726.1Marinobacterium stanieri[NiFe] Group 3bGammaproteobacteriaAlteromonadalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_020412786.1Microbulbifer variabilis[NiFe] Group 3bGammaproteobacteriaAlteromonadalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_008286766.1Hydrogenivirga sp. 128-5-R1-1[NiFe] Group 3bAquificaeAquificalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_012963143.1Hydrogenobacter thermophilus[NiFe] Group 3bAquificaeAquificalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_012676609.1Persephonella marina[NiFe] Group 3bAquificaeAquificalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_012674555.1Sulfurihydrogenibium azorense[NiFe] Group 3bAquificaeAquificalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_028949840.1Sulfurihydrogenibium subterraneum[NiFe] Group 3bAquificaeAquificalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_017774733.1Burkholderia kururiensis[NiFe] Group 3bBetaproteobacteriaBurkholderialesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_028214587.1Burkholderia mimosarum[NiFe] Group 3bBetaproteobacteriaBurkholderialesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_020653150.1Massilia niastensis[NiFe] Group 3bBetaproteobacteriaBurkholderialesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_014433201.1Caldilinea aerophila[NiFe] Group 3bChloroflexiCaldilinealesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_006926982.1Caldithrix abyssi[NiFe] Group 3bCaldithrixCaldithrixalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_012501574.1Chlorobaculum parvum[NiFe] Group 3bChlorobiChlorobialesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_010933552.1Chlorobaculum tepidum[NiFe] Group 3bChlorobiChlorobialesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_011361294.1Chlorobium chlorochromatii[NiFe] Group 3bChlorobiChlorobialesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_006366269.1Chlorobium ferrooxidans[NiFe] Group 3bChlorobiChlorobialesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_012466994.1Chlorobium limicola[NiFe] Group 3bChlorobiChlorobialesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_011745973.1Chlorobium phaeobacteroides[NiFe] Group 3bChlorobiChlorobialesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_012498899.1Chloroherpeton thalassium[NiFe] Group 3bChlorobiChlorobialesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_012509156.1Pelodictyon phaeoclathratiforme[NiFe] Group 3bChlorobiChlorobialesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_012506474.1Prosthecochloris aestuarii[NiFe] Group 3bChlorobiChlorobialesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_012970030.1Allochromatium vinosum[NiFe] Group 3bGammaproteobacteriaChromatialesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_025280829.1Halorhodospira halochloris[NiFe] Group 3bGammaproteobacteriaChromatialesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_005000139.1Nitrococcus mobilis[NiFe] Group 3bGammaproteobacteriaChromatialesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_013032567.1Nitrosococcus halophilus[NiFe] Group 3bGammaproteobacteriaChromatialesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_015258948.1Thioalkalivibrio nitratireducens[NiFe] Group 3bGammaproteobacteriaChromatialesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_012637708.1Thioalkalivibrio sulfidiphilus[NiFe] Group 3bGammaproteobacteriaChromatialesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_006786889.1Thiorhodospira sibirica[NiFe] Group 3bGammaproteobacteriaChromatialesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_012628086.1Cyanothece sp. PCC 7425[NiFe] Group 3bCyanobacteriaChroococcalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_008515176.1Dethiobacter alkaliphilus[NiFe] Group 3bFirmicutesClostridialesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_022739737.1Adlercreutzia equolifaciens[NiFe] Group 3bActinobacteriaCoriobacterialesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_015760489.1Eggerthella lenta[NiFe] Group 3bActinobacteriaCoriobacterialesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_022363293.1Eggerthella sp. CAG:298[NiFe] Group 3bActinobacteriaCoriobacterialesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_013979629.1Eggerthella sp. YY7918[NiFe] Group 3bActinobacteriaCoriobacterialesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_016308610.1Enterorhabdus caecimuris[NiFe] Group 3bActinobacteriaCoriobacterialesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_028027114.1Enterorhabdus mucosicola[NiFe] Group 3bActinobacteriaCoriobacterialesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_009139266.1Slackia piriformis[NiFe] Group 3bActinobacteriaCoriobacterialesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_013218375.1Dehalogenimonas lykanthroporepellens[NiFe] Group 3bChloroflexiDehalogenimonasBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_028322239.1Desulfobacterium anilini[NiFe] Group 3bDeltaproteobacteriaDesulfobacteralesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_015403594.1Desulfocapsa sulfexigens[NiFe] Group 3bDeltaproteobacteriaDesulfobacteralesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_027366709.1Desulfovibrio africanus[NiFe] Group 3bDeltaproteobacteriaDesulfovibrionalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_013638346.1Desulfurobacterium thermolithotrophum[NiFe] Group 3bAquificaeDesulfurobacterialesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_013537242.1Thermovibrio ammonificans[NiFe] Group 3bAquificaeDesulfurobacterialesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_014737726.1Thermogladius cellulolyticus[NiFe] Group 3bCrenarchaeotaDesulfurococcalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_027716793.1Desulfuromonas sp. TF[NiFe] Group 3bDeltaproteobacteriaDesulfuromonadalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_012530401.1Geobacter bemidjiensis[NiFe] Group 3bDeltaproteobacteriaDesulfuromonadalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_026841827.1Geobacter bremensis[NiFe] Group 3bDeltaproteobacteriaDesulfuromonadalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein

Literature

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