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Escherichia coli K-12 substr. MG1655 Polypeptide: reduced ferredoxin

Gene: fdx Accession Numbers: EG11328 (EcoCyc), b2525, ECK2522

Regulation Summary Diagram: ?

Regulation summary diagram for fdx

Alternative forms of reduced ferredoxin: oxidized ferredoxin

Ferredoxin (Fdx) contains a [2Fe-2S] cluster [Knoell74, Kakuta01] and functions in Fe-S cluster assembly [Takahashi99, Tokumoto01]. Fdx interacts directly with IscS and supplies one of the two electrons needed for reduction of S0 to IscS. Fdx and IscU compete for overlapping binding sites on IscS [Kim13a].

Holo-IscA [OllagnierdeChou01], holo-GrxD, and the GrxD-BolA heterodimer [Yeung11] can transfer an [2Fe-2S] cluster to apo-Fdx in vitro.

A crystal structure of Fdx has been solved at 1.7 Å resolution. The [2Fe-2S] cluster is located near the surface of the protein and is coordinated by the Sγ atoms of Cys42, Cys48, Cys51, and Cys87; another cysteine residue, Cys46, is exposed on the surface near the Fe-S cluster [Kakuta01].

Fdx is synthesized in under both aerobic and anaerobic growth conditions [Knoell74]. An fdx null mutant strain grows with a significantly increased doubling time compared to wild type [Tokumoto01].

Review: [Roche13]

Citations: [Vetter71, Ta92, Nakamura99, Tokumoto02, Tokumoto04]

Gene Citations: [Lelivelt95, Tokumoto02]

Locations: cytosol

Map Position: [2,654,770 <- 2,655,105] (57.22 centisomes, 206°)
Length: 336 bp / 111 aa

Molecular Weight of Polypeptide: 12.331 kD (from nucleotide sequence), 12.0 kD (experimental) [Knoell74 ]

pI: 4.69

Unification Links: ASAP:ABE-0008311 , CGSC:32984 , DIP:DIP-48512N , EchoBASE:EB1304 , EcoGene:EG11328 , EcoliWiki:b2525 , OU-Microarray:b2525 , PortEco:fdx , PR:PRO_000022588 , Pride:P0A9R4 , Protein Model Portal:P0A9R4 , RegulonDB:EG11328 , SMR:P0A9R4 , String:511145.b2525 , UniProt:P0A9R4

Relationship Links: InterPro:IN-FAMILY:IPR001041 , InterPro:IN-FAMILY:IPR001055 , InterPro:IN-FAMILY:IPR011536 , InterPro:IN-FAMILY:IPR012675 , InterPro:IN-FAMILY:IPR018298 , Panther:IN-FAMILY:PTHR23426:SF8 , PDB:Structure:1I7H , Pfam:IN-FAMILY:PF00111 , Prints:IN-FAMILY:PR00355 , Prosite:IN-FAMILY:PS00814 , Prosite:IN-FAMILY:PS51085

Reactions known to consume the compound:

biotin biosynthesis from 8-amino-7-oxononanoate I :
a sulfurated [sulfur carrier] + dethiobiotin + 2 S-adenosyl-L-methionine + 2 a reduced [2Fe-2S] ferredoxin → an unsulfurated [sulfur carrier] + biotin + 2 5'-deoxyadenosine + 2 L-methionine + 2 an oxidized [2Fe-2S] ferredoxin

lipoate biosynthesis and incorporation I , lipoate biosynthesis and incorporation II :
a [lipoyl-carrier protein] N6-octanoyl-L-lysine + 2 S-adenosyl-L-methionine + 2 a sulfurated [sulfur carrier] + 2 a reduced [2Fe-2S] ferredoxin → a [lipoyl-carrier protein] N6-lipoyl-L-lysine + 2 5'-deoxyadenosine + 2 L-methionine + 2 an unsulfurated [sulfur carrier] + 2 an oxidized [2Fe-2S] ferredoxin

Not in pathways:
2 S-adenosyl-L-methionine + an adenine37 in tRNA + 2 a reduced [2Fe-2S] ferredoxinS-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + a 2-methyladenine37 in tRNA + 2 an oxidized [2Fe-2S] ferredoxin
2 S-adenosyl-L-methionine + adenine2503 in 23S rRNA + 2 a reduced [2Fe-2S] ferredoxinS-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 2-methyladenine2503 in 23S rRNA + 2 an oxidized [2Fe-2S] ferredoxin

thiazole biosynthesis I (E. coli) :
an S-sulfanyl-[ThiI sulfur-carrier protein] + a carboxy-adenylated-[ThiS sulfur-carrier protein] + 2 a reduced ferredoxin → a thiocarboxy-[ThiS-Protein] + a ThiI sulfur-carrier protein + AMP + 2 an oxidized ferredoxin

Not in pathways:
a reduced flavoprotein (FMNH2) + an iron-sulfur protein → an oxidized flavoprotein (FMN) + a reduced iron-sulfur protein + 2 H+

Reactions known to produce the compound:

Not in pathways:
a menaquinone oxidoreductase (menaquinone-8) + a reduced iron-sulfur protein + 2 H+ → a menaquinone oxidoreductase (menaquinol-8) + an iron-sulfur protein + 2 H+
a menaquinone oxidoreductase (demethylmenaquinone) + a reduced iron-sulfur protein + 2 H+ → a menaquinone oxidoreductase (demethylmenaquinol) + an iron-sulfur protein + 2 H+
a reduced iron-sulfur protein + a ubiquinone-8 oxidoreductase + 2 H+an iron-sulfur protein + a ubiquinol-8 oxidoreductase + 2 H+

Reactions known to both consume and produce the compound:

Not in pathways:
pyruvate + 2 an oxidized ferredoxin + coenzyme A ↔ acetyl-CoA + CO2 + 2 a reduced ferredoxin + H+

In Reactions of unknown directionality:

Not in pathways:
2 a reduced [2Fe-2S] ferredoxin + NAD+ + H+ = 2 an oxidized [2Fe-2S] ferredoxin + NADH

Not in pathways:
an iron-sulfur protein + 2 e- = a reduced iron-sulfur protein

GO Terms:

Biological Process: GO:0016226 - iron-sulfur cluster assembly Inferred from experiment [Tokumoto01, Kim13a]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Kim13a, OllagnierdeChou01]
GO:0009055 - electron carrier activity Inferred from experiment Inferred by computational analysis [GOA01a, Kim13a]
GO:0051537 - 2 iron, 2 sulfur cluster binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA01a, Knoell74]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]

MultiFun Terms: metabolism energy production/transport electron carriers

Essentiality data for fdx knockouts: ?

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

Last-Curated ? 13-Jun-2013 by Keseler I , SRI International

Sequence Features

Protein sequence of reduced ferredoxin with features indicated

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Ta92a, Knoell74, UniProt11, Ta92a]
UniProt: Removed.
Conserved-Region 2 -> 104
UniProt: 2Fe-2S ferredoxin-type;
Chain 2 -> 111
UniProt: 2Fe-2S ferredoxin;
Sequence-Conflict 8
[Knoell74, UniProt10a]
UniProt: (in Ref. 6; AA sequence);
Metal-Binding-Site 42
UniProt: Iron-sulfur (2Fe-2S).
Metal-Binding-Site 48
UniProt: Iron-sulfur (2Fe-2S).
Metal-Binding-Site 51
UniProt: Iron-sulfur (2Fe-2S).
Sequence-Conflict 63
[Kawula94, UniProt10a]
UniProt: (in Ref. 2);
Sequence-Conflict 68 -> 69
[Kawula94, UniProt10a]
UniProt: (in Ref. 2);
Sequence-Conflict 74
[Kawula94, UniProt10a]
UniProt: (in Ref. 2);
Sequence-Conflict 77
[Kawula94, UniProt10a]
UniProt: (in Ref. 2);
Metal-Binding-Site 87
UniProt: Iron-sulfur (2Fe-2S).
Sequence-Conflict 91 -> 93
[Kawula94, UniProt10a]
UniProt: (in Ref. 2);

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


10/20/97 Gene b2525 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11328; confirmed by SwissProt match.


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

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

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

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

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

Kakuta01: Kakuta Y, Horio T, Takahashi Y, Fukuyama K (2001). "Crystal structure of Escherichia coli Fdx, an adrenodoxin-type ferredoxin involved in the assembly of iron-sulfur clusters." Biochemistry 40(37);11007-12. PMID: 11551196

Kawula94: Kawula TH, Lelivelt MJ (1994). "Mutations in a gene encoding a new Hsp70 suppress rapid DNA inversion and bgl activation, but not proU derepression, in hns-1 mutant Escherichia coli." J Bacteriol 176(3);610-9. PMID: 8300516

Kim13a: Kim JH, Frederick RO, Reinen NM, Troupis AT, Markley JL (2013). "[2Fe-2S]-ferredoxin binds directly to cysteine desulfurase and supplies an electron for iron-sulfur cluster assembly but is displaced by the scaffold protein or bacterial frataxin." J Am Chem Soc 135(22);8117-20. PMID: 23682711

Knoell74: Knoell HE, Knappe J (1974). "Escherichia coli ferredoxin, an iron-sulfur protein of the adrenodoxin type." Eur J Biochem 1974;50(1);245-52. PMID: 4375562

Lelivelt95: Lelivelt MJ, Kawula TH (1995). "Hsc66, an Hsp70 homolog in Escherichia coli, is induced by cold shock but not by heat shock." J Bacteriol 1995;177(17);4900-7. PMID: 7665466

Nakamura99: Nakamura M, Saeki K, Takahashi Y (1999). "Hyperproduction of recombinant ferredoxins in escherichia coli by coexpression of the ORF1-ORF2-iscS-iscU-iscA-hscB-hs cA-fdx-ORF3 gene cluster." J Biochem (Tokyo) 126(1);10-8. PMID: 10393315

OllagnierdeChou01: Ollagnier-de-Choudens S, Mattioli T, Takahashi Y, Fontecave M (2001). "Iron-sulfur cluster assembly: characterization of IscA and evidence for a specific and functional complex with ferredoxin." J Biol Chem 276(25);22604-7. PMID: 11319236

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

Roche13: Roche B, Aussel L, Ezraty B, Mandin P, Py B, Barras F (2013). "Iron/sulfur proteins biogenesis in prokaryotes: formation, regulation and diversity." Biochim Biophys Acta 1827(3);455-69. PMID: 23298813

Seaton94: Seaton BL, Vickery LE (1994). "A gene encoding a DnaK/hsp70 homolog in Escherichia coli." Proc Natl Acad Sci U S A 1994;91(6);2066-70. PMID: 8134349

Ta92: Ta DT, Seaton BL, Vickery LE (1992). "Localization of the ferredoxin (fdx) gene on the physical map of the Escherichia coli chromosome." J Bacteriol 174(17);5760-1. PMID: 1512212

Ta92a: Ta DT, Vickery LE (1992). "Cloning, sequencing, and overexpression of a [2Fe-2S] ferredoxin gene from Escherichia coli." J Biol Chem 1992;267(16);11120-5. PMID: 1317854

Takahashi99: Takahashi Y, Nakamura M (1999). "Functional assignment of the ORF2-iscS-iscU-iscA-hscB-hscA-fdx-ORF3 gene cluster involved in the assembly of Fe-S clusters in Escherichia coli." J Biochem (Tokyo) 1999;126(5);917-26. PMID: 10544286

Tokumoto01: Tokumoto U, Takahashi Y (2001). "Genetic analysis of the isc operon in Escherichia coli involved in the biogenesis of cellular iron-sulfur proteins." J Biochem (Tokyo) 130(1);63-71. PMID: 11432781

Tokumoto02: Tokumoto U, Nomura S, Minami Y, Mihara H, Kato S, Kurihara T, Esaki N, Kanazawa H, Matsubara H, Takahashi Y (2002). "Network of protein-protein interactions among iron-sulfur cluster assembly proteins in Escherichia coli." J Biochem (Tokyo) 131(5);713-9. PMID: 11983079

Tokumoto04: Tokumoto U, Kitamura S, Fukuyama K, Takahashi Y (2004). "Interchangeability and distinct properties of bacterial Fe-S cluster assembly systems: functional replacement of the isc and suf operons in Escherichia coli with the nifSU-like operon from Helicobacter pylori." J Biochem (Tokyo) 136(2);199-209. PMID: 15496591

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

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

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

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

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

Vetter71: Vetter H, Knappe J (1971). "Flavodoxin and ferredoxin of Escherichia coli." Hoppe Seylers Z Physiol Chem 352(3);433-46. PMID: 4927832

Yeung11: Yeung N, Gold B, Liu NL, Prathapam R, Sterling HJ, Willams ER, Butland G (2011). "The E. coli monothiol glutaredoxin GrxD forms homodimeric and heterodimeric FeS cluster containing complexes." Biochemistry 50(41);8957-69. PMID: 21899261

Other References Related to Gene Regulation

Giel06: Giel JL, Rodionov D, Liu M, Blattner FR, Kiley PJ (2006). "IscR-dependent gene expression links iron-sulphur cluster assembly to the control of O-regulated genes in Escherichia coli." Mol Microbiol 60(4);1058-75. PMID: 16677314

Kaleta10: Kaleta C, Gohler A, Schuster S, Jahreis K, Guthke R, Nikolajewa S (2010). "Integrative inference of gene-regulatory networks in Escherichia coli using information theoretic concepts and sequence analysis." BMC Syst Biol 4;116. PMID: 20718955

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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 19.0 on Sun Aug 30, 2015, biocyc13.