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CO2 + reduced benzyl viologen
formate + benzyl viologen
-
-
-
r
formate + acceptor
CO2 + reduced acceptor
formate + benzyl viologen
CO2 + reduced benzyl viologen
formate + FAD
CO2 + FADH2
formate + FMN
CO2 + FMNH2
formate + HycB
CO2 + reduced HycB
-
the hydrogenase 3 Fe-S subunit HycB may represent the electron transfer partner of FDH-H
-
-
?
formate + methyl viologen
CO2 + reduced methyl viologen
-
-
-
?
formate + oxidized coenzyme F420
CO2 + reduced coenzyme F420
formate + [NiFe]-hydrogenase 3
CO2 + a [reduced hydrogenase]
-
-
-
-
?
formate + [NiFe]-hydrogenase 3
CO2 + reduced [NiFe]-hydrogenase 3
-
-
-
-
?
additional information
?
-
formate + acceptor
CO2 + reduced acceptor
-
-
-
?
formate + acceptor
CO2 + reduced acceptor
-
formate dehydrogenase H (FDHH) catalyses the first step in the formate hydrogen lyase (FHL) system
-
-
?
formate + acceptor
CO2 + reduced acceptor
-
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)
-
-
?
formate + acceptor
CO2 + reduced acceptor
-
the reinterpretation of the crystal structure suggests a new reaction mechanism: In step I, formate binds directly to Mo, displacing Se-Cys140. In step II, the alpha-proton from formate may be transferred to the nearby His141 that acts as general base. In this step the CO2 molecule can be released and two electrons transferred to Mo. Alternatively, step II may involve a selenium-carboxylated intermediate. In step III, electrons from Mo(IV) are transferred via the [4Fe-4S] center to an external electron acceptor and the catalytic cycle is completed
-
-
?
formate + benzyl viologen
CO2 + reduced benzyl viologen
-
-
-
-
?
formate + benzyl viologen
CO2 + reduced benzyl viologen
-
the enzyme may have a role in formate reuptake
-
-
?
formate + benzyl viologen
CO2 + reduced benzyl viologen
-
-
-
-
?
formate + benzyl viologen
CO2 + reduced benzyl viologen
-
-
-
?
formate + benzyl viologen
CO2 + reduced benzyl viologen
-
-
-
r
formate + benzyl viologen
CO2 + reduced benzyl viologen
-
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)
-
-
?
formate + benzyl viologen
CO2 + reduced benzyl viologen
-
FDH-H remains essentially unchanged when deuteroformate is used as a substrate
-
-
?
formate + benzyl viologen
CO2 + reduced benzyl viologen
-
formate oxidation is not rate-limiting in the overall coupled reaction of formate oxidation and benzyl viologen reduction
-
-
?
formate + benzyl viologen
CO2 + reduced benzyl viologen
-
ping-pong bi-bi kinetic mechanism
-
-
?
formate + FAD
CO2 + FADH2
-
-
-
-
?
formate + FAD
CO2 + FADH2
-
-
-
-
?
formate + FMN
CO2 + FMNH2
-
-
-
-
?
formate + FMN
CO2 + FMNH2
-
-
-
-
?
formate + oxidized coenzyme F420
CO2 + reduced coenzyme F420
-
-
-
-
?
formate + oxidized coenzyme F420
CO2 + reduced coenzyme F420
-
-
-
-
?
additional information
?
-
-
Escherichia coli possesses two hydrogenases, Hyd-3 and Hyd-4. These, in conjunction with formate dehydrogenase H (Fdh-H), constitute distinct membrane-associated formate hydrogenlyases, FHL-1 and FHL-2, both catalyzing the decomposition of formate to H2 and CO2 during fermentative growth. FHL-1 is the major pathway at acidic pH. At alkaline pH formate increases an activity of Fdh-H and of Hyd-3 both but not of Hyd-4
-
-
?
additional information
?
-
-
hydrogenase 3 but not hydrogenase 4 is the major enzyme in hydrogen gas production by Escherichia coli formate hydrogenlyase at acidic pH and in the presence of external formate
-
-
?
additional information
?
-
-
physiological role of FSH-O is to ensure rapid adaptation during a shift from aerobiosis to anaerobiosis
-
-
?
additional information
?
-
-
the enzyme catalyzes carbon exchange between carbon dioxide and formate in the absence of other electron acceptors, confirming the ping-pong reaction mechanism
-
-
?
additional information
?
-
-
no activity with NADP+ or NAD+
-
-
?
additional information
?
-
-
no activity with NADP+ or NAD+
-
-
?
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formate + acceptor
CO2 + reduced acceptor
formate + benzyl viologen
CO2 + reduced benzyl viologen
-
the enzyme may have a role in formate reuptake
-
-
?
formate + HycB
CO2 + reduced HycB
-
the hydrogenase 3 Fe-S subunit HycB may represent the electron transfer partner of FDH-H
-
-
?
formate + oxidized coenzyme F420
CO2 + reduced coenzyme F420
formate + [NiFe]-hydrogenase 3
CO2 + a [reduced hydrogenase]
-
-
-
-
?
additional information
?
-
formate + acceptor
CO2 + reduced acceptor
-
formate dehydrogenase H (FDHH) catalyses the first step in the formate hydrogen lyase (FHL) system
-
-
?
formate + acceptor
CO2 + reduced acceptor
-
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)
-
-
?
formate + oxidized coenzyme F420
CO2 + reduced coenzyme F420
-
-
-
-
?
formate + oxidized coenzyme F420
CO2 + reduced coenzyme F420
-
-
-
-
?
additional information
?
-
-
Escherichia coli possesses two hydrogenases, Hyd-3 and Hyd-4. These, in conjunction with formate dehydrogenase H (Fdh-H), constitute distinct membrane-associated formate hydrogenlyases, FHL-1 and FHL-2, both catalyzing the decomposition of formate to H2 and CO2 during fermentative growth. FHL-1 is the major pathway at acidic pH. At alkaline pH formate increases an activity of Fdh-H and of Hyd-3 both but not of Hyd-4
-
-
?
additional information
?
-
-
hydrogenase 3 but not hydrogenase 4 is the major enzyme in hydrogen gas production by Escherichia coli formate hydrogenlyase at acidic pH and in the presence of external formate
-
-
?
additional information
?
-
-
physiological role of FSH-O is to ensure rapid adaptation during a shift from aerobiosis to anaerobiosis
-
-
?
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Molybdenum
contains molybdenum
selenium
-
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
-
the enzyme contains selenocysteine
Fe
-
each mole of enzyme contains 3.3 gatoms of iron
Fe
-
Mo(IV)- and the reduced FeS cluster-containing form of the enzyme is crystallized and this can be converted into Mo(VI)- and oxidized FeS cluster form upon oxidation
Fe
-
oxidation of Mo(IV) centers by the Fe4S4 is used for deprotonation of YH(formate) and transfer of the formate proton H+(formate) against the thermodynamic potential. The Mo-Se bond is estimated to be covalent to the extent of 17-27% of the unpaired electron spin density residing in the valence 4s and 4p selenium orbitals, based on comparison of the scalar and dipolar hyperfine components to atomic 77Se. Two electron oxidation of formate by the Mo(VI) state converts Mo to the reduced Mo(IV) state with the formate proton, H+(formate), transferring to a nearby base Y-. Transfer of one electron to the Fe4S4 center converts Mo(IV) to the EPR detectable Mo(V) state. The Y- is located within magnetic contact to the [Mo-Se] center, as shown by its strong dipolar 1Hf hyperfine couplings. Photolysis of the formate-induced Mo(V) state abolishes the 1Hf hyperfine splitting from YH(formate), suggesting photoisomerization of this group or phototransfer of the proton to a more distant proton acceptor group A-. The minor effect of photolysis on the 77Se-hyperfine interaction with [77Se] selenocysteine suggests that the Y- group is not the Se atom, but instead might be the imidazole ring of the His141 residue which is located in the putative substrate-binding pocket close to the [Mo-Se] center. It is proposed that the transfer of 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
Fe
-
the enzyme may contain one 4Fe-4S cluster
Fe
-
the reinterpretation of the crystal structure suggests a new reaction mechanism: In step I, formate binds directly to Mo, displacing Se-Cys140. In step II, the alpha-proton from formate may be transferred to the nearby His141 that acts as general base. In this step the CO2 molecule can be released and two electrons transferred to Mo. Alternatively, step II may involve a selenium-carboxylated intermediate. In step III, electrons from Mo(IV) are transferred via the [4Fe-4S] center to an external electron acceptor and the catalytic cycle is completed
Mo
-
contains bis-molybdopterin guanine dinucleotide
Mo
-
enzyme contains a bis-molybdopterin guanine dinucleotide cofactor. EPR spectroscopy of the Mo(V) state indicates a square pyramidal geometry analogous to that of the Mo(IV) center. The strongest ligand field component is likely the single axial Se atom producing a ground orbital configuration Mo(dxy). The Mo-Se bond is estimated to be covalent to the extent of 17-27% of the unpaired electron spin density residing in the valence 4s and 4p selenium orbitals, based on comparison of the scalar and dipolar hyperfine components to atomic 77Se. Two electron oxidation of formate by the Mo(VI) state converts Mo to the reduced Mo(IV) state with the formate proton, H+(formate), transferring to a nearby base Y-. Transfer of one electron to the Fe4S4 center converts Mo(IV) to the EPR detectable Mo(V) state. The Y- is located within magnetic contact to the [Mo-Se] center, as shown by its strong dipolar 1Hf hyperfine couplings. Photolysis of the formate-induced Mo(V) state abolishes the 1Hf hyperfine splitting from YH(formate), suggesting photoisomerization of this group or phototransfer of the proton to a more distant proton acceptor group A-. The minor effect of photolysis on the 77Se-hyperfine interaction with [77Se] selenocysteine suggests that the Y- group is not the Se atom, but instead might be the imidazole ring of the His141 residue which is located in the putative substrate-binding pocket close to the [Mo-Se] center. It is proposed that the transfer of 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
Mo
-
Mo(IV)- and the reduced FeS cluster-containing form of the enzyme is crystallized and this can be converted into Mo(VI)- and oxidized FeS cluster form upon oxidation
Mo
-
molybdopterin containg enzyme, Mo is coordinated with the Se atom of selenocysteine
Mo
-
the reinterpretation of the crystal structure suggests a new reaction mechanism: In step I, formate binds directly to Mo, displacing Se-Cys140. In step II, the alpha-proton from formate may be transferred to the nearby His141 that acts as general base. In this step the CO2 molecule can be released and two electrons transferred to Mo. Alternatively, step II may involve a selenium-carboxylated intermediate. In step III, electrons from Mo(IV) are transferred via the [4Fe-4S] center to an external electron acceptor and the catalytic cycle is completed
Se
-
formate dehydrogenase H contains selenocysteine as an integral amino acid. Selenium of formate dehydrogenase H is directly involved in formate oxidation
Se
-
Mo of the molybdopterin is coordinated with the Se atom of selenocysteine
Se
-
selenocysteine is located at amino acid position 140
Se
-
selenocysteine-containing enzyme. The molybdenum-coordinated selenocysteine is essential for catalytic activity of the native enzyme
Se
selenocysteine-containing polypeptide
Se
-
the enzyme contains selenocysteine
Se
-
the enzyme contains selenocysteine. The Mo-Se bond is estimated to be covalent to the extent of 17-27% of the unpaired electron spin density residing in the valence 4s and 4p selenium orbitals, based on comparison of the scalar and dipolar hyperfine components to atomic 77Se. Two electron oxidation of formate by the Mo(VI) state converts Mo to the reduced Mo(IV) state with the formate proton, H+(formate), transferring to a nearby base Y-. Transfer of one electron to the Fe4S4 center converts Mo(IV) to the EPR detectable Mo(V) state. The Y- is located within magnetic contact to the [Mo-Se] center, as shown by its strong dipolar 1Hf hyperfine couplings. Photolysis of the formate-induced Mo(V) state abolishes the 1Hf hyperfine splitting from YH(formate), suggesting photoisomerization of this group or phototransfer of the proton to a more distant proton acceptor group A-. The minor effect of photolysis on the 77Se-hyperfine interaction with [77Se] selenocysteine suggests that the Y- group is not the Se atom, but instead might be the imidazole ring of the His141 residue which is located in the putative substrate-binding pocket close to the [Mo-Se] center. It is proposed that the transfer of 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
Se
-
the enzyme contains selenocysteine.The trxB gene is required for the formation of selenocysteine containing FDHH polypeptide
Se
-
the fdhF gene of Escherichia coli codes for the selenocysteine-including protein subunit of formate dehydrogenase H
Se
-
the reinterpretation of the crystal structure suggests a new reaction mechanism: In step I, formate binds directly to Mo, displacing Se-Cys140. In step II, the alpha-proton from formate may be transferred to the nearby His141 that acts as general base. In this step the CO2 molecule can be released and two electrons transferred to Mo. Alternatively, step II may involve a selenium-carboxylated intermediate. In step III, electrons from Mo(IV) are transferred via the [4Fe-4S] center to an external electron acceptor and the catalytic cycle is completed
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1,2-dihydroxybenzene-3,5-disulfonic acid
-
-
4,5-dihydroxybenzene-1,3-disulfonate
-
-
azide
-
0.3 mM NaN3, about 80% inhibition
N3-
formate oxidation is inhibited strongly and competitively whereas CO2 reduction is inhibited weakly and not competitively; strongly inhibits the oxidation of formate, whereas CO2 reduction is inhibited only weakly and not competitively
NaNO3
-
competitive with respect to formate
nitrate
-
10 mM NaNO3, 50% inhibition
nitrite
-
10 mM NaNO2, 55% inhibition
NO2-
formate oxidation is inhibited strongly and competitively whereas CO2 reduction is inhibited weakly and not competitively; strongly inhibits the oxidation of formate, whereas CO2 reduction is inhibited only weakly and not competitively
NO3-
formate oxidation is inhibited strongly and competitively whereas CO2 reduction is inhibited weakly and not competitively; strongly inhibits the oxidation of formate, whereas CO2 reduction is inhibited only weakly and not competitively
OCN-
formate oxidation is inhibited strongly and competitively whereas CO2 reduction is inhibited weakly and not competitively; strongly inhibits the oxidation of formate, whereas CO2 reduction is inhibited only weakly and not competitively
SCN-
formate oxidation is inhibited strongly and competitively whereas CO2 reduction is inhibited weakly and not competitively; strongly inhibits the oxidation of formate, whereas CO2 reduction is inhibited only weakly and not competitively
Sodium azide
-
competitive with respect to formate
iodoacetamide
-
inhibition is enhanced in the presence of formate
iodoacetamide
-
iodoacetamide-dependent loss of activity occurrs only when formate is present
iodoacetamide
-
addition of 1 mM iodoacetamide, to enzyme preparations in pH 7 buffer containing 2 mM 2-mercaptoethanol inactivates
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Raaijmakers, H.C.; Romao, M.J.
Formate-reduced E. coli formate dehydrogenase H: The reinterpretation of the crystal structure suggests a new reaction mechanism
J. Biol. Inorg. Chem.
11
849-854
2006
Escherichia coli
brenda
Takahata, M.; Tamura, T.; Abe, K.; Mihara, H.; Kurokawa, S.; Yamamoto, Y.; Nakano, R.; Esaki, N.; Inagaki, K.
Selenite assimilation into formate dehydrogenase H depends on thioredoxin reductase in Escherichia coli
J. Biochem.
143
467-473
2008
Escherichia coli
brenda
Sawers, G.
The hydrogenases and formate dehydrogenases of Escherichia coli
Antonie van Leeuwenhoek
66
57-88
1994
Escherichia coli
brenda
Khangulov, S.V.; Gladyshev, V.N.; Dismukes, G.C.; Stadtman, T.C.
Selenium-containing formate dehydrogenase H from Escherichia coli: A molybdopterin enzyme that catalyzes formate oxidation without oxygen transfer
Biochemistry
37
3518-3528
1998
Escherichia coli
brenda
Mnatsakanyan, N.; Bagramyan, K.; Trchounian, A.
Hydrogenase 3 but not hydrogenase 4 is major in hydrogen gas production by Escherichia coli formate hydrogenlyase at acidic pH and in the presence of external formate
Cell Biochem. Biophys.
41
357-366
2004
Escherichia coli
brenda
Mnatsakanyan. N.; Vassilian, A.; Navasardyan, L.; Bagramyan, K.; Trchounian, A.
Regulation of Escherichia coli formate hydrogenlyase activity by formate at alkaline pH
Curr. Microbiol.
45
281-286
2002
Escherichia coli
brenda
Benoit, S.; Abaibou, H.; Mandrand-Berthelot, M.A.
Topological analysis of the aerobic membrane-bound formate dehydrogenase of Escherichia coli
J. Bacteriol.
180
6625-6634
1998
Escherichia coli
brenda
Axley, M.J.; Grahame, D.A.; Stadtman, T.C.
Escherichia coli formate-hydrogen lyase. Purification and properties of the selenium-dependent formate dehydrogenase component
J. Biol. Chem.
265
18213-18218
1990
Escherichia coli
brenda
Axley, M.J.; Grahame, D.A.
Kinetics for formate dehydrogenase of Escherichia coli formate-hydrogenlyase
J. Biol. Chem.
266
13731-13736
1991
Escherichia coli
brenda
Gladyshev, V.N.; Boyington, J.C.; Khangulov, S.V.; Grahame, D.A.; Stadtman, T.C.; Sun, P.D.
Characterization of crystalline formate dehydrogenase H from Escherichia coli
J. Biol. Chem.
271
8095-8100
1996
Escherichia coli
brenda
Andrews, S.C.; Berks, B.C.; McClay, J.; Ambler, A.; Quail, M.A.; Golby, P.; Guest, J.R.
A 12-cistron Escherichia coli operon (hyf) encoding a putative proton-translocating formate hydrogenlyase system
Microbiology
143
3633-3647
1997
Escherichia coli
brenda
Chen, G.T.; Axley, M.J.; Hacia, J.; Inouye, M.
Overproduction of a selenocysteine-containing polypeptide in Escherichia coli: the fdhFgene product
Mol. Microbiol.
6
781-785
1992
Escherichia coli
brenda
Zinoni, F.; Birkmann, A.; Stadtman, T.C.; Bck, A.
Nucleotide sequence and expression of the selenocysteine-containing polypeptide of formate dehydrogenase (formate-hydrogen-lyase-linked) from Escherichia coli
Proc. Natl. Acad. Sci. USA
83
4650-4654
1986
Escherichia coli (P07658), Escherichia coli
brenda
Axley, M.J.; Bck, A.; Stadtman, T.C.
Catalytic properties of an Escherichia coli formate dehydrogenase mutant in which sulfur replaces selenium
Proc. Natl. Acad. Sci. USA
88
8450-8454
1991
Escherichia coli
brenda
Gladyshev, V.N.; Khangulov, S.V.; Axley, M.J.; Stadtman, T.C.
Coordination of selenium to molybdenum in formate dehydrogenase H from Escherichia coli
Proc. Natl. Acad. Sci. USA
91
7708-7711
1994
Escherichia coli
brenda
Vornolt, J.; Kunow, J.; Stetter, K.; Thauer, R.
Enzymes and coenzymes of the carbon monoxide dehydrogenase pathway for autotrophic CO2 fixation in Archaeoglobus lithotrophicus and the lack of carbon monoxide dehydrogenase in the heterotrophic A. profundus
Arch. Microbiol.
163
112-118
1995
Archaeoglobus fulgidus, Archaeoglobus profundus, Archaeoglobus profundus DSM 5631
-
brenda
Henstra, A.M.; Dijkema, C.; Stams, A.J.
Archaeoglobus fulgidus couples CO oxidation to sulfate reduction and acetogenesis with transient formate accumulation
Environ. Microbiol.
9
1836-1841
2007
Archaeoglobus fulgidus
brenda
Jones, J.B.; Dilworth, G.L.; Stadtman, T.C.
Occurrence of selenocysteine in the selenium-dependent formate dehydrogenase of Methanococcus vannielii
Arch. Biochem. Biophys.
195
255-260
1979
Methanococcus vannielii
brenda
Sparling, R.; Daniels, L.
Regulation of formate dehydrogenase activity in Methanococcus thermolithotrophicus
J. Bacteriol.
172
1464-1469
1990
Methanothermococcus thermolithotrophicus, Methanothermococcus thermolithotrophicus HF
brenda
Jones, J.B.; Stadtman, T.C.
Selenium-dependent and selenium-independent formate dehydrogenases of Methanococcus vannielii. Separation of the two forms and characterization of the purified selenium-independent form
J. Biol. Chem.
256
656-663
1981
Methanococcus vannielii, Methanococcus vannielii DSM 1224
brenda
Bassegoda, A.; Madden, C.; Wakerley, D.W.; Reisner, E.; Hirst, J.
Reversible interconversion of CO2 and formate by a molybdenum-containing formate dehydrogenase
J. Am. Chem. Soc.
136
15473-15476
2014
Escherichia coli (P07658)
brenda
Robinson, W.E.; Bassegoda, A.; Reisner, E.; Hirst, J.
Oxidation-state-dependent binding properties of the active site in a Mo-containing formate dehydrogenase
J. Am. Chem. Soc.
139
9927-9936
2017
Escherichia coli, Escherichia coli (P07658)
brenda
Pinske, C.
The ferredoxin-like proteins HydN and YsaA enhance redox dye-linked activity of the formate dehydrogenase H component of the formate hydrogenlyase complex
Front. Microbiol.
9
1238
2018
Escherichia coli
brenda