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Escherichia coli K-12 substr. MG1655 Transporter: formate dehydrogenase N

Synonyms: Fdh-N

Subunit composition of formate dehydrogenase N = [(FdnI)(FdnH)(FdnG)]3
         formate dehydrogenase N, subcomplex = (FdnI)(FdnH)(FdnG)
                 formate dehydrogenase N, γ subunit = FdnI (summary available)
                 formate dehydrogenase N, β subunit = FdnH (summary available)
                 formate dehydrogenase N, α subunit = FdnG (extended summary available)

Summary:
fdnGHI encodes membrane bound formate dehydrogenase N (FDH-N) - a respiratory enzyme that catalyses the oxidation of formate to carbon dioxide, donating electrons to the quinone pool for the reduction of anaerobic respiratory substrates such as nitrate and trimethylamine N-oxide. FDH-N is a member of the complex iron sulfur molybdoenzyme (CISM) family [Rothery08].

The oxidation of formate by FDH-N is electrogenic (H+/e- = 1); oxidation of formate in the periplasm is accompanied by menaquinone reduction at the cytoplasmic face of the inner membrane [Jones80, Jormakka02]. Expression of formate dehydrogenase-N is induced by nitrate and anaerobiosis, mediated by NarL and Fnr, respectively [Berg90, Wang03b].

Purified FDH-N contains three subunits, designated α (FdnG), β (FdnH) and γ (FdnI) [Enoch75]. A crystal structure, resolved at 1.6 Å, indicates that this subcomplex is further organised into physiologically relevant trimers with the α and β subunits located towards the periplasmic face of the inner membrane and the γ subunits located towards the cytoplasm. Electrons are tranferred from the site of formate oxidation in the α subunit across the membrane to the site of menaquinone reduction in the γ subunit. Protons are taken up from the cytoplasm at the menaquinone reduction site [Jormakka02].

E. coli K-12 contains two other formate dehydrogenases - formate dehydrogenase-O (low level constitutive expression) and formate dehydrogenase-H - a component of the fermentative formate-hydrogenlyase complex.

Reviews: [Sawers94, Jormakka03]

Citations: [RuizHerrera69, Scott76, Lester71, RuizHerrera69a, Enoch74, Barker00, Berg91a, Zorn13, Cox81a, Enoch72, Haddock82, Boxer82]

Locations [Comment 1Comment 1]: inner membrane

Relationship Links: PDB:Structure:1KQF , PDB:Structure:1KQG

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0009061 - anaerobic respiration Inferred from experiment [Berg90]
GO:0015944 - formate oxidation Inferred from experiment [Enoch75]
GO:0019645 - anaerobic electron transport chain Inferred from experiment [Enoch74]
Molecular Function: GO:0009055 - electron carrier activity Inferred from experiment [Jormakka02]
GO:0036397 - formate dehydrogenase (quinone) activity Inferred from experiment [Enoch75]
Cellular Component: GO:0009326 - formate dehydrogenase complex Inferred from experiment [Jormakka02, Enoch75]
GO:0016021 - integral component of membrane Inferred from experiment [Enoch82]
GO:0071575 - integral component of external side of plasma membrane Inferred from experiment [Jormakka02]

Credits:
Revised 01-Dec-2014 by Mackie A , Macquarie University
Last-Curated ? 01-Dec-2014 by Mackie A , Macquarie University


Enzymatic reaction of: formate dehydrogenase-N (formate dehydrogenase N)

Synonyms: formate dehydrogenase, nitrate inducible, Fdh-N

EC Number: 1.1.5.6

Transport reaction diagram for formate dehydrogenase-N

In Pathways: nitrate reduction III (dissimilatory) , formate to dimethyl sulfoxide electron transfer , formate to trimethylamine N-oxide electron transfer

Summary:

Cofactors or Prosthetic Groups: bis(guanylyl molybdopterin cofactor) [Jormakka02], heme b [Jormakka02]

Inhibitors (Unknown Mechanism): azide [Enoch75] , p-hydroxymercuribenzoate [Enoch75] , iodoacetamide [Enoch75] , oxygen [Enoch75] , hydrogen cyanide [Enoch75]


Subunit of formate dehydrogenase N, subcomplex: formate dehydrogenase N, γ subunit

Synonyms: FdnI

Gene: fdnI Accession Numbers: EG11229 (EcoCyc), b1476, ECK1470

Locations: inner membrane

Sequence Length: 217 AAs

Molecular Weight: 25.368 kD (from nucleotide sequence)

Molecular Weight: 20.0 kD (experimental) [Enoch75]

pI: 9.68

GO Terms:

Biological Process: GO:0009061 - anaerobic respiration Inferred from experiment [Berg90]
GO:0015944 - formate oxidation Inferred from experiment [Enoch75]
GO:0022904 - respiratory electron transport chain Inferred by computational analysis [GOA01]
GO:0045333 - cellular respiration Inferred by computational analysis [GOA01]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Jormakka02]
GO:0009055 - electron carrier activity Inferred from experiment [Jormakka02]
GO:0020037 - heme binding Inferred from experiment [Jormakka02]
GO:0036397 - formate dehydrogenase (quinone) activity Inferred from experiment [Enoch75]
GO:0008863 - formate dehydrogenase (NAD+) activity Inferred by computational analysis [GOA01]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, DiazMejia09, Daley05]
GO:0005887 - integral component of plasma membrane Inferred from experiment [Jormakka02]
GO:0009326 - formate dehydrogenase complex Inferred from experiment Inferred by computational analysis [GOA01, Jormakka02, Enoch75]
GO:0016021 - integral component of membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01, Enoch82]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11, GOA01]

MultiFun Terms: cell structure membrane
metabolism biosynthesis of macromolecules (cellular constituents) large molecule carriers cytochromes
metabolism energy metabolism, carbon anaerobic respiration
metabolism energy production/transport electron donors

Isozyme Sequence Similarity:
formate dehydrogenase-O, γ subunit: YES

Unification Links: EcoliWiki:b1476 , ModBase:P0AEK7 , PR:PRO_000022583 , Protein Model Portal:P0AEK7 , RefSeq:NP_415993 , SMR:P0AEK7 , String:511145.b1476 , Swiss-Model:P0AEK7 , UniProt:P0AEK7

Relationship Links: InterPro:IN-FAMILY:IPR006471 , InterPro:IN-FAMILY:IPR016174 , Panther:IN-FAMILY:PTHR30074:SF2 , PDB:Structure:1KQF , PDB:Structure:1KQG , Pfam:IN-FAMILY:PF00033

Reactions known to consume the compound:

Not in pathways:
a ubiquinol-8 oxidoreductase + a b-type cytochrome → a ubiquinone-8 oxidoreductase + a reduced b-type cytochrome
a b-type cytochrome + a menaquinone oxidoreductase (demethylmenaquinol) → a reduced b-type cytochrome + a menaquinone oxidoreductase (demethylmenaquinone)
a b-type cytochrome + a menaquinone oxidoreductase (menaquinol-8) → a reduced b-type cytochrome + a menaquinone oxidoreductase (menaquinone-8)
a reduced b-type cytochrome + a b-type cytochromea b-type cytochrome + a reduced cytochrome o

Summary:
fdnI encodes the γ subunit of formate dehydrogenase-N (Fhd-N); it is an integral membrane protein with four transmembrane helices, which, together with the single transmembrane helix of FdnH and a cardiolipin molecule, form a tightly packed trimer in the inner membrane. The γ subunit contains two heme b groups - heme bP located towards the periplasmic side of the membrane and heme bC located towards the cytoplasmic face of the membrane - and a site for menaquinone reduction [Berg91a, Jormakka02].

Essentiality data for fdnI knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 2]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 3]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 4]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 3]
Yes [Feist07, Comment 5]

Subunit of formate dehydrogenase N, subcomplex: formate dehydrogenase N, β subunit

Synonyms: FdnH

Gene: fdnH Accession Numbers: EG11228 (EcoCyc), b1475, ECK1469

Locations: inner membrane

Sequence Length: 294 AAs

Molecular Weight: 32.239 kD (from nucleotide sequence)

Molecular Weight: 32.0 kD (experimental) [Enoch75]

pI: 5.67

GO Terms:

Biological Process: GO:0009061 - anaerobic respiration Inferred from experiment [Berg90]
GO:0015944 - formate oxidation Inferred from experiment [Enoch75]
GO:0045333 - cellular respiration Inferred by computational analysis [GOA01]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0009055 - electron carrier activity Inferred from experiment Inferred by computational analysis [Gaudet10, Jormakka02]
GO:0036397 - formate dehydrogenase (quinone) activity Inferred from experiment [Enoch75]
GO:0008863 - formate dehydrogenase (NAD+) activity Inferred by computational analysis [GOA01]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred by computational analysis [UniProtGOA11, Jormakka02]
Cellular Component: GO:0009326 - formate dehydrogenase complex Inferred from experiment [Jormakka02, Enoch75]
GO:0016020 - membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11, Lasserre06]
GO:0071575 - integral component of external side of plasma membrane Inferred from experiment [Jormakka02]
GO:0005886 - plasma membrane Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, DiazMejia09]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11, GOA01]

MultiFun Terms: cell structure membrane
metabolism energy metabolism, carbon anaerobic respiration
metabolism energy production/transport electron donors

Isozyme Sequence Similarity:
formate dehydrogenase-O, β subunit: YES

Unification Links: DIP:DIP-35836N , EcoliWiki:b1475 , Mint:MINT-1286317 , ModBase:P0AAJ3 , PR:PRO_000022582 , Pride:P0AAJ3 , Protein Model Portal:P0AAJ3 , RefSeq:NP_415992 , SMR:P0AAJ3 , String:511145.b1475 , UniProt:P0AAJ3

Relationship Links: InterPro:IN-FAMILY:IPR001450 , InterPro:IN-FAMILY:IPR006470 , InterPro:IN-FAMILY:IPR014603 , InterPro:IN-FAMILY:IPR015246 , InterPro:IN-FAMILY:IPR017896 , InterPro:IN-FAMILY:IPR017900 , PDB:Structure:1KQF , PDB:Structure:1KQG , Pfam:IN-FAMILY:PF00037 , Pfam:IN-FAMILY:PF09163 , Pfam:IN-FAMILY:PF12798 , Pfam:IN-FAMILY:PF12838 , Prosite:IN-FAMILY:PS00198 , Prosite:IN-FAMILY:PS51379

Summary:
fdnH encodes the β subunit of formate dehydrogenase N (Fdh-N); it contains four [4Fe-4S] clusters (FS1, FS2, FS3 and FS4) and one C-terminal transmembrane helix [Berg91a, Jormakka02]. FdnH serves as a conduit for electrons that are transferred from the formate oxidation site in the α subunit (FdnG) to the menaquinone associated with the β (FdnI) subunit of formate dehydrogenase-N [Jormakka02].

Essentiality data for fdnH knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 2]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 3]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 4]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 3]
Yes [Feist07, Comment 5]

Subunit of formate dehydrogenase N, subcomplex: formate dehydrogenase N, α subunit

Synonyms: FdnG

Gene: fdnG Accession Numbers: EG11227 (EcoCyc), b1474, ECK1468

Locations: periplasmic space, cytosol, membrane

Sequence Length: 1015 AAs

Molecular Weight: 112.96 kD (from nucleotide sequence)

Molecular Weight: 110.0 kD (experimental) [Enoch75]

pI: 6.97

GO Terms:

Biological Process: GO:0009061 - anaerobic respiration Inferred from experiment [Berg90]
GO:0015944 - formate oxidation Inferred from experiment [Enoch75]
GO:0045333 - cellular respiration Inferred by computational analysis [GOA01]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11, GOA01]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Jormakka02, Rajagopala14, Chan09, Butland05]
GO:0008430 - selenium binding Inferred from experiment [Enoch75, Jormakka02]
GO:0009055 - electron carrier activity Inferred from experiment Inferred by computational analysis [GOA01, Jormakka02]
GO:0030151 - molybdenum ion binding Inferred from experiment Inferred by computational analysis [GOA01, Enoch75, Jormakka02]
GO:0036397 - formate dehydrogenase (quinone) activity Inferred from experiment Inferred by computational analysis [GOA01a, Enoch75]
GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01, Jormakka02]
GO:0008863 - formate dehydrogenase (NAD+) activity Inferred by computational analysis [GOA01]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0009326 - formate dehydrogenase complex Inferred from experiment [Jormakka02, Enoch75]
GO:0016020 - membrane Inferred from experiment [Lasserre06]
GO:0030288 - outer membrane-bounded periplasmic space Inferred by computational analysis Inferred from experiment [Stanley02, DiazMejia09]
GO:0005737 - cytoplasm Inferred by computational analysis [GOA01]
GO:0042597 - periplasmic space Inferred by computational analysis [UniProtGOA11a, UniProtGOA11]

MultiFun Terms: metabolism energy metabolism, carbon anaerobic respiration
metabolism energy production/transport electron donors

Isozyme Sequence Similarity:
formate dehydrogenase-O, α subunit: YES

Unification Links: DIP:DIP-9573N , EcoliWiki:b1474 , Mint:MINT-1236143 , ModBase:P24183 , PR:PRO_000022581 , Pride:P24183 , Protein Model Portal:P24183 , RefSeq:NP_415991 , SMR:P24183 , String:511145.b1474 , UniProt:P24183

Relationship Links: InterPro:IN-FAMILY:IPR006311 , InterPro:IN-FAMILY:IPR006443 , InterPro:IN-FAMILY:IPR006655 , InterPro:IN-FAMILY:IPR006656 , InterPro:IN-FAMILY:IPR006657 , InterPro:IN-FAMILY:IPR006963 , InterPro:IN-FAMILY:IPR009010 , InterPro:IN-FAMILY:IPR027467 , PDB:Structure:1KQF , PDB:Structure:1KQG , Pfam:IN-FAMILY:PF00384 , Pfam:IN-FAMILY:PF01568 , Pfam:IN-FAMILY:PF04879 , Prosite:IN-FAMILY:PS00551 , Prosite:IN-FAMILY:PS00932 , Prosite:IN-FAMILY:PS51318 , Prosite:IN-FAMILY:PS51669 , Smart:IN-FAMILY:SM00926

Summary:
fdnG encodes the α subunit of formate dehydrogenase N (Fdh-N). The α subunit is the site of formate oxidation; it contains a bis-molybdopterin guanine dinucleotide (MGD) cofactor, a selenocysteine residue and a (4Fe-4S) cluster (FS0). Electrons are transferred from formate to the molybdenum cofactor and then passed to the β subunit possibly via the FS0 cluster [Berg91a, Jormakka02].

FdnG is translocated to the periplasm via the Tat system; interaction with the FdnI subunit localizes the protein to the periplasmic face of the cytoplasmic membrane [Sargent98a, Stanley02].

Production of FdnG is regulated at the translational level. A segment of the mRNA encoding the N terminus of FdnG is able to form a stable stem-loop structure; disruption of the structure by site-directed mutagenesis leads to overproduction of FdnG-β-galactosidase and FdnG-CAT translational fusion proteins; if such mutations are introduced at the chromosomal fdnG locus, formate dehydrogenase-N activity increases [Punginelli04].

Essentiality data for fdnG knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 2]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 3]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 4]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 3]
Yes [Feist07, Comment 5]

References

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Barker00: Barker HC, Kinsella N, Jaspe A, Friedrich T, O'Connor CD (2000). "Formate protects stationary-phase Escherichia coli and Salmonella cells from killing by a cationic antimicrobial peptide." Mol Microbiol 35(6);1518-29. PMID: 10760151

Berg90: Berg BL, Stewart V (1990). "Structural genes for nitrate-inducible formate dehydrogenase in Escherichia coli K-12." Genetics 1990;125(4);691-702. PMID: 2168848

Berg91a: Berg BL, Li J, Heider J, Stewart V (1991). "Nitrate-inducible formate dehydrogenase in Escherichia coli K-12. I. Nucleotide sequence of the fdnGHI operon and evidence that opal (UGA) encodes selenocysteine." J Biol Chem 1991;266(33);22380-5. PMID: 1834669

Boxer82: Boxer D, Malcolm A, Graham A (1982). "Escherichia coli formate to nitrate respiratory pathway: structural analysis." Biochem Soc Trans 10(6);480-1. PMID: 6759195

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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