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Escherichia coli K-12 substr. MG1655 Polypeptide: formate dehydrogenase N, γ subunit



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

Regulation Summary Diagram: ?

Regulation summary diagram for fdnI

Component of:
formate dehydrogenase N, subcomplex
formate dehydrogenase N (extended summary available)

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 [Berg91, Jormakka02].

Gene Citations: [Li92, Li94]

Locations: inner membrane

Map Position: [1,549,362 -> 1,550,015] (33.39 centisomes, 120°)
Length: 654 bp / 217 aa

Molecular Weight of Polypeptide: 25.368 kD (from nucleotide sequence), 20.0 kD (experimental) [Enoch75 ]

pI: 9.68

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

Unification Links: ASAP:ABE-0004921 , CGSC:32168 , EchoBASE:EB1211 , EcoGene:EG11229 , EcoliWiki:b1476 , ModBase:P0AEK7 , OU-Microarray:b1476 , PortEco:fdnI , PR:PRO_000022583 , Protein Model Portal:P0AEK7 , RefSeq:NP_415993 , RegulonDB:EG11229 , 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

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for fdnI

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 [GOA01a]
GO:0045333 - cellular respiration Inferred by computational analysis [GOA01a]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a]
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 [GOA01a]
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:0005887 - integral component of plasma membrane Inferred from experiment [Jormakka02]
GO:0009326 - formate dehydrogenase complex Inferred from experiment Inferred by computational analysis [GOA01a, Jormakka02, Enoch75]
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

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 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Credits:
Curated 21-Apr-2008 by Nolan L , Macquarie University
Last-Curated ? 02-Dec-2014 by Mackie A , Macquarie University


Subunit of: formate dehydrogenase N, subcomplex

Subunit composition of 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)

Component of: formate dehydrogenase N (extended summary available)

Locations [Comment 5]:


Subunit of: formate dehydrogenase N

Synonyms: Fdh-N, formate:menaquinone oxidoreductase

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 [Jones80b, Jormakka02]. Expression of formate dehydrogenase-N is induced by nitrate and anaerobiosis, mediated by NarL and Fnr, respectively [Berg90, Wang03a].

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: [RuizHerrera69a, Scott76, Lester71, RuizHerrera69, Enoch74, Barker00, Berg91, Zorn13, Cox81a, Enoch72, Haddock82, Boxer82]

Locations [Comment 5]: inner membrane

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

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

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 , formate to nitrite electron transfer

Cofactors or Prosthetic Groups: a [4Fe-4S] iron-sulfur cluster [Jormakka02], ferroheme b [Jormakka02], bis(guanylyl molybdopterin cofactor) [Jormakka02]

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


Sequence Features

Protein sequence of formate dehydrogenase N, gamma subunit with features indicated

Feature Class Location Citations Comment
Transmembrane-Region 12 -> 36
[UniProt15]
UniProt: Helical.
Metal-Binding-Site 18
[UniProt10a, Jormakka02]
UniProt: Iron (heme B 1 axial ligand); heme bc ligand
Transmembrane-Region 53 -> 74
[UniProt15]
UniProt: Helical.
Metal-Binding-Site 57
[UniProt10a, Jormakka02]
UniProt: Iron (heme B 2 axial ligand); heme bp ligand
Transmembrane-Region 111 -> 134
[UniProt15]
UniProt: Helical.
Transmembrane-Region 151 -> 175
[UniProt15]
UniProt: Helical.
Metal-Binding-Site 155
[UniProt10a, Jormakka02]
UniProt: Iron (heme B 2 axial ligand); heme bp ligand
Sequence-Conflict 160 -> 217
[Berg91, UniProt10a]
UniProt: (in Ref. 1);
Metal-Binding-Site 169
[UniProt10a, Jormakka02]
UniProt: Iron (heme B 1 axial ligand); heme bc ligand


Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram

Notes:

History:
10/20/97 Gene b1476 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11229; confirmed by SwissProt match.


References

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

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

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

Cox81a: Cox JC, Edwards ES, DeMoss JA (1981). "Resolution of distinct selenium-containing formate dehydrogenases from Escherichia coli." J Bacteriol 145(3);1317-24. PMID: 7009577

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

Enoch72: Enoch HG, Lester RL (1972). "Effects of molybdate, tungstate, and selenium compounds on formate dehydrogenase and other enzyme systems in Escherichia coli." J Bacteriol 110(3);1032-40. PMID: 4555402

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

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

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

Haddock82: Haddock BA, Mandrand-Berthelot MA (1982). "Escherichia coli formate-to-nitrate respiratory chain: genetic analysis." Biochem Soc Trans 10(6);478-80. PMID: 6759194

Jones80b: Jones RW "Proton translocation by the membrane-bound formate dehydrogenase of Escherichia coli." FEMS Microbiology Letters 8 (1980), 167-171.

Jormakka02: Jormakka M, Tornroth S, Byrne B, Iwata S (2002). "Molecular basis of proton motive force generation: structure of formate dehydrogenase-N." Science 295(5561);1863-8. PMID: 11884747

Jormakka03: Jormakka M, Byrne B, Iwata S (2003). "Protonmotive force generation by a redox loop mechanism." FEBS Lett 545(1);25-30. PMID: 12788488

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Lester71: Lester RL, DeMoss JA (1971). "Effects of molybdate and selenite on formate and nitrate metabolism in Escherichia coli." J Bacteriol 105(3);1006-14. PMID: 4926673

Li92: Li J, Stewart V (1992). "Localization of upstream sequence elements required for nitrate and anaerobic induction of fdn (formate dehydrogenase-N) operon expression in Escherichia coli K-12." J Bacteriol 1992;174(15);4935-42. PMID: 1629153

Li94: Li J, Kustu S, Stewart V (1994). "In vitro interaction of nitrate-responsive regulatory protein NarL with DNA target sequences in the fdnG, narG, narK and frdA operon control regions of Escherichia coli K-12." J Mol Biol 1994;241(2);150-65. PMID: 8057356

Rothery08: Rothery RA, Workun GJ, Weiner JH (2008). "The prokaryotic complex iron-sulfur molybdoenzyme family." Biochim Biophys Acta 1778(9);1897-929. PMID: 17964535

RuizHerrera69: Ruiz-Herrera J, DeMoss JA (1969). "Nitrate reductase complex of Escherichia coli K-12: participation of specific formate dehydrogenase and cytochrome b1 components in nitrate reduction." J Bacteriol 99(3);720-9. PMID: 4905536

RuizHerrera69a: Ruiz-Herrera J, Showe MK, DeMoss JA (1969). "Nitrate reductase complex of Escherichia coli K-12: isolation and characterization of mutants unable to reduce nitrate." J Bacteriol 97(3);1291-7. PMID: 4887509

Sawers94: Sawers G (1994). "The hydrogenases and formate dehydrogenases of Escherichia coli." Antonie Van Leeuwenhoek 1994;66(1-3);57-88. PMID: 7747941

Scott76: Scott RH, DeMoss JA (1976). "Formation of the formate-nitrate electron transport pathway from inactive components in Escherichia coli." J Bacteriol 126(1);478-86. PMID: 770433

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Wang03a: Wang H, Gunsalus RP (2003). "Coordinate regulation of the Escherichia coli formate dehydrogenase fdnGHI and fdhF genes in response to nitrate, nitrite, and formate: roles for NarL and NarP." J Bacteriol 185(17);5076-85. PMID: 12923080

Zorn13: Zorn M, Ihling CH, Golbik R, Sawers RG, Sinz A (2013). "Selective selC-independent selenocysteine incorporation into formate dehydrogenases." PLoS One 8(4);e61913. PMID: 23634217

Other References Related to Gene Regulation

Campagne14: Campagne S, Marsh ME, Capitani G, Vorholt JA, Allain FH (2014). "Structural basis for -10 promoter element melting by environmentally induced sigma factors." Nat Struct Mol Biol 21(3);269-76. PMID: 24531660

Darwin97: Darwin AJ, Tyson KL, Busby SJ, Stewart V (1997). "Differential regulation by the homologous response regulators NarL and NarP of Escherichia coli K-12 depends on DNA binding site arrangement." Mol Microbiol 1997;25(3);583-95. PMID: 9302020

Rabin93: Rabin RS, Stewart V (1993). "Dual response regulators (NarL and NarP) interact with dual sensors (NarX and NarQ) to control nitrate- and nitrite-regulated gene expression in Escherichia coli K-12." J Bacteriol 1993;175(11);3259-68. PMID: 8501030

Spiro91: Spiro S, Guest JR (1991). "Adaptive responses to oxygen limitation in Escherichia coli." Trends Biochem Sci 1991;16(8);310-4. PMID: 1957353


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