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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
         trimer complex of formate dehydrogenase-N α, β and γ subunits = (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 (summary available)

Summary:
The proton motive force (PMF), composed of an electrochemical gradient and a concentration difference of protons across the inner membrane, allows generation of the ubiquitous energy carrier ATP by ATP synthase. The PMF itself can be generated by oxidative phosphorylation, using molecular oxygen as the terminal electron acceptor.

In addition to molecular oxygen, E. coli can use alternative terminal electron acceptors to generate the PMF. Formate dehydrogenase-N is part of one such system. Expression of formate dehydrogenase-N is induced by nitrate and anaerobiosis, mediated by NarL and Fnr, respectively [Berg90, Wang03c]. Formate dehydrogenase-N oxidizes formate in the periplasm, transferring electrons via the menaquinone pool in the cytoplasmic membrane to nitrate reductase, which transfers electrons to nitrate in the cytoplasm [RuizHerrera69, Enoch74, Jones80a].

Formate dehydrogenase-N is one of three formate dehydrogenases in E. coli [Sawers94].

A crystal structure of formate dehydrogenase-N has been determined at 1.6 Å resolution [Jormakka02].

Review: [Jormakka03]

Locations [Comment 1Comment 1]: inner membrane

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

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0009061 - anaerobic respiration Inferred from experiment [Enoch75]
Molecular Function: GO:0008863 - formate dehydrogenase (NAD+) activity Inferred from experiment [Jormakka02a]
GO:0009055 - electron carrier activity Inferred from experiment [Boonstra75]
Cellular Component: GO:0009326 - formate dehydrogenase complex Inferred from experiment [Jormakka02a]
GO:0016021 - integral component of membrane Inferred from experiment [Enoch82]
GO:0005886 - plasma membrane

Credits:
Reviewed 15-Apr-2008 by Nolan L , Macquarie University
Last-Curated ? 21-Apr-2008 by Nolan L , Macquarie University


Enzymatic reaction of: formate dehydrogenase-N

Synonyms: formate dehydrogenase, nitrate inducible, Fdh-N

EC Number: 1.1.5.6

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

Summary:
Formate dehydrogenase-N catalyzes the oxidation of formate during nitrate respiration, where formate serves as a major electron donor. [Enoch75, Berg90, Berg91, Sawers94]

Formate dehydrogenase may may play a role in infection, as the enzyme is necessary for protection by formate of stationary-phase cells from killing by a derivative of a human antimicrobial peptide (BPI) [Barker00].

Cofactors or Prosthetic Groups: Mo2+

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


Subunit of trimer complex of formate dehydrogenase-N α, β and γ subunits: 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)

pI: 9.68

GO Terms:

Biological Process: GO:0009061 - anaerobic respiration Inferred from experiment [Enoch75]
GO:0017004 - cytochrome complex assembly Inferred from experiment [Enoch75]
GO:0045333 - cellular respiration Inferred from experiment Inferred by computational analysis [GOA01a, Garland75]
GO:0022904 - respiratory electron transport chain Inferred by computational analysis [GOA01a]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0008863 - formate dehydrogenase (NAD+) activity Inferred from experiment Inferred by computational analysis [GOA01a, Jormakka02a]
GO:0009055 - electron carrier activity Inferred from experiment [Boonstra75]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, DiazMejia09, Daley05]
GO:0009326 - formate dehydrogenase complex Inferred from experiment Inferred by computational analysis [GOA01a, Jormakka02a]
GO:0016021 - integral component of membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA01a, Enoch82]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11a, GOA01a]

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 , 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, the membrane subunit of formate dehydrogenase-N, contains two heme b556 groups and a site for menaquinone reduction. It contains 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 [Berg91, 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 trimer complex of formate dehydrogenase-N α, β and γ subunits: 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)

pI: 5.67

GO Terms:

Biological Process: GO:0009061 - anaerobic respiration Inferred from experiment [Enoch75]
GO:0045333 - cellular respiration Inferred from experiment Inferred by computational analysis [GOA01a, Garland75]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0008863 - formate dehydrogenase (NAD+) activity Inferred from experiment Inferred by computational analysis [GOA01a, Jormakka02a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0009326 - formate dehydrogenase complex Inferred from experiment [Jormakka02a]
GO:0016020 - membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Lasserre06]
GO:0005886 - plasma membrane Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, DiazMejia09]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11a, GOA01a]

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 contains four [4Fe-4S] clusters and one C-terminal transmembrane helix [Berg91, Jormakka02]. FdnH serves as a conduit for electrons that are transferred from the formate oxidation site in FdnG to the menaquinone associated with the 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 trimer complex of formate dehydrogenase-N α, β and γ subunits: 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)

pI: 6.97

GO Terms:

Biological Process: GO:0009061 - anaerobic respiration Inferred from experiment [Enoch75]
GO:0045333 - cellular respiration Inferred from experiment Inferred by computational analysis [GOA01a, Garland75]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Chan09, Butland05]
GO:0008430 - selenium binding Inferred from experiment [Sawers91]
GO:0008863 - formate dehydrogenase (NAD+) activity Inferred from experiment Inferred by computational analysis [GOA01a, Jormakka02a]
GO:0009055 - electron carrier activity Inferred from experiment Inferred by computational analysis [GOA01a, Boonstra75]
GO:0030151 - molybdenum ion binding Inferred from experiment Inferred by computational analysis [GOA01a, Jormakka02a]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0036397 - formate dehydrogenase (quinone) activity Inferred by computational analysis [GOA01]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [UniProtGOA11a]
GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
Cellular Component: GO:0009326 - formate dehydrogenase complex Inferred from experiment [Jormakka02a]
GO:0016020 - membrane Inferred from experiment [Lasserre06]
GO:0005737 - cytoplasm Inferred by computational analysis [GOA01a]
GO:0030288 - outer membrane-bounded periplasmic space Inferred by computational analysis [DiazMejia09]
GO:0042597 - periplasmic space Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]

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:PS00490 , Prosite:IN-FAMILY:PS00551 , Prosite:IN-FAMILY:PS00932 , Prosite:IN-FAMILY:PS51318 , Prosite:IN-FAMILY:PS51669 , Smart:IN-FAMILY:SM00926

Summary:
FdnG is the catalytic subunit of formate dehydrogenase-N. It contains the bis-molybdopterin guanine dinucleotide (MGD) cofactor and selenocysteine [Berg91].

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 [Sargent98, 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

Berg91: 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

Boonstra75: Boonstra J, Huttunen MT, Konings WN (1975). "Anaerobic transport in Escherichia coli membrane vesicles." J Biol Chem 250(17);6792-8. PMID: 1099094

Butland05: Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005). "Interaction network containing conserved and essential protein complexes in Escherichia coli." Nature 433(7025);531-7. PMID: 15690043

Chan09: Chan CS, Chang L, Rommens KL, Turner RJ (2009). "Differential interactions between Tat-specific redox enzyme peptides and their chaperones." J Bacteriol 191(7):2091-101. PMID: 19151138

Daley05: Daley DO, Rapp M, Granseth E, Melen K, Drew D, von Heijne G (2005). "Global topology analysis of the Escherichia coli inner membrane proteome." Science 308(5726);1321-3. PMID: 15919996

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Enoch74: Enoch HG, Lester RL (1974). "The role of a novel cytochrome b-containing nitrate reductase and quinone in the in vitro reconstruction of formate-nitrate reductase activity of E. coli." Biochem Biophys Res Commun 61(4);1234-41. PMID: 4616697

Enoch75: Enoch HG, Lester RL (1975). "The purification and properties of formate dehydrogenase and nitrate reductase from Escherichia coli." J Biol Chem 1975;250(17);6693-705. PMID: 1099093

Enoch82: Enoch HG, Lester RL (1982). "Formate dehydrogenase from Escherichia coli." Methods Enzymol 89 Pt D;537-43. PMID: 6755185

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Garland75: Garland PB, Downie JA, Haddock BA (1975). "Proton translocation and the respiratory nitrate reductase of Escherichia coli." Biochem J 152(3);547-59. PMID: 5996

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Jones80a: Jones RW "Proton translocation by the membrane-bound formate dehydrogenase of Escherichia coli." FEMS Microbiology Letters 8 (1980), 167-171.

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Jormakka02a: Jormakka M, Tornroth S, Abramson J, Byrne B, Iwata S (2002). "Purification and crystallization of the respiratory complex formate dehydrogenase-N from Escherichia coli." Acta Crystallogr D Biol Crystallogr 58(Pt 1);160-2. PMID: 11752799

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Punginelli04: Punginelli C, Ize B, Stanley NR, Stewart V, Sawers G, Berks BC, Palmer T (2004). "mRNA secondary structure modulates translation of Tat-dependent formate dehydrogenase N." J Bacteriol 186(18);6311-5. PMID: 15342602

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

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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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