[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_028300037.1Oceanospirillum beijerinckii[NiFe] Group 3bGammaproteobacteriaAeromonadalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_026375374.1Aestuariibacter salexigens[NiFe] Group 3bGammaproteobacteriaAlteromonadalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_012136580.1Marinobacter lipolyticus[NiFe] Group 3bGammaproteobacteriaAlteromonadalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
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_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_019350089.1Fluoribacter dumoffii[NiFe] Group 3bGammaproteobacteriaLegionellalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_028379943.1Legionella cherrii[NiFe] Group 3bGammaproteobacteriaLegionellalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_006871434.1Legionella drancourtii[NiFe] Group 3bGammaproteobacteriaLegionellalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_028385762.1Legionella geestiana[NiFe] Group 3bGammaproteobacteriaLegionellalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_003635857.1Legionella longbeachae[NiFe] Group 3bGammaproteobacteriaLegionellalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_028383773.1Legionella moravica[NiFe] Group 3bGammaproteobacteriaLegionellalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_025386399.1Legionella oakridgensis[NiFe] Group 3bGammaproteobacteriaLegionellalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_027222572.1Legionella pneumophila[NiFe] Group 3bGammaproteobacteriaLegionellalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_027271172.1Legionella sainthelensi[NiFe] Group 3bGammaproteobacteriaLegionellalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_026610481.1Methylocaldum szegediense[NiFe] Group 3bGammaproteobacteriaMethylococcalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_007021942.1Neptuniibacter caesariensis[NiFe] Group 3bGammaproteobacteriaOceanospirillalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_027709971.1Zooshikella ganghwensis[NiFe] Group 3bGammaproteobacteriaOceanospirillalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_012699124.1Azotobacter vinelandii[NiFe] Group 3bGammaproteobacteriaPseudomonadalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_002691721.1Beggiatoa alba[NiFe] Group 3bGammaproteobacteriaThiotrichalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_018300187.1Fangia hongkongensis[NiFe] Group 3bGammaproteobacteriaThiotrichalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_012280244.1Francisella philomiragia[NiFe] Group 3bGammaproteobacteriaThiotrichalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_013923702.1Francisella sp. TX077308[NiFe] Group 3bGammaproteobacteriaThiotrichalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_028490240.1Thiothrix lacustris[NiFe] Group 3bGammaproteobacteriaThiotrichalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_002708355.1Thiothrix nivea[NiFe] Group 3bGammaproteobacteriaThiotrichalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_009021278.1Luminiphilus syltensis[NiFe] Group 3bGammaproteobacteriaUnclassifiedBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_012308976.1Korarchaeum cryptofilum[NiFe] Group 3bKorarchaeotaUnclassifiedBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_005006913.1Nitrospina gracilis[NiFe] Group 3bNitrospinaNitrospinalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_028842337.1Thermodesulfovibrio islandicus[NiFe] Group 3bNitrospiraeNitrospiralesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_028844226.1Thermodesulfovibrio thiophilus[NiFe] Group 3bNitrospiraeNitrospiralesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_012544964.1 Thermodesulfovibrio yellowstonii[NiFe] Group 3bNitrospiraeNitrospiralesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_022808428.1Omnitrophus fodinae[NiFe] Group 3bOmnitrophicaUnclassifiedBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_002644708.1Planctomyces maris[NiFe] Group 3bPlanctomycetesPlanctomycetalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_007219971.1Planctomycete KSU-1[NiFe] Group 3bPlanctomycetesPlanctomycetalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_009094014.1Rhodopirellula sp. SWK7[NiFe] Group 3bPlanctomycetesPlanctomycetalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_010585297.1Schlesneria paludicola[NiFe] Group 3bPlanctomycetesPlanctomycetalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_020864100.1Caldiarchaeum subterraneum[NiFe] Group 3bThaumarchaeotaUnclassifiedBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_012464725.1Methylacidiphilum infernorum[NiFe] Group 3bVerrucomicrobiaMethylacidiphilalesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_009061764.1Methylacidiphilum fumariolicum[NiFe] Group 3bVerrucomicrobiaVerrucomicrobialesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_008098529.1Verrucomicrobiae bacterium DG1235[NiFe] Group 3bVerrucomicrobiaVerrucomicrobialesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein
WP_024807859.1Verrucomicrobiae bacterium LP2A[NiFe] Group 3bVerrucomicrobiaVerrucomicrobialesBidirectionalTolerant4[NiFe]-centre, 3 x [4Fe4S] clustersDiaphorase, [FeS] protein

Literature

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