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discounted EARLY registration ends Dec 31, 2014
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Escherichia coli K-12 substr. MG1655 Transporter: 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

Gene-Reaction Schematic: ?

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)


Component enzyme of ferric dicitrate transport system : ferric dicitrate ABC transporter

Synonyms: iron dicitrate ABC transporter, ferric citrate ABC transporter

Catalyzes:
ATP + ferric dicitrate[periplasmic space] + H2O → ADP + ferric dicitrate[cytosol] + phosphate + H+

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].


Subunit of ferric dicitrate ABC transporter: ferric dicitrate ABC transporter - ATP binding subunit

Gene: fecE Accession Numbers: EG10290 (EcoCyc), b4287, ECK4277

Locations: inner membrane

Sequence Length: 255 AAs

Molecular Weight: 28.191 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006200 - ATP catabolic process Inferred by computational analysis [GOA01]
GO:0006810 - transport Inferred by computational analysis [UniProtGOA11]
GO:0006811 - ion transport Inferred by computational analysis [UniProtGOA11]
GO:0055072 - iron ion homeostasis Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016887 - ATPase activity Inferred by computational analysis [GOA01]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, Staudenmaier89]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell processes adaptations Fe aquisition
transport Channel-type Transporters Pyrophosphate Bond (ATP; GTP; P2) Hydrolysis-driven Active Transporters The ATP-binding Cassette (ABC) Superfamily + ABC-type Uptake Permeases ABC superfamily ATP binding cytoplasmic component

Unification Links: EcoliWiki:b4287 , ModBase:P15031 , PR:PRO_000022595 , Protein Model Portal:P15031 , RefSeq:NP_418707 , SMR:P15031 , String:511145.b4287 , UniProt:P15031

Relationship Links: EcoO157Cyc:Homolog:Z1964-MONOMER , EcoO157Cyc:Homolog:Z4385-MONOMER , EcoO157Cyc:Homolog:Z4919-MONOMER , InterPro:IN-FAMILY:IPR003439 , InterPro:IN-FAMILY:IPR003593 , InterPro:IN-FAMILY:IPR017871 , InterPro:IN-FAMILY:IPR027417 , Pfam:IN-FAMILY:PF00005 , Prosite:IN-FAMILY:PS00211 , Prosite:IN-FAMILY:PS50893 , Smart:IN-FAMILY:SM00382

Summary:
ATP binding component of the iron dicitrate ABC transporter

Essentiality data for fecE 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]

Subunit of ferric dicitrate ABC transporter: ferric dicitrate ABC transporter - membrane subunit

Gene: fecC Accession Numbers: EG10288 (EcoCyc), b4289, ECK4279

Locations: inner membrane

Sequence Length: 332 AAs

Molecular Weight: 34.893 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006810 - transport Inferred by computational analysis [UniProtGOA11]
GO:0006811 - ion transport Inferred by computational analysis [UniProtGOA11]
GO:0055072 - iron ion homeostasis Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0005215 - transporter activity Inferred by computational analysis [GOA01]
GO:0015623 - iron-chelate-transporting ATPase activity Inferred by computational analysis
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, DiazMejia09, Daley05]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell processes adaptations Fe aquisition
cell structure membrane
transport Channel-type Transporters Pyrophosphate Bond (ATP; GTP; P2) Hydrolysis-driven Active Transporters The ATP-binding Cassette (ABC) Superfamily + ABC-type Uptake Permeases ABC superfamily, membrane component

Unification Links: EcoliWiki:b4289 , ModBase:P15030 , PR:PRO_000022593 , Pride:P15030 , Protein Model Portal:P15030 , RefSeq:NP_418709 , SMR:P15030 , String:511145.b4289 , UniProt:P15030

Relationship Links: EcoO157Cyc:Homolog:CHUU-MONOMER , EcoO157Cyc:Homolog:Z1965-MONOMER , EcoO157Cyc:Homolog:Z4383-MONOMER , EcoO157Cyc:Homolog:Z4384-MONOMER , InterPro:IN-FAMILY:IPR000522 , Pfam:IN-FAMILY:PF01032

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

Essentiality data for fecC 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]

Subunit of ferric dicitrate ABC transporter: ferric dicitrate ABC transporter - membrane subunit

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

Locations: inner membrane

Sequence Length: 318 AAs

Molecular Weight: 34.131 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006810 - transport Inferred by computational analysis [UniProtGOA11]
GO:0006811 - ion transport Inferred by computational analysis [UniProtGOA11]
GO:0055072 - iron ion homeostasis Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0005215 - transporter activity Inferred by computational analysis [GOA01]
GO:0015623 - iron-chelate-transporting ATPase activity Inferred by computational analysis
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, DiazMejia09, Daley05]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure membrane
transport Channel-type Transporters Pyrophosphate Bond (ATP; GTP; P2) Hydrolysis-driven Active Transporters The ATP-binding Cassette (ABC) Superfamily + ABC-type Uptake Permeases ABC superfamily, membrane component

Unification Links: EcoliWiki:b4288 , ModBase:P15029 , PR:PRO_000022594 , Pride:P15029 , Protein Model Portal:P15029 , RefSeq:NP_418708 , SMR:P15029 , String:511145.b4288 , UniProt:P15029

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

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

Essentiality data for fecD 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]

Subunit of ferric dicitrate ABC transporter: ferric dicitrate ABC transporter - periplasmic binding protein

Gene: fecB Accession Numbers: EG10287 (EcoCyc), b4290, ECK4280

Locations: periplasmic space

Sequence Length: 300 AAs

Molecular Weight: 33.146 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006810 - transport Inferred by computational analysis [UniProtGOA11]
GO:0006811 - ion transport Inferred by computational analysis [UniProtGOA11]
GO:0055072 - iron ion homeostasis Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0015623 - iron-chelate-transporting ATPase activity Inferred by computational analysis
Cellular Component: GO:0030288 - outer membrane-bounded periplasmic space Inferred by computational analysis [DiazMejia09]
GO:0042597 - periplasmic space Inferred by computational analysis [UniProtGOA11a, UniProtGOA11]

MultiFun Terms: cell processes adaptations Fe aquisition
transport Channel-type Transporters Pyrophosphate Bond (ATP; GTP; P2) Hydrolysis-driven Active Transporters The ATP-binding Cassette (ABC) Superfamily + ABC-type Uptake Permeases ABC superfamily, periplasmic binding component

Unification Links: DIP:DIP-9584N , EcoliWiki:b4290 , Mint:MINT-1275090 , ModBase:P15028 , PR:PRO_000022592 , Protein Model Portal:P15028 , RefSeq:NP_418710 , SMR:P15028 , String:511145.b4290 , UniProt:P15028

Relationship Links: InterPro:IN-FAMILY:IPR002491 , Pfam:IN-FAMILY:PF01497 , Prosite:IN-FAMILY:PS50983

Summary:
Periplasmic substrate binding component of the iron dicitrate ABC transporter

Essentiality data for fecB knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
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]

Component enzyme of ferric dicitrate transport system : ferric citrate outer membrane transport complex

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

Catalyzes:
ferric dicitrate[extracellular space] → ferric dicitrate[periplasmic space]

Summary:
The outer membrane ferric citrate transport system is responsible for the transport of ferric citrate across the outer membrane by FecA energized by the TonB energy transducing system.


Subunit of ferric citrate outer membrane transport complex: ferric citrate outer membrane porin FecA

Synonyms: FecA

Gene: fecA Accession Numbers: EG10286 (EcoCyc), b4291, ECK4281

Locations: outer membrane

Sequence Length: 774 AAs

Molecular Weight: 85.321 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0015682 - ferric iron transport Inferred from experiment [Harle95]
GO:0006810 - transport Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0006811 - ion transport Inferred by computational analysis [UniProtGOA11]
GO:0044718 - siderophore transmembrane transport Inferred by computational analysis [GOA01]
GO:0055072 - iron ion homeostasis Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0015091 - ferric iron transmembrane transporter activity Inferred from experiment [Harle95]
GO:0004872 - receptor activity Inferred by computational analysis [GOA01]
GO:0005215 - transporter activity Inferred by computational analysis [GOA01]
GO:0005506 - iron ion binding Inferred by computational analysis [GOA01]
GO:0015343 - siderophore transmembrane transporter activity Inferred by computational analysis [GOA01]
Cellular Component: GO:0009279 - cell outer membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, DiazMejia09, Han12, LopezCampistrou05, Pressler88, Harle95]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11]
GO:0019867 - outer membrane Inferred by computational analysis [GOA01]

MultiFun Terms: cell processes adaptations Fe aquisition
transport Channel-type Transporters Beta barrel porins (The Outer Membrane Porin (OMP) Functional Superfamily)

Unification Links: DIP:DIP-9583N , EcoliWiki:b4291 , Mint:MINT-119307 , ModBase:P13036 , PR:PRO_000022591 , Pride:P13036 , Protein Model Portal:P13036 , RefSeq:NP_418711 , SMR:P13036 , String:511145.b4291 , UniProt:P13036

Relationship Links: EcoO157Cyc:Homolog:Z1178-MONOMER , EcoO157Cyc:Homolog:Z1617-MONOMER , EcoO157Cyc:Homolog:Z4386-MONOMER , InterPro:IN-FAMILY:IPR000531 , InterPro:IN-FAMILY:IPR010105 , InterPro:IN-FAMILY:IPR010916 , InterPro:IN-FAMILY:IPR010917 , InterPro:IN-FAMILY:IPR011662 , InterPro:IN-FAMILY:IPR012910 , PDB:Structure:1KMO , PDB:Structure:1KMP , PDB:Structure:1PNZ , PDB:Structure:1PO0 , PDB:Structure:1PO3 , PDB:Structure:1ZZV , PDB:Structure:2D1U , Pfam:IN-FAMILY:PF00593 , Pfam:IN-FAMILY:PF07660 , Pfam:IN-FAMILY:PF07715 , Prosite:IN-FAMILY:PS00430 , Prosite:IN-FAMILY:PS01156 , Smart:IN-FAMILY:SM00965

Summary:
FecA is the TonB energy transducing system-dependent ferric citrate uptake receptor. The structure of the periplasmic signaling domain of the FecA protein has been solved by multidimensional NMR spectroscopy [GarciaHerrero05]. The crystallographic structures of FecA with and without bound ferric citrate have been determined to resolutions of 2.5 and 2.0 angstroms [Ferguson02]. Bipartite gating of the protein is described [vanderHelm02].

Citations: [Yue03]

Essentiality data for fecA 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]

Subunit of ferric citrate outer membrane transport complex: TonB energy transducing system

Locations: inner membrane, periplasmic space

GO Terms:

Biological Process: GO:0015682 - ferric iron transport Inferred from experiment [Gresock11]
GO:0015889 - cobalamin transport Inferred from experiment [Bassford76]
Molecular Function: GO:0031992 - energy transducer activity Inferred from experiment [Letain97]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment [Skare93]
GO:0042597 - periplasmic space Inferred from experiment [Postle88]

Summary:
TonB is a cytoplasmic membrane protein which transduces the proton motive force (pmf) of the cytoplasmic membrane to the outer membrane active transporters thus providing the energy source required for the import of iron-siderophore complexes and vitamin B12 across the outer membrane [Letain97]. The amino-terminal signal sequence of TonB is thought to span the cytoplasmic membrane, with the rest of the protein residing within the periplasmic space [Karlsson93]. TonB has been shown to come into close contact with proteins located in both membranes [Skare93]. Sucrose density gradient centrifugation studies found that TonB is distributed approximately equally in the inner and outer membrane fractions [Letain97]. In conjunction with cytoplasmic membrane proteins ExbB and ExbD, TonB forms an energy transduction complex which interacts with a variety of outer membrane active transporter proteins [Braun02]. When complexed with ExbB and ExbD, TonB is thought to adopt an energized conformation which is subsequently released from the cytoplasmic membrane to the outer membrane whereupon it interacts with an array of outer membrane proteins [Higgs02]. TonB is then thought to respond to the conformational changes induced in the active transport proteins upon substrate binding [Moeck97], releasing its stored energy to the active transporters and reassociating with ExbB and ExbD at the cytoplasmic membrane to be re-energized [Larsen03].


Subunit of TonB energy transducing system: TonB energy transducing system - TonB subunit

Synonyms: ExbA, TonB

Gene: tonB Accession Numbers: EG11012 (EcoCyc), b1252, ECK1246

Locations: periplasmic space, inner membrane

Sequence Length: 239 AAs

Molecular Weight: 26.094 kD (from nucleotide sequence)

Molecular Weight: 25.0 kD (experimental) [James09]

GO Terms:

Biological Process: GO:0015889 - cobalamin transport Inferred from experiment [Cadieux02, Bassford76]
GO:0006810 - transport Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0015031 - protein transport Inferred by computational analysis [UniProtGOA11]
GO:0015891 - siderophore transport Author statement [Braun95]
GO:0042914 - colicin transport Author statement [Braun95]
GO:0043213 - bacteriocin transport Inferred by computational analysis [UniProtGOA11]
GO:0044718 - siderophore transmembrane transport Inferred by computational analysis [GOA01]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Ollis12, Ollis12a, Ollis11, Brinkman08, VakhariaRao07, James09]
GO:0031992 - energy transducer activity Inferred from experiment Inferred by computational analysis [GOA01, Letain97, Bassford76]
GO:0015343 - siderophore transmembrane transporter activity Inferred by computational analysis [GOA01]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, Postle88]
GO:0031233 - intrinsic component of external side of plasma membrane Inferred from experiment [Skare93]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11]
GO:0030288 - outer membrane-bounded periplasmic space Inferred by computational analysis [GOA01, DiazMejia09]

MultiFun Terms: cell structure membrane
extrachromosomal prophage genes and phage related functions

Unification Links: DIP:DIP-11010N , DIP:DIP-48111N , DisProt:DP00043 , EcoliWiki:b1252 , ModBase:P02929 , PR:PRO_000024083 , Pride:P02929 , Protein Model Portal:P02929 , RefSeq:NP_415768 , SMR:P02929 , UniProt:P02929

Relationship Links: InterPro:IN-FAMILY:IPR003538 , InterPro:IN-FAMILY:IPR006260 , PDB:Structure:1IHR , PDB:Structure:1QXX , PDB:Structure:1U07 , PDB:Structure:1XX3 , PDB:Structure:2GRX , PDB:Structure:2GSK , Pfam:IN-FAMILY:PF03544 , Prints:IN-FAMILY:PR01374

Summary:
TonB is a cytoplasmic membrane protein which transduces the proton motive force (pmf) of the cytoplasmic membrane to the outer membrane active transporters thus providing the energy source required for the import of iron-siderophore complexes and vitamin B12 across the outer membrane [Letain97]. TonB functions as part of an energy transduction complex with ExbB and ExbD [Braun02].

TonB induces conformational changes in outer exposed-surface loops of the outer-membrane receptor FhuA, which promotes binding to and transport of hydroxamate-type siderophores into the periplasm [James08]. TonB also interacts with the periplasmic binding protein BtuF. This interaction has a stoichiometry of 1:1 and is independent of cyanocobalamin binding by BtuF [James09].

Hybrid protein studies indicate that the TonB N terminus remains associated with the inner membrane, while the downstream region bridges the cell envelope due to the affinity of the C terminus for peptidoglycan. This suggests that TonB searches for occupied receptor proteins from underneath the peptidoglycan-associated outer membrane proteins [Kaserer08].

The crystal structure of a 92-residue fragment of TonB (TonB-92) has been determined to 1.13 Å resolution [Kodding04].

Essentiality data for tonB knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
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]

Subunit of TonB energy transducing system: TonB energy transducing system - ExbB subunit

Synonyms: ExbB

Gene: exbB Accession Numbers: EG10271 (EcoCyc), b3006, ECK2999

Locations: inner membrane

Sequence Length: 244 AAs

Molecular Weight: 26.287 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0050821 - protein stabilization Inferred from experiment [Ahmer95]
GO:0006810 - transport Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0015031 - protein transport Inferred by computational analysis [UniProtGOA11]
GO:0043213 - bacteriocin transport Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Ollis12, Ollis11, Brinkman08, VakhariaRao07, Higgs98]
GO:0031992 - energy transducer activity Inferred from experiment [Letain97]
GO:0008565 - protein transporter activity Inferred by computational analysis [GOA01]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, DiazMejia09, Zhang07, Daley05, Letain97]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell processes adaptations Fe aquisition
cell structure membrane
transport Electrochemical potential driven transporters Ion-gradient-driven energizers

Unification Links: DIP:DIP-47841N , EcoliWiki:b3006 , PR:PRO_000022554 , Pride:P0ABU7 , Protein Model Portal:P0ABU7 , RefSeq:NP_417479 , String:511145.b3006 , UniProt:P0ABU7

Relationship Links: InterPro:IN-FAMILY:IPR002898 , InterPro:IN-FAMILY:IPR014164 , Pfam:IN-FAMILY:PF01618

Summary:
ExbB and ExbD proteins function as part of the TonB-dependent energy transduction system for the import of iron-siderophore complexes and vitamin B12 across the outer membrane. ExbB and ExbD are encoded by the exb operon in Escherichia coli [Held02].

Essentiality data for exbB 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]

Subunit of TonB energy transducing system: tonB energy transducing system - ExbD subunit

Synonyms: ExbD

Gene: exbD Accession Numbers: EG10272 (EcoCyc), b3005, ECK2998

Locations: inner membrane

Sequence Length: 141 AAs

Molecular Weight: 15.527 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0050821 - protein stabilization Inferred from experiment [Ahmer95]
GO:0006810 - transport Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0015031 - protein transport Inferred by computational analysis [UniProtGOA11]
GO:0043213 - bacteriocin transport Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Ollis12, Ollis12a, Ollis11]
GO:0031992 - energy transducer activity Inferred from experiment [Letain97]
GO:0042802 - identical protein binding Inferred from experiment [Rajagopala14, Ollis12, Ollis11]
GO:0005215 - transporter activity Inferred by computational analysis [GOA01]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, DiazMejia09, Zhang07, Letain97]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell processes adaptations Fe aquisition
transport Electrochemical potential driven transporters Ion-gradient-driven energizers

Unification Links: DIP:DIP-47973N , EcoliWiki:b3005 , PR:PRO_000022555 , Protein Model Portal:P0ABV2 , RefSeq:NP_417478 , SMR:P0ABV2 , String:511145.b3005 , UniProt:P0ABV2

Relationship Links: InterPro:IN-FAMILY:IPR003400 , InterPro:IN-FAMILY:IPR014170 , PDB:Structure:2PFU , Pfam:IN-FAMILY:PF02472

Summary:
ExbB and ExbD proteins function as part of the TonB-dependent energy transduction system for the import of iron-siderophore complexes and vitamin B12 across the outer membrane. ExbB and ExbD are encoded by the exb operon in Escherichia coli [Held02].

Essentiality data for exbD 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]

References

Ahmer95: Ahmer BM, Thomas MG, Larsen RA, Postle K (1995). "Characterization of the exbBD operon of Escherichia coli and the role of ExbB and ExbD in TonB function and stability." J Bacteriol 1995;177(16);4742-7. PMID: 7642501

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

Bassford76: Bassford PJ, Bradbeer C, Kadner RJ, Schnaitman CA (1976). "Transport of vitamin B12 in tonB mutants of Escherichia coli." J Bacteriol 128(1);242-7. PMID: 135755

Braun02: Braun V, Braun M (2002). "Active transport of iron and siderophore antibiotics." Curr Opin Microbiol 5(2);194-201. PMID: 11934617

Braun95: Braun V (1995). "Energy-coupled transport and signal transduction through the gram-negative outer membrane via TonB-ExbB-ExbD-dependent receptor proteins." FEMS Microbiol Rev 16(4);295-307. PMID: 7654405

Brinkman08: Brinkman KK, Larsen RA (2008). "Interactions of the energy transducer TonB with noncognate energy-harvesting complexes." J Bacteriol 190(1);421-7. PMID: 17965155

Cadieux02: Cadieux N, Bradbeer C, Reeger-Schneider E, Koster W, Mohanty AK, Wiener MC, Kadner RJ (2002). "Identification of the periplasmic cobalamin-binding protein BtuF of Escherichia coli." J Bacteriol 2002;184(3);706-17. PMID: 11790740

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

Ferguson02: Ferguson AD, Chakraborty R, Smith BS, Esser L, van der Helm D, Deisenhofer J (2002). "Structural basis of gating by the outer membrane transporter FecA." Science 295(5560);1715-9. PMID: 11872840

GarciaHerrero05: Garcia-Herrero A, Vogel HJ (2005). "Nuclear magnetic resonance solution structure of the periplasmic signalling domain of the TonB-dependent outer membrane transporter FecA from Escherichia coli." Mol Microbiol 58(5);1226-37. PMID: 16313612

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."

Gresock11: Gresock MG, Savenkova MI, Larsen RA, Ollis AA, Postle K (2011). "Death of the TonB Shuttle Hypothesis." Front Microbiol 2;206. PMID: 22016747

Han12: Han MJ, Lee SY, Hong SH (2012). "Comparative analysis of envelope proteomes in Escherichia coli B and K-12 strains." J Microbiol Biotechnol 22(4);470-8. PMID: 22534293

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

Held02: Held KG, Postle K (2002). "ExbB and ExbD do not function independently in TonB-dependent energy transduction." J Bacteriol 184(18);5170-3. PMID: 12193634

Higgs02: Higgs PI, Letain TE, Merriam KK, Burke NS, Park H, Kang C, Postle K (2002). "TonB interacts with nonreceptor proteins in the outer membrane of Escherichia coli." J Bacteriol 184(6);1640-8. PMID: 11872715

Higgs98: Higgs PI, Myers PS, Postle K (1998). "Interactions in the TonB-dependent energy transduction complex: ExbB and ExbD form homomultimers." J Bacteriol 180(22);6031-8. PMID: 9811664

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

James08: James KJ, Hancock MA, Moreau V, Molina F, Coulton JW (2008). "TonB Induces Conformational Changes in Surface-exposed Loops of FhuA, Outer Membrane Receptor of Escherichia coli." Protein Sci NIL. PMID: 18653801

James09: James KJ, Hancock MA, Gagnon JN, Coulton JW (2009). "TonB Interacts with BtuF, the Escherichia coli periplasmic binding protein for cyanocobalamin." Biochemistry 48(39);9212-20. PMID: 19708689

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

Karlsson93: Karlsson M, Hannavy K, Higgins CF (1993). "A sequence-specific function for the N-terminal signal-like sequence of the TonB protein." Mol Microbiol 8(2);379-88. PMID: 8316087

Kaserer08: Kaserer WA, Jiang X, Xiao Q, Scott DC, Bauler M, Copeland D, Newton SM, Klebba PE (2008). "Insight from TonB hybrid proteins into the mechanism of iron transport through the outer membrane." J Bacteriol 190(11);4001-16. PMID: 18390658

Kodding04: Kodding J, Killig F, Polzer P, Howard SP, Diederichs K, Welte W (2004). "Crystal structure of a 92-residue C-terminal fragment of TonB from Escherichia coli reveals significant conformational changes compared to structures of smaller TonB fragments." J Biol Chem 280(4):3022-8. PMID: 15522863

Larsen03: Larsen RA, Letain TE, Postle K (2003). "In vivo evidence of TonB shuttling between the cytoplasmic and outer membrane in Escherichia coli." Mol Microbiol 49(1);211-8. PMID: 12823822

Letain97: Letain TE, Postle K (1997). "TonB protein appears to transduce energy by shuttling between the cytoplasmic membrane and the outer membrane in Escherichia coli." Mol Microbiol 24(2);271-83. PMID: 9159515

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Moeck97: Moeck GS, Coulton JW, Postle K (1997). "Cell envelope signaling in Escherichia coli. Ligand binding to the ferrichrome-iron receptor fhua promotes interaction with the energy-transducing protein TonB." J Biol Chem 272(45);28391-7. PMID: 9353297

Ollis11: Ollis AA, Postle K (2011). "The same periplasmic ExbD residues mediate in vivo interactions between ExbD homodimers and ExbD-TonB heterodimers." J Bacteriol 193(24);6852-63. PMID: 21984795

Ollis12: Ollis AA, Kumar A, Postle K (2012). "The ExbD periplasmic domain contains distinct functional regions for two stages in TonB energization." J Bacteriol 194(12);3069-77. PMID: 22493019

Ollis12a: Ollis AA, Postle K (2012). "Identification of functionally important TonB-ExbD periplasmic domain interactions in vivo." J Bacteriol 194(12);3078-87. PMID: 22493017

Postle88: Postle K, Skare JT (1988). "Escherichia coli TonB protein is exported from the cytoplasm without proteolytic cleavage of its amino terminus." J Biol Chem 263(22);11000-7. PMID: 2839513

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

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

Skare93: Skare JT, Ahmer BM, Seachord CL, Darveau RP, Postle K (1993). "Energy transduction between membranes. TonB, a cytoplasmic membrane protein, can be chemically cross-linked in vivo to the outer membrane receptor FepA." J Biol Chem 268(22);16302-8. PMID: 8344918

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

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."

VakhariaRao07: Vakharia-Rao H, Kastead KA, Savenkova MI, Bulathsinghala CM, Postle K (2007). "Deletion and substitution analysis of the Escherichia coli TonB Q160 region." J Bacteriol 189(13);4662-70. PMID: 17483231

vanderHelm02: van der Helm D, Chakraborty R, Ferguson AD, Smith BS, Esser L, Deisenhofer J (2002). "Bipartite gating in the outer membrane protein FecA." Biochem Soc Trans 30(4);708-10. PMID: 12196171

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

Yue03: Yue WW, Grizot S, Buchanan SK (2003). "Structural evidence for iron-free citrate and ferric citrate binding to the TonB-dependent outer membrane transporter FecA." J Mol Biol 332(2);353-68. PMID: 12948487

Zhang07: Zhang N, Chen R, Young N, Wishart D, Winter P, Weiner JH, Li L (2007). "Comparison of SDS- and methanol-assisted protein solubilization and digestion methods for Escherichia coli membrane proteome analysis by 2-D LC-MS/MS." Proteomics 7(4);484-93. PMID: 17309111

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


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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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