Information on EC 1.1.99.33 - formate dehydrogenase (acceptor)

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The expected taxonomic range for this enzyme is: Archaea, Bacteria

EC NUMBER
COMMENTARY hide
1.1.99.33
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RECOMMENDED NAME
GeneOntology No.
formate dehydrogenase (acceptor)
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
formate + acceptor = CO2 + reduced acceptor
show the reaction diagram
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-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
methanol oxidation to carbon dioxide
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reductive acetyl coenzyme A pathway
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SYSTEMATIC NAME
IUBMB Comments
formate:acceptor oxidoreductase
Formate dehydrogenase H is a cytoplasmic enzyme that oxidizes formate without oxygen transfer, transferring electrons to a hydrogenase. The two enzymes form the formate-hydrogen lyase complex [1]. The enzyme contains an [4Fe-4S] cluster, a selenocysteine residue and a molybdopterin cofactor [1].
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
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the enzyme may have a role in formate reuptake
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
formate + acceptor
CO2 + reduced acceptor
show the reaction diagram
formate + benzyl viologen
CO2 + benzyl viologen
show the reaction diagram
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the transfer of the formate proton, H+(formate), from formate to the active site base Y- is thermodynamically coupled to two-electron oxidation of the formate molecule, thereby facilitating formation of CO2. Under normal physiological conditions, when electron flow is not limited by the terminal acceptor of electrons, the energy released upon oxidation of Mo(IV) centers by the Fe4S4 is used for deprotonation of YH(formate) and transfer of H+(formate) against the thermodynamic potential. This mechanism of proton release from FDH(Se) may play a physiological role in delivery of the formate proton H+(formate) to hydrogenase 3, which is the natural terminal acceptor of electrons for FDH(Se)
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-
?
formate + benzyl viologen
CO2 + reduced benzyl viologen
show the reaction diagram
formate + FAD
CO2 + FADH2
show the reaction diagram
formate + FMN
CO2 + FMNH2
show the reaction diagram
formate + HycB
CO2 + reduced HycB
show the reaction diagram
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the hydrogenase 3 Fe-S subunit HycB may represent the electron transfer partner of FDH-H
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-
?
formate + oxidized coenzyme F420
CO2 + reduced coenzyme F420
show the reaction diagram
additional information
?
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
formate + acceptor
CO2 + reduced acceptor
show the reaction diagram
formate + benzyl viologen
CO2 + reduced benzyl viologen
show the reaction diagram
-
the enzyme may have a role in formate reuptake
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-
?
formate + HycB
CO2 + reduced HycB
show the reaction diagram
-
the hydrogenase 3 Fe-S subunit HycB may represent the electron transfer partner of FDH-H
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-
?
formate + oxidized coenzyme F420
CO2 + reduced coenzyme F420
show the reaction diagram
additional information
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
bis(molybdopterin guanine dinucleotide)molybdenum cofactor
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molybdopterin
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molybdopterin containg enzyme, Mo is coordinated with the Se atom of selenocysteine
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
selenium
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anaerobic oxidation of formate by Methanococcus vannielii is catalyzed by two readily separable formate dehydrogenases. One of these is a 105000 Da protein that contains molybdenum, iron, and acid-labile sulfide, but not selenium. The other is a high molecular weight complex composed of selenoprotein and molybdo-iron sulfur protein subunits
selenocysteine
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the enzyme contains selenocysteine
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1,10-phenanthroline
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1,2-dihydroxybenzene-3,5-disulfonic acid
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2,2'-dipyridyl
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4,5-dihydroxybenzene-1,3-disulfonate
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azide
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0.3 mM NaN3, about 80% inhibition
formate
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iodoacetamide
NaNO3
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competitive with respect to formate
nitrate
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10 mM NaNO3, 50% inhibition
nitrite
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10 mM NaNO2, 55% inhibition
Sodium azide
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competitive with respect to formate
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
15
benzyl viologen
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pH 7.5, 24°C
9 - 26
formate
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
9 - 2833
formate
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
7.1
formate
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pH 7.5, 24°C
0.08
Sodium azide
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pH 7.5, 24°C
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.5 - 9.7
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pH 6.5: about 40% of maximal activity, pH 9.7: about 40% of maximal activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
additional information
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FDH-H synthesis is optimal when Escherichia coli grows fermentatively
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
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bound to. The alphabeta catalytic dimer is located in the cytoplasm, with a C-terminal anchor for beta protruding into the periplasm. The gamma subunit, which specifies cytochrome b, crosses the cytoplasmic membrane four times, with the N and C termini exposed to the cytoplasm
Manually annotated by BRENDA team
PDB
SCOP
CATH
ORGANISM
UNIPROT
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
105000
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anaerobic oxidation of formate by Methanococcus vannielii is catalyzed by two readily separable formate dehydrogenases. One of these is a 105000 Da protein that contains molybdenum, iron, and acid-labile sulfide, but not selenium. The other is a high molecular weight complex composed of selenoprotein and molybdo-iron sulfur protein subunits
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
crystals diffract to 2.6 A resolution and belong to a space group of P4(1)2(1)2 or P4(3)2(1)2 with unit cell dimensions a = b = 146.1 A and c = 82.7 A. There is one monomer of FDH per crystallographic asymmetric unit. Similar diffraction quality crystals of oxidized FDH can be obtained by oxidation of crystals of formate-reduced enzyme with benzyl viologen. Mo(IV)- and the reduced FeS cluster containing form of the enzyme was crystallized and this can be converted into Mo(VI)- and oxidized FeS cluster form upon oxidation
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reinterpretation of the crystal structure
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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4.8
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room temperature, 20 h, about 45% loss of activity
698686, 701023
5.3 - 6.4
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room temperature, 20 h, stable
698686, 701023
6
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maximum stability
698704
7
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room temperature, 20 h, about 60% loss of activity
698686, 701023
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
azide protects the enzyme from inactivation by O2
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enzyme in dilute solutions (30 mg/ml) is rapidly inactivated at basic pH or in the presence of formate under anaerobic conditions, but at higher enzyme concentrations (3 mg/ml) the enzyme is relatively stable
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OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
azide protects the enzyme from inactivation by O2
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698686
enzyme is extremely oxygen-sensitive
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701024
extremely oxygen-sensitive
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727803
the formate-reduced enzyme is extremely sensitive to air inactivation
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698704
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
the formate dehydrogenase component of the formate-hydrogen lyase complex
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
overproduction of the selenocysteine-containing fdhF gene product
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
high levels of formate dehydrogenase are observed in strain HF only when these cells are grown with formate in the absence of H2. In all strains two- to threefold fluctuations of both hydrogenase and formate dehydrogenase cell-free activities are observed during growth, with peak activities reached in the middle of the exponential phase
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Sec140Cys
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mutant enzyme with cysteine substituted at position 140 for the selenocysteine residue has decreased catalytic activity and exhibits a different EPR signal
additional information
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mutant form of the enzyme in which cysteine replaces selenocysteine. The mutant and wild-type enzymes display similar pH dependencies with respect to activity and stability, although the mutant enzyme profiles are slightly shifted to more alkaline pH. The mutant enzyme binds formate with greater affinity than does the wild-type enzyme, as shown by reduced values of Km and Kd. The mutant enzyme has a turnover number which is more than two orders of magnitude lower than that of the native selenium-containing enzyme. The lower turnover number results from a diminished reaction rate for the initial step of the overall reaction
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