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Information on EC 1.17.98.3 - formate dehydrogenase (coenzyme F420)
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1.17.98.3 formate dehydrogenase (coenzyme F420)IUBMB Comments
The enzyme, characterized from methanogenic archaea, is involved in formate-dependent H2 production. It contains noncovalently bound FAD .
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The enzyme appears in viruses and cellular organisms
Synonyms
coenzyme f420-dependent formate dehydrogenase, coenzyme f420-reducing formate dehydrogenase, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
coenzyme F420-dependent formate dehydrogenase
EC 1.2.99.9
-
-
formerly
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
formate + oxidized coenzyme F420 = CO2 + reduced coenzyme F420
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-
-
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formate + oxidized coenzyme F420 = CO2 + reduced coenzyme F420
the enzyme is specific for the si face hydride transfer to C5 of coenzyme F420. While catalysis probably occurs by hydride transfer from formate to the enzyme to generate an enzyme-H2 species and then by hydride transfer back out to F420, the formate-derived hydrogen exchanges with solvent protons before transfer back out to coenzyme F420. The kinetics of hydride transfer from formate reveals that this step is not rate determining
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PATHWAY SOURCE
PATHWAYS
BRENDA
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SYSTEMATIC NAME
IUBMB Comments
formate:coenzyme-F420 oxidoreductase
The enzyme, characterized from methanogenic archaea, is involved in formate-dependent H2 production. It contains noncovalently bound FAD [1].
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
formate + FAD
CO2 + FADH2
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specific activity 5.4fold lower than for the reaction with coenzyme F420. Vmax /Km is 11fold as compared to reaction with coenzyme F420
-
-
?
formate + FMN
CO2 + FMNH2
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specific activity 9.1fold lower than for the reaction with coenzyme F420. Vmax /Km is 6.4fold as compared to reaction with coenzyme F420
-
-
?
formate + oxidized benzyl viologen
CO2 + reduced benzyl viologen
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-
-
-
?
formate + 2,3,5-triphenyltetrazoIium chloride
CO2 + ?
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-
-
-
?
formate + oxidized coenzyme F420
CO2 + reduced coenzyme F420
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-
-
-
?
formate + oxidized coenzyme F420
CO2 + reduced coenzyme F420
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no activity with NAD+ or NADP*
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-
?
formate + oxidized coenzyme F420
CO2 + reduced coenzyme F420
-
-
-
-
?
formate + oxidized coenzyme F420
CO2 + reduced coenzyme F420
-
-
-
-
?
formate + oxidized coenzyme F420
CO2 + reduced coenzyme F420
-
reduced coenzyme F420 obtained from the formate dehydrogenase can be further linked to the formation of hydrogen via the F420-dependent hydrogenase reaction
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-
?
formate + oxidized coenzyme F420
CO2 + reduced coenzyme F420
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-
-
-
?
formate + oxidized coenzyme F420
CO2 + reduced coenzyme F420
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a key enzyme for formate-dependent H2 production
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-
?
formate + oxidized coenzyme F420
CO2 + reduced coenzyme F420
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-
-
-
?
formate + oxidized coenzyme F420
CO2 + reduced coenzyme F420
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i.e. 8-hydroxy-5-deazaflavin
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-
?
formate + oxidized coenzyme F420
CO2 + reduced coenzyme F420
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-
-
-
?
formate + oxidized coenzyme F420
CO2 + reduced coenzyme F420
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i.e. 8-hydroxy-5-deazaflavin
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-
?
formate + oxidized methyl viologen
CO2 + reduced methyl viologen
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-
-
-
?
formate + oxidized methyl viologen
CO2 + reduced methyl viologen
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the enzyme is specific for the si face hydride transfer to C5 of coenzyme F420
-
-
?
formate + oxidized methyl viologen
CO2 + reduced methyl viologen
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-
-
-
?
formate + oxidized methyl viologen
CO2 + reduced methyl viologen
-
-
-
-
?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
formate + oxidized coenzyme F420
CO2 + reduced coenzyme F420
-
-
-
-
?
formate + oxidized coenzyme F420
CO2 + reduced coenzyme F420
-
reduced coenzyme F420 obtained from the formate dehydrogenase can be further linked to the formation of hydrogen via the F420-dependent hydrogenase reaction
-
-
?
formate + oxidized coenzyme F420
CO2 + reduced coenzyme F420
-
-
-
-
?
formate + oxidized coenzyme F420
CO2 + reduced coenzyme F420
-
a key enzyme for formate-dependent H2 production
-
-
?
formate + oxidized coenzyme F420
CO2 + reduced coenzyme F420
-
-
-
-
?
formate + oxidized coenzyme F420
CO2 + reduced coenzyme F420
-
-
-
-
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
molybdopterin
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denaturation of the enzyme releases a molybdopterin cofactor, the enzyme contains 1 mol of molybdenum
FAD
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FAD stimulates activity about 1.3fold in the presence of coenzyme F420 but can not replace coenzyme F420
FAD
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nonheme iron-sulfur flavoprotein, contains 1 FAD molecule. Reduction of the enzyme facilitates dissociation of FAD, and the FAD-depleted enzyme is unable to reduce coenzyme F420. Preincubation of the FAD-depleted enzyme with FAD restores coenzyme F420-dependent activity
FAD
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the enzyme contains noncovalently bound FAD that is required for coenzyme F420-dependent activity. Neither flavin mononucleotide nor FADH2 can replace FAD
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Molybdenum
-
the purified enzyme contains 0.0074 mM of molybdenum per g of protein
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.006
oxidized coenzyme F420
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pH 7.5, temperature not specified in the publication
0.009
formate
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pH 7.5, temperature not specified in the publication, substrate: deuterioformate
0.012
formate
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pH 7.5, temperature not specified in the publication, substrate: protioformate
0.83
formate
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pH 8.0, temperature not specified in the publication
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.039
azide
-
pH 7.5, temperature not specified in the publication
0.006
cyanide
-
pH 7.5, temperature not specified in the publication
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
0.0009
-
substrate: FMN, pH 7.5, temperature not specified in the publication
0.0016
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substrate: FAD, pH 7.5, temperature not specified in the publication
0.0082
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substrate: oxidized coenzyme F420, pH 7.5, temperature not specified in the publication
0.059
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substrate: oxidized methyl viologen, pH 7.5, temperature not specified in the publication
0.1 - 1
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substrate: coenzyme F420, pH 8.0, temperature not specified in the publication
36.2
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substrate: coenzyme F420, pH and temperature not specified in the publication
447
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substrate: methyl viologen, pH and temperature not specified in the publication
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7.3 - 8.3
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pH 7.3: about 40% of maximal activity, pH 8.3: about 70% of maximal activity
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Q877E3: alpha subunit fdhA2, Q877C5: beta subunit fdhB2, the Methanococcus maripaludis genome contains two gene clusters important for formate utilization. Phylogenetic analysis suggests that the two formate dehydrogenase gene sets arise from duplication events within the methanococcal lineage. The first gene cluster encodes homologs of formate dehydrogenase (FdhA1) and (FdhB1) subunits and a putative formate transporter (FdhC) as well as a carbonic anhydrase analog. The second gene cluster encodes only FdhA2 and FdhB2 homologs. Mutants lacking either fdhA gene exhibit a partial growth defect on formate, whereas a double mutant is completely unable to grow on formate as a sole methanogenic substrate
Q877E3; Q877C5
UniProt
brenda
Q877E4: alpha subunit fdhA1, Q877C6: beta subunit fdhB1, the Methanococcus maripaludis genome contains two gene clusters important for formate utilization. Phylogenetic analysis suggests that the two formate dehydrogenase gene sets arise from duplication events within the methanococcal lineage. The first gene cluster encodes homologs of formate dehydrogenase (FdhA1) and (FdhB1) subunits and a putative formate transporter (FdhC) as well as a carbonic anhydrase analog. The second gene cluster encodes only FdhA2 and FdhB2 homologs. Mutants lacking either fdhA gene exhibit a partial growth defect on formate, whereas a double mutant is completely unable to grow on formate as a sole methanogenic substrate
Q877E4; Q877C6
UniProt
brenda
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
malfunction
-
H2 production and growth are severely reduced in a mutant containing a deletion of the gene encoding the Fdh1 isozyme, indicating that it was the primary Fdh. In contrast, a mutant containing a deletion of the gene encoding the Fdh2 isozyme possesses near-wild-type activities, indicating that this isozyme does not play a major role
physiological function
-
a key enzyme for formate-dependent H2 production
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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). A0A8B3S242_9EURY
382
0
42974
TrEMBL
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
53000
-
1 * 85000 (alpha-subunit) + 1 * 53000 (beta-subunit), SDS-PAGE
85000
-
1 * 85000 (alpha-subunit) + 1 * 53000 (beta-subunit), SDS-PAGE
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
dimer
-
1 * 85000 (alpha-subunit) + 1 * 53000 (beta-subunit), SDS-PAGE
dimer
-
1 * 85000 (alpha-subunit) + 1 * 53000 (beta-subunit), SDS-PAGE
-
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GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
azide, FAD, glycerol, and 2-mercaptoethanol stabilize during purification
-
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OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
the enzyme is extremely sensitive to oxygen. The exposure of crude cell-free extract to 101.3 kPa (1 atm) of air results in rapid loss of activity. The removal of air by vacuum degassing with O2-free N2 and the addition of 1 mM sodium dithionite does not restore activity.Sodium azide (10 mM) partially protected the against inactivation by air
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727711
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Lupa, B.; Hendrickson, E.L.; Leigh, J.A.; Whitman, W.B.
Formate-dependent H2 production by the mesophilic methanogen Methanococcus maripaludis
Appl. Environ. Microbiol.
74
6584-6590
2008
Methanococcus maripaludis
brenda
Schauer, N.L.; Ferry, J.G.; Honek, J.F.; Orme-Johnson, W.H.; Walsh, C.
Mechanistic studies of the coenzyme F420 reducing formate dehydrogenase from Methanobacterium formicicum
Biochemistry
25
:7163-7168
1986
Methanobacterium formicicum
brenda
Tzing, S.F.; Bryant, M.P.; Wolfe, R.S.
Factor 420-dependent pyridine nucleotide-linked formate metabolism of Methanobacterium ruminantium
J. Bacteriol.
121
192-196
1975
Methanobrevibacter ruminantium
brenda
Schauer, N.L.; Ferry, J.G.
Properties of formate dehydrogenase in Methanobacterium formicicum
J. Bacteriol.
150
1-7
1982
Methanobacterium formicicum
brenda
Schauer, N.L.; Ferry, J.G.
FAD requirement for the reduction of coenzyme F420 by formate dehydrogenase from Methanobacterium formicicum
J. Bacteriol.
155
467-472
1983
Methanobacterium formicicum
brenda
Schauer, N.L.; Ferry, J.G.
Composition of the coenzyme F420-dependent formate dehydrogenase from Methanobacterium formicicum
J. Bacteriol.
165
405-411
1986
Methanobacterium formicicum, Methanobacterium formicicum DSM 2639
brenda
Baron, S.F.; Ferry, J.G.
Reconstitution and properties of a coenzyme F420-mediated formate hydrogenlyase system in Methanobacterium formicicum
J. Bacteriol.
171
3854-3859
1989
Methanobacterium formicicum
brenda
Wood, G.E.; Haydock, A.K.; Leigh, J.A.
Function and regulation of the formate dehydrogenase genes of the methanogenic archaeon Methanococcus maripaludis
J. Bacteriol.
185
2548-2554
2003
Methanococcus maripaludis (Q877E3 and Q877C5), Methanococcus maripaludis (Q877E4 and Q877C6)
brenda
Jones, J.B.; Stadtman, T.C.
Reconstitution of a formate-NADP+ oxidoreductase from formate dehydrogenase and a 5-deazaflavin-linked NADP+ reductase isolated from Methanococcus vannielii
J. Biol. Chem.
255
1049-1053
1980
Methanococcus vannielii, Methanococcus vannielii DSM 1224
brenda
Costa, K.C.; Yoon, S.H.; Pan, M.; Burn, J.A.; Baliga, N.S.; Leigh, J.A.
Effects of H2 and formate on growth yield and regulation of methanogenesis in Methanococcus maripaludis
J. Bacteriol.
195
1456-1462
2013
Methanococcus maripaludis
brenda
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