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 . The enzyme contains an [4Fe-4S] cluster, a selenocysteine residue and a molybdopterin cofactor .
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SYSTEMATIC NAME
IUBMB Comments
formate:[oxidized hydrogenase] 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].
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)
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
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)
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
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
the enzyme catalyzes carbon exchange between carbon dioxide and formate in the absence of other electron acceptors, confirming the ping-pong reaction mechanism
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)
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
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
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
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
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
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
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(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
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 dehydrogenase H contains selenocysteine as an integral amino acid. Selenium of formate dehydrogenase H is directly involved in formate oxidation
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
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 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
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
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
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
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
the ferredoxin-like proteins HydN and YsaA enhance redox dye-linked activity of the formate dehydrogenase H component of the formate hydrogenlyase complex
the ferredoxin-like proteins HydN and YsaA enhance redox dye-linked activity of the formate dehydrogenase H component of the formate hydrogenlyase complex
Components of the Rv0081-Rv0088 locus encoding a predicted formate hydrogenlyase complex are co-regulated by Rv0081, MprA, and DosR in Mycobacterium tuberculosis.
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
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
x * 80000, formate dehydrogenase component, the formate-hydrogen lyase complex of Escherichia coli decomposes formic acid to hydrogen and carbon dioxide under anaerobic conditions in the absence of exogenous electron acceptors. The complex consists of two separable enzymatic activities: a formate dehydrogenase and a hydrogenase, SDS-PAGE
x * 80000, formate dehydrogenase component, the formate-hydrogen lyase complex of Escherichia coli decomposes formic acid to hydrogen and carbon dioxide under anaerobic conditions in the absence of exogenous electron acceptors. The complex consists of two separable enzymatic activities: a formate dehydrogenase and a hydrogenase, SDS-PAGE
formate dehydrogenase H (FDH-H) and [NiFe]-hydrogenase 3 (Hyd-3) form the catalytic components of the hydrogen-producing formate hydrogenlyase (FHL) complex
hydrogenase 4 (Hyf), in conjunction with formate dehydrogenase H (Fdh-H), forms a respiration-linked proton-translocating formate hydrogenlyase (FHL-2)
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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
mutant enzyme with cysteine substituted at position 140 for the selenocysteine residue has decreased catalytic activity and exhibits a different EPR signal
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
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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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
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
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