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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: ?

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

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].

Gene Citations: [Li92, Li94]

Locations: inner membrane

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

Molecular Weight of Polypeptide: 25.368 kD (from nucleotide sequence)

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 , 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: ?

Genetic Regulation Schematic: ?

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 [GOA01, Garland75]
GO:0022904 - respiratory electron transport chain Inferred by computational analysis [GOA01]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0008863 - formate dehydrogenase (NAD+) activity Inferred from experiment Inferred by computational analysis [GOA01, Jormakka02a]
GO:0009055 - electron carrier activity Inferred from experiment [Boonstra75]
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:0009326 - formate dehydrogenase complex Inferred from experiment Inferred by computational analysis [GOA01, Jormakka02a]
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

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


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

Subunit composition of 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)

Component of: formate dehydrogenase-N (extended summary available)

Locations [Comment 5]:


Subunit of: 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, Wang03]. 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, Jones80].

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 5]: inner membrane

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

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


Sequence Features

Feature Class Location Citations Comment
Transmembrane-Region 12 -> 36
[UniProt10]
UniProt: Helical;
Metal-Binding-Site 18
[UniProt10]
UniProt: Iron (heme B 1 axial ligand);
Transmembrane-Region 53 -> 74
[UniProt10]
UniProt: Helical;
Metal-Binding-Site 57
[UniProt10]
UniProt: Iron (heme B 2 axial ligand);
Transmembrane-Region 111 -> 134
[UniProt10]
UniProt: Helical;
Transmembrane-Region 151 -> 175
[UniProt10]
UniProt: Helical;
Metal-Binding-Site 155
[UniProt10]
UniProt: Iron (heme B 2 axial ligand);
Sequence-Conflict 160 -> 217
[Berg91, UniProt10]
Alternate sequence: IILIHAILIHMYMAFWVKGSIKGMIEGKVSRRWAKKHHPRWYREIEKAEAKKESEEGI → YHPDPRHPDPYVYGILGERID; UniProt: (in Ref. 1);
Metal-Binding-Site 169
[UniProt10]
UniProt: Iron (heme B 1 axial ligand);


Gene Local Context (not to scale): ?

Transcription Unit:

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

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

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

Jones80: 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

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

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

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

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

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

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

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

Wang03: 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

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


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Wed Nov 26, 2014, biocyc11.