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Escherichia coli K-12 substr. MG1655 Polypeptide: ferric dicitrate ABC transporter - membrane subunit




Gene: fecD Accession Numbers: EG10289 (EcoCyc), b4288, ECK4278

Regulation Summary Diagram

Regulation summary diagram for fecD

Component of:
ferric dicitrate ABC transporter (summary available)
ferric dicitrate transport system

Summary:
FecD is one of two (along with FecC) integral membrane protein components of the iron dicitrate ABC transporter.

Gene Citations: [Braun97]

Locations: inner membrane

Map Position: [4,509,481 <- 4,510,437] (97.19 centisomes, 350°)
Length: 957 bp / 318 aa

Molecular Weight of Polypeptide: 34.131 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0014059, CGSC:18394, EchoBASE:EB0285, EcoGene:EG10289, EcoliWiki:b4288, ModBase:P15029, OU-Microarray:b4288, PortEco:fecD, PR:PRO_000022594, Pride:P15029, Protein Model Portal:P15029, RefSeq:NP_418708, RegulonDB:EG10289, SMR:P15029, String:511145.b4288, UniProt:P15029

Relationship Links: EcoO157Cyc:Homolog:CHUU, EcoO157Cyc:Homolog:CHUU-MONOMER, EcoO157Cyc:Homolog:Z1965, EcoO157Cyc:Homolog:Z1965-MONOMER, EcoO157Cyc:Homolog:Z4384, EcoO157Cyc:Homolog:Z4384-MONOMER, InterPro:IN-FAMILY:IPR000522, InterPro:IN-FAMILY:IPR029022, Panther:IN-FAMILY:PTHR30472, Pfam:IN-FAMILY:PF01032

In Paralogous Gene Group: 53 (5 members)

Gene-Reaction Schematic

Gene-Reaction Schematic

Genetic Regulation Schematic

Genetic regulation schematic for fecD


GO Terms:
Biological Process:
Inferred by computational analysisGO:0006810 - transport [UniProtGOA11a]
Inferred by computational analysisGO:0006811 - ion transport [UniProtGOA11a]
Inferred by computational analysisGO:0055072 - iron ion homeostasis [UniProtGOA11a]
Molecular Function:
Inferred by computational analysisGO:0005215 - transporter activity [GOA01a]
Inferred by computational analysisGO:0015623 - iron-chelate-transporting ATPase activity []
Cellular Component:
Inferred from experimentInferred by computational analysisGO:0005886 - plasma membrane [UniProtGOA11, UniProtGOA11a, DiazMejia09, Daley05]
Inferred by computational analysisGO:0016020 - membrane [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0016021 - integral component of membrane [UniProtGOA11a]

MultiFun Terms: cell structuremembrane
transportChannel-type TransportersPyrophosphate Bond (ATP; GTP; P2) Hydrolysis-driven Active TransportersThe ATP-binding Cassette (ABC) Superfamily + ABC-type Uptake PermeasesABC superfamily, membrane component

Essentiality data for fecD knockouts:

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

Subunit of: ferric dicitrate ABC transporter

Synonyms: iron dicitrate ABC transporter, ferric citrate ABC transporter

Subunit composition of ferric dicitrate ABC transporter = [FecE]2[FecC][FecD][FecB]
         ferric dicitrate ABC transporter - ATP binding subunit = FecE (summary available)
         ferric dicitrate ABC transporter - membrane subunit = FecC (summary available)
         ferric dicitrate ABC transporter - membrane subunit = FecD (summary available)
         ferric dicitrate ABC transporter - periplasmic binding protein = FecB (summary available)

Component of: ferric dicitrate transport system

Summary:
FecBCDE is an ATP Binding Cassette (ABC) citrate-dependent iron (III) transport system. Sequence homology and hydropathy analyses indicate that FecB is the periplasmic binding protein, FecC and FecD are integral membrane proteins and FecE is the ATP-binding protein [Pressler88]. Mutation and induction studies indicate that exogenous ferric citrate induces the expression of fec transport genes through a signaling mechanism which does not require ferric citrate to enter the cytoplasm [Hussein81]. [Wagegg81], or to cross the outer membrane into the periplasmic space [Harle95]. Rather, induction of fec transport genes is a function of FecA-ferric citrate binding and is coupled through the TonB, ExbB and ExbD proteins independent of their role in uptake [Harle95].


Enzymatic reaction of: transport of ferric dicitrate (ferric dicitrate ABC transporter)

Inferred from experimentInferred by computational analysis

EC Number: 3.6.3.34

Transport reaction diagram for transport of ferric dicitrate


Subunit of: ferric dicitrate transport system

Subunit composition of ferric dicitrate transport system = [(FecE)2(FecC)(FecD)(FecB)][(FecA)([TonB][ExbB][ExbD])]
         ferric dicitrate ABC transporter = (FecE)2(FecC)(FecD)(FecB) (summary available)
                 ferric dicitrate ABC transporter - ATP binding subunit = FecE (summary available)
                 ferric dicitrate ABC transporter - membrane subunit = FecC (summary available)
                 ferric dicitrate ABC transporter - membrane subunit = FecD (summary available)
                 ferric dicitrate ABC transporter - periplasmic binding protein = FecB (summary available)
         ferric citrate outer membrane transport complex = (FecA)([TonB][ExbB][ExbD]) (summary available)
                 ferric citrate outer membrane porin FecA = FecA (summary available)
                 TonB energy transducing system = (TonB)(ExbB)(ExbD) (extended summary available)
                         TonB energy transducing system - TonB subunit = TonB (extended summary available)
                         TonB energy transducing system - ExbB subunit = ExbB (summary available)
                         tonB energy transducing system - ExbD subunit = ExbD (summary available)

Locations: outer membrane, inner membrane, periplasmic space


GO Terms:
Cellular Component:
GO:0005886 - plasma membrane []
GO:0009279 - cell outer membrane []
GO:0030288 - outer membrane-bounded periplasmic space []

Enzymatic reaction of: transport of ferric dicitrate (ferric dicitrate transport system)

Inferred from experimentInferred by computational analysis

Transport reaction diagram for transport of ferric dicitrate


Sequence Features

Protein sequence of ferric dicitrate ABC transporter - membrane subunit with features indicated

Feature Class Location Citations Comment
Transmembrane-Region 3 -> 23
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Sequence-Conflict 41
Inferred by curator[Staudenmaier89, UniProt15]
UniProt: (in Ref. 1; AAA23764).
Transmembrane-Region 56 -> 76
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Transmembrane-Region 85 -> 105
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Transmembrane-Region 106 -> 126
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Transmembrane-Region 138 -> 158
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Transmembrane-Region 180 -> 200
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Transmembrane-Region 226 -> 246
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Transmembrane-Region 270 -> 290
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Transmembrane-Region 295 -> 315
Inferred by computational analysis[UniProt15]
UniProt: Helical.


Sequence Pfam Features

Protein sequence of ferric dicitrate ABC transporter - membrane subunit with features indicated

Feature Class Location Citations Comment
Pfam PF01032 14 -> 316
Inferred by computational analysis[Finn14]
FecCD : FecCD transport family


Gene Local Context (not to scale -- see Genome Browser for correct scale)

Gene local context diagram

Transcription Unit

Transcription-unit diagram

Notes:

History:
10/20/97 Gene b4288 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10289; 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

Braun97: Braun V (1997). "Surface signaling: novel transcription initiation mechanism starting from the cell surface." Arch Microbiol 167(6);325-31. PMID: 9148773

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

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

Finn14: Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M (2014). "Pfam: the protein families database." Nucleic Acids Res 42(Database issue);D222-30. PMID: 24288371

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."

Harle95: Harle C, Kim I, Angerer A, Braun V (1995). "Signal transfer through three compartments: transcription initiation of the Escherichia coli ferric citrate transport system from the cell surface." EMBO J 14(7);1430-8. PMID: 7729419

Hussein81: Hussein S, Hantke K, Braun V (1981). "Citrate-dependent iron transport system in Escherichia coli K-12." Eur J Biochem 1981;117(2);431-7. PMID: 6268411

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

Pressler88: Pressler U, Staudenmaier H, Zimmermann L, Braun V (1988). "Genetics of the iron dicitrate transport system of Escherichia coli." J Bacteriol 170(6);2716-24. PMID: 2836368

Staudenmaier89: Staudenmaier H, Van Hove B, Yaraghi Z, Braun V (1989). "Nucleotide sequences of the fecBCDE genes and locations of the proteins suggest a periplasmic-binding-protein-dependent transport mechanism for iron(III) dicitrate in Escherichia coli." J Bacteriol 171(5);2626-33. PMID: 2651410

UniProt15: UniProt Consortium (2015). "UniProt version 2015-08 released on 2015-07-22." 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."

Wagegg81: Wagegg W, Braun V (1981). "Ferric citrate transport in Escherichia coli requires outer membrane receptor protein fecA." J Bacteriol 145(1);156-63. PMID: 7007312

Zimmermann84: Zimmermann L, Hantke K, Braun V (1984). "Exogenous induction of the iron dicitrate transport system of Escherichia coli K-12." J Bacteriol 159(1);271-7. PMID: 6376472

Other References Related to Gene Regulation

Angerer98: Angerer A, Braun V (1998). "Iron regulates transcription of the Escherichia coli ferric citrate transport genes directly and through the transcription initiation proteins." Arch Microbiol 1998;169(6);483-90. PMID: 9575233

Chen07: Chen Z, Lewis KA, Shultzaberger RK, Lyakhov IG, Zheng M, Doan B, Storz G, Schneider TD (2007). "Discovery of Fur binding site clusters in Escherichia coli by information theory models." Nucleic Acids Res 35(20);6762-77. PMID: 17921503

Drazic13: Drazic A, Miura H, Peschek J, Le Y, Bach NC, Kriehuber T, Winter J (2013). "Methionine oxidation activates a transcription factor in response to oxidative stress." Proc Natl Acad Sci U S A 110(23);9493-8. PMID: 23690622

Enz03: Enz S, Mahren S, Menzel C, Braun V (2003). "Analysis of the ferric citrate transport gene promoter of Escherichia coli." J Bacteriol 185(7);2387-91. PMID: 12644513

Enz95: Enz S, Braun V, Crosa JH (1995). "Transcription of the region encoding the ferric dicitrate-transport system in Escherichia coli: similarity between promoters for fecA and for extracytoplasmic function sigma factors." Gene 163(1);13-8. PMID: 7557462

Faith07: Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, Kasif S, Collins JJ, Gardner TS (2007). "Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles." PLoS Biol 5(1);e8. PMID: 17214507

Gebendorfer12: Gebendorfer KM, Drazic A, Le Y, Gundlach J, Bepperling A, Kastenmuller A, Ganzinger KA, Braun N, Franzmann TM, Winter J (2012). "Identification of a Hypochlorite-specific Transcription Factor from Escherichia coli." J Biol Chem 287(9);6892-903. PMID: 22223481

Newman99: Newman DL, Shapiro JA (1999). "Differential fiu-lacZ fusion regulation linked to Escherichia coli colony development." Mol Microbiol 33(1);18-32. PMID: 10411720

Silva98: Silva AA, Barbieri MA, Gomes UA, Bettiol H (1998). "Trends in low birth weight: a comparison of two birth cohorts separated by a 15-year interval in Ribeirao Preto, Brazil." Bull World Health Organ 76(1);73-84. PMID: 9615499

Zhang05: Zhang Z, Gosset G, Barabote R, Gonzalez CS, Cuevas WA, Saier MH (2005). "Functional interactions between the carbon and iron utilization regulators, Crp and Fur, in Escherichia coli." J Bacteriol 187(3);980-90. PMID: 15659676


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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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