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Information on EC 1.12.1.4 - hydrogenase (NAD+, ferredoxin)
for references in articles please use BRENDA:EC1.12.1.4
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EC Tree 1 Oxidoreductases
1.12 Acting on hydrogen as donor
1.12.1 With NAD+ or NADP+ as acceptor
1.12.1.4 hydrogenase (NAD+, ferredoxin)
IUBMB Comments
The enzyme from Thermotoga maritima contains a [FeFe] cluster (H-cluster) and iron-sulfur clusters. It works in the direction evolving hydrogen as a means of eliminating excess reducing equivalents.
The enzyme appears in viruses and cellular organisms
- 1.12.1.4
-
desulfovibrio
- hydrogenases
- desulfuricans
-
nickel-iron
-
diiron
-
dinuclear
- fructosovorans
showSynonyms
iron hydrogenase, [fefe]-type hydrogenase, more
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
bifurcating [FeFe] hydrogenase
Fe-only hydrogenase
HydABC
HydC
NAD(P)+-linked [FeFe]-hydrogenase
bifurcating [FeFe] hydrogenase
-
-
-
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
2 H2 + NAD+ + 2 oxidized ferredoxin = 5 H+ + NADH + 2 reduced ferredoxin
-
-
-
-
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PATHWAY SOURCE
PATHWAYS
MetaCyc
hydrogen production I
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SYSTEMATIC NAME
IUBMB Comments
hydrogen:NAD+, ferredoxin oxidoreductase
The enzyme from Thermotoga maritima contains a [FeFe] cluster (H-cluster) and iron-sulfur clusters. It works in the direction evolving hydrogen as a means of eliminating excess reducing equivalents.
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
NAD+ + 2 oxidized methyl viologen + 2 H2
NADH + 3 H+ + 2 reduced methyl viologen
-
Substrates: -
Products: -
Products: -
?
NADH + 3 H+ + 2 reduced ferredoxin
NAD+ + 2 oxidized ferredoxin + 2 H2
-
Substrates: -
Products: per mol NADH, about 2 mol H2 is formed
Products: per mol NADH, about 2 mol H2 is formed
?
NADH + 3 H+ + 2 reduced methyl viologen
NAD+ + 2 oxidized methyl viologen + 2 H2
-
Substrates: -
Products: -
Products: -
?
NADH + H+ + reduced methyl viologen
H2 + NAD+ + oxidized methyl viologen
-
Substrates: -
Products: -
Products: -
?
sodium dithionite + H+ + reduced anthraquinone-2,6-disulfonic acid
H2 + oxidized anthraquinone-2,6-disulfonic acid + ?
H2 + NAD+ + oxidized ferredoxin
H+ + NADH + reduced ferredoxin
-
Substrates: -
Products: -
Products: -
?
H2 + NAD+ + oxidized ferredoxin
H+ + NADH + reduced ferredoxin
Thermotoga maritima MSB8 / DSM 3109 / ATCC 43589
-
Substrates: -
Products: -
Products: -
?
NAD+ + 2 oxidized ferredoxin + 2 H2
NADH + 3 H+ + 2 reduced ferredoxin
-
Substrates: -
Products: ferredoxin reduction with H2 is driven by the exergonic reduction of NAD+ (E0 -320 mV) with H2. In the absence of NAD+, ferredoxin is not reduced
Products: ferredoxin reduction with H2 is driven by the exergonic reduction of NAD+ (E0 -320 mV) with H2. In the absence of NAD+, ferredoxin is not reduced
?
NAD+ + 2 oxidized ferredoxin + 2 H2
NADH + 3 H+ + 2 reduced ferredoxin
-
Substrates: -
Products: -
Products: -
?
NAD+ + 2 oxidized ferredoxin + 2 H2
NADH + 3 H+ + 2 reduced ferredoxin
-
Substrates: -
Products: -
Products: -
?
NADH + H+ + reduced ferredoxin
H2 + NAD+ + oxidized ferredoxin
-
Substrates: -
Products: -
Products: -
?
NADH + H+ + reduced ferredoxin
H2 + NAD+ + oxidized ferredoxin
-
Substrates: the iron hydrogenase requires the presence of both electron carriers, NADH and ferredoxin, for catalysis of H2 production
Products: -
Products: -
?
NADH + H+ + reduced ferredoxin
H2 + NAD+ + oxidized ferredoxin
-
Substrates: the iron hydrogenase requires the presence of both electron carriers, NADH and ferredoxin, for catalysis of H2 production
Products: -
Products: -
?
NADH + H+ + reduced ferredoxin
H2 + NAD+ + oxidized ferredoxin
-
Substrates: -
Products: -
Products: -
?
sodium dithionite + H+ + reduced anthraquinone-2,6-disulfonic acid
H2 + oxidized anthraquinone-2,6-disulfonic acid + ?
-
Substrates: -
Products: -
Products: -
?
sodium dithionite + H+ + reduced anthraquinone-2,6-disulfonic acid
H2 + oxidized anthraquinone-2,6-disulfonic acid + ?
-
Substrates: -
Products: -
Products: -
?
sodium dithionite + H+ + reduced methyl viologen
H2 + oxidized methyl viologen + ?
-
Substrates: -
Products: -
Products: -
?
sodium dithionite + H+ + reduced methyl viologen
H2 + oxidized methyl viologen + ?
-
Substrates: -
Products: -
Products: -
?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
H2 + NAD+ + oxidized ferredoxin
H+ + NADH + reduced ferredoxin
-
Substrates: -
Products: -
Products: -
?
H2 + NAD+ + oxidized ferredoxin
H+ + NADH + reduced ferredoxin
Thermotoga maritima MSB8 / DSM 3109 / ATCC 43589
-
Substrates: -
Products: -
Products: -
?
NADH + H+ + reduced ferredoxin
H2 + NAD+ + oxidized ferredoxin
-
Substrates: -
Products: -
Products: -
?
NADH + H+ + reduced ferredoxin
H2 + NAD+ + oxidized ferredoxin
-
Substrates: the iron hydrogenase requires the presence of both electron carriers, NADH and ferredoxin, for catalysis of H2 production
Products: -
Products: -
?
NADH + H+ + reduced ferredoxin
H2 + NAD+ + oxidized ferredoxin
-
Substrates: the iron hydrogenase requires the presence of both electron carriers, NADH and ferredoxin, for catalysis of H2 production
Products: -
Products: -
?
NADH + H+ + reduced ferredoxin
H2 + NAD+ + oxidized ferredoxin
-
Substrates: -
Products: -
Products: -
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
4Fe-4S-center
-
displays electron paramagnetic resonance signals characteristic of oxidized [3Fe-4S]+ cluster. Cysteine residues C302, C353, and C356 are strictly required for the binding of the [4Fe-4S] cluster, whereas the fourth ligand of the coordination sphere can vary depending on the molecular environment created by local residues and/or experimental conditions
iron-sulfur centre
-
the alpha subunit contains two [2Fe-2S] clusters and three [4Fe-4S] clusters, the beta subunit contains three [4Fe-4S] clusters and one [2Fe-2S] clusters, the gamma subunit contains one [2Fe-2S] cluster
iron-sulfur centre
-
subunit HydA (63 kDa) is predicted to harbor the H cluster, i.e., the [6Fe4S] hydrogenase active site, three [4Fe4S] clusters, and one [2Fe2S] cluster. Subunit HydB (67 kDa) is predicted to harbor three [4Fe4S] clusters, a flavin binding site, and an NAD binding site. HydC (17 kDa) is predicted to harbor one [2Fe2S] cluster
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
H2
-
apparent Km value for H2 is about 6% in the gas phase, pH 7.5, 45Ā°C
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
Highest Expressing Human Cell Lines
Cell Line LinksPlease wait a moment until the data is sorted. This message will disappear when the data is sorted.
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
-
an active HydF GTPase domain is essential to produce a functional [FeFe]-hydrogenase
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UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). A0A7I8MQ26_9DELT
648
0
70069
TrEMBL
-
A0A3B0UPD4_9ZZZZ
780
0
85165
TrEMBL
other Location (Reliability: 1)
G4FFG1_THEMA
Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)
645
0
72254
TrEMBL
-
G4FFG0_THEMA
Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)
626
0
68681
TrEMBL
other Location (Reliability: 5)
Q9S5X7_THEMA
Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)
164
0
18324
TrEMBL
Mitochondrion (Reliability: 1)
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
18025
-
1 * 72248 + 1 * 68676 + 1 * 18025, calculated from amino acid sequence
68000
68676
-
1 * 72248 + 1 * 68676 + 1 * 18025, calculated from amino acid sequence
72248
-
1 * 72248 + 1 * 68676 + 1 * 18025, calculated from amino acid sequence
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
heterohexamer
-
2 * 67000, subunit HydB, plus 2 * 63000, subunit HydA, plus 2 * 17000, subunit HydC, SDS-PAGE
heterotrimer
multimer
heterotrimer
-
1 * 72248 + 1 * 68676 + 1 * 18025, calculated from amino acid sequence
heterotrimer
-
1 * 72248 + 1 * 68676 + 1 * 18025, calculated from amino acid sequence
-
multimer
-
x * 68000, subunit HdB, plus x * 64000, subunit HydA, plus x * 18000, subunit HydC
multimer
-
x * 68000, subunit HdB, plus x * 64000, subunit HydA, plus x * 18000, subunit HydC
-
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
A85P
-
the mutant has an altered reduction potential compared to the wild type enzyme
V131N
-
the mutant has an altered reduction potential compared to the wild type enzyme
A85P
Thermotoga maritima MSB8 / DSM 3109 / ATCC 43589
-
the mutant has an altered reduction potential compared to the wild type enzyme
-
V131N
Thermotoga maritima MSB8 / DSM 3109 / ATCC 43589
-
the mutant has an altered reduction potential compared to the wild type enzyme
-
C302S
-
mutant displays a very weak electron paramagnetic resonance signal
C353S
-
mutant displays a very weak electron paramagnetic resonance signal
C356S
-
mutant displays a very weak electron paramagnetic resonance signal
H304A
-
similar to wild-type, mutant exhibits electron paramagnetic resonance signals characteristic of oxidized [3Fe-4S]+ cluster
H352A
-
similar to wild-type, mutant exhibits electron paramagnetic resonance signals characteristic of oxidized [3Fe-4S]+ cluster
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
DEAE-Sepharose column chromatography, Q-Sepharose column chromatography, hydroxyapatite column chromatography, phenyl-Sepharose column chromatography, and Superdex 200 gel filtration
-
nickel affinity column chromatography and Superdex 200 gel filtration
-
nickel affinity column chromatography, and Superose 12 gel filtration
-
under strictly anoxic conditions, the enzyme is inactivated in the presence of even trace amounts of O2
-
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Schut, G.J.; Adams, M.W.
The iron-hydrogenase of Thermotoga maritima utilizes ferredoxin and NADH synergistically: a new perspective on anaerobic hydrogen production
J. Bacteriol.
191
4451-4457
2009
Thermotoga maritima, Thermotoga maritima DSM 3109
brenda
Verhagen, M.; Adams, M.
Fe-only hydrogenase from Thermotoga maritima
Methods Enzymol.
331
216-226
2001
Thermotoga maritima, Thermotoga maritima DSM 3109
brenda
Berto, P.; Di Valentin, M.; Cendron, L.; Vallese, F.; Albertini, M.; Salvadori, E.; Giacometti, G.M.; Carbonera, D.; Costantini, P.
The [4Fe-4S]-cluster coordination of [FeFe]-hydrogenase maturation protein HydF as revealed by EPR and HYSCORE spectroscopies
Biochim. Biophys. Acta
1817
2149-2157
2012
Thermotoga neapolitana
brenda
Wang, S.; Huang, H.; Kahnt, J.; Thauer, R.K.
A reversible electron-bifurcating ferredoxin- and NAD-dependent [FeFe]-hydrogenase (HydABC) in Moorella thermoacetica
J. Bacteriol.
195
1267-1275
2013
Moorella thermoacetica
brenda
Zheng, Y.; Kahnt, J.; Kwon, I.H.; Mackie, R.I.; Thauer, R.K.
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
2014
Ruminococcus albus, Ruminococcus albus DSM 20455
brenda
Maso, L.; Galazzo, L.; Vallese, F.; Di Valentin, M.; Albertini, M.; De Rosa, E.; Giacometti, G.; Costantini, P.; Carbonera, D.
A conformational study of the GTPase domain of [FeFe]-hydrogenase maturation protein HydF by PELDOR spectroscopy
Appl. Magn. Reson.
46
465-479
2015
Thermotoga neapolitana
-
brenda
Birrell, J.A.; Laurich, C.; Reijerse, E.J.; Ogata, H.; Lubitz, W.
Importance of hydrogen bonding in fine tuning the [2Fe-2S] cluster redox potential of HydC from Thermotoga maritima
Biochemistry
55
4344-4355
2016
Thermotoga maritima, Thermotoga maritima MSB8 / DSM 3109 / ATCC 43589
brenda
Albertini, M.; Vallese, F.; Di Valentin, M.; Berto, P.; Giacometti, G.; Costantini, P.; Carbonera, D.
The proton iron-sulfur cluster environment of the [FeFe]-hydrogenase maturation protein HydF from Thermotoga neapolitana
Int. J. Hydrogen Energy
39
18574-18582
2014
Thermotoga neapolitana
-
brenda
EXTERNAL LINKS (specific for EC-Number 1.12.1.4)
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