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Escherichia coli K-12 substr. MG1655 Transporter: Colicin E9 translocon
Inferred from experiment

Subunit composition of Colicin E9 translocon = [TolB][(OmpF)3]
         TolB - periplasmic protein of the Tol-Pal system = TolB (extended summary available)
         outer membrane porin F = (OmpF)3
                 OmpF monomer = OmpF

Gene-Reaction Schematic

Gene-Reaction Schematic

Instance reaction of [a monosaccharide[periplasm] ↔ a monosaccharide[extracellular space]] (no EC#):
i2: N-acetylneuraminate[extracellular space]N-acetylneuraminate[periplasm] (no EC#)

Instance reaction of [N-acetylneuraminate[extracellular space]N-acetylneuraminate[periplasm]] (no EC#):
i1: N-acetyl-β-neuraminate[extracellular space]N-acetyl-β-neuraminate[periplasm] (no EC#)

Subunit of Colicin E9 translocon: TolB - periplasmic protein of the Tol-Pal system

Synonyms: Lky, LkyA

Gene: tolB Accession Numbers: EG11008 (EcoCyc), b0740, ECK0729

Locations: periplasmic space

Sequence Length: 430 AAs

Molecular Weight: 45.956 kD (from nucleotide sequence)

GO Terms:
Biological Process:
Inferred by computational analysisInferred from experimentGO:0015031 - protein transport [Clavel98, UniProtGOA11a, GOA01a]
Inferred by computational analysisInferred from experimentGO:0017038 - protein import [Clavel98, GOA06, GOA01a]
Inferred by computational analysisInferred from experimentGO:0043213 - bacteriocin transport [Clavel98, UniProtGOA11a]
Inferred from experimentGO:0051301 - cell division [Gerding07]
Inferred from experimentGO:0071237 - cellular response to bacteriocin [Loftus06, Walburger02]
Inferred by computational analysisGO:0006810 - transport [UniProtGOA11a]
Molecular Function:
Inferred from experimentGO:0005515 - protein binding [Walburger02, Rigal97, Bouveret95, Bonsor09, Clavel98]
Cellular Component:
Inferred from experimentInferred by computational analysisGO:0030288 - outer membrane-bounded periplasmic space [DiazMejia09, Han14, Zhang07, Molloy00, LopezCampistrou05, Isnard94, Levengood89]
Inferred from experimentGO:0032153 - cell division site [Gerding07]
Inferred by computational analysisInferred from experimentGO:0042597 - periplasmic space [Isnard94, UniProtGOA11, UniProtGOA11a, GOA06, GOA01a]

MultiFun Terms: extrachromosomalcolicin related
extrachromosomalprophage genes and phage related functions
transportChannel-type TransportersBeta barrel porins (The Outer Membrane Porin (OMP) Functional Superfamily)

Unification Links: DIP:DIP-48262N, EcoliWiki:b0740, Mint:MINT-7888580, ModBase:P0A855, PR:PRO_000024079, Pride:P0A855, Protein Model Portal:P0A855, RefSeq:NP_415268, SMR:P0A855, UniProt:P0A855

Relationship Links: InterPro:IN-FAMILY:IPR002469, InterPro:IN-FAMILY:IPR007195, InterPro:IN-FAMILY:IPR011659, InterPro:IN-FAMILY:IPR014167, InterPro:IN-FAMILY:IPR015943, PDB:Structure:1C5K, PDB:Structure:1CRZ, PDB:Structure:2HQS, PDB:Structure:2IVZ, PDB:Structure:2W8B, PDB:Structure:3IAX, Pfam:IN-FAMILY:PF04052, Pfam:IN-FAMILY:PF07676

TolB is a periplasmic component of the Tol-Pal system - a group of interacting proteins which span the cell envelope of E. coli K-12. The Tol-Pal system plays a role in outer membrane invagination during cell division and is important for maintaining outer membrane integrity. It also has a role in facilitating phage infection and colicin uptake.

TolB is a periplasmic protein [Isnard94]; TolB interacts with the peptidoglycan associated lipoprotein, Pal in vivo [Bouveret95, Walburger02]. TolB interacts with the major outer membrane lipoprotein, Lpp and with OmpA in a Pal-dependent manner [Clavel98]. Purified TolB interacts with the trimeric outer membrane porins, OmpF, OmpC, PhoE and LamB in vitro [Rigal97]. TolB may form homodimers in vivo [Walburger02]. TolB interacts with TolA; disrupting this interaction results in cells that are hypersensitive to SDS and tolerant to colicin A [Walburger02].

TolB accumulates at the site of constriction in dividing cells; this localisation is dependent on FtsN [Gerding07].

TolB consists of two domains - an N-terminal domain with an αβ structure and a large C-terminal domain that adopts a 6-bladed β propeller structure [Abergel99, Carr00].

Colicin E9 binds to the propeller domain of TolB; colicin E9 competes with Pal for binding to TolB; colicin E9 can dislodge Pal from its complex with TolB but this requires Ca2+ or Mg2+ ions [Loftus06, Papadakos12]. Colicin A and colicin E9 interact in subtly different ways with TolB [Zhang10a]. TolB, TolA and proton motive force are required for release of the immunity protein (Im9) from colicin E9 [Vankemmelbeke09]

tolB mutants release periplasmic proteins into the extracellular medium [Lazzaroni81, FogniniLefebvre87].

Targeting of TolB to the Sec-translocase for transport across the inner membrane is SecB-dependent [Baars06].

tol: colicin tolerant [Nagel67, Nomura67]
lky: leaky [Lazzaroni81]

Comments: [Uversky12]

Citations: [Benedetti91, Bouveret98, Duche06]

Essentiality data for tolB 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]

Component enzyme of Colicin E9 translocon : outer membrane porin F

Synonyms: nfxB, tolF, cmlB, cry, outer membrane protein F, colB, outer membrane protein A1, outer membrane protein 1a, outer membrane protein 4, outer membrane protein b, outer membrane protein 0-9

Gene: ompF Accession Numbers: EG10671 (EcoCyc), b0929, ECK0920

Locations: outer membrane

Subunit composition of outer membrane porin F = [OmpF]3
         OmpF monomer = OmpF

Map Position: [985,117 <- 986,205] (21.23 centisomes, 76°)
Length: 1089 bp / 362 aa

Molecular Weight of Polypeptide: 39.333 kD (from nucleotide sequence)

GO Terms:
Biological Process:
Inferred from experimentGO:0006855 - drug transmembrane transport [Harder81]
Inferred from experimentGO:0043213 - bacteriocin transport [Bourdineaud90]
Inferred by computational analysisGO:0006810 - transport [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0006811 - ion transport [UniProtGOA11a]
Author statementGO:0034220 - ion transmembrane transport [Nikaido85]
Molecular Function:
Inferred from experimentGO:0015238 - drug transmembrane transporter activity [Harder81]
Inferred from experimentAuthor statementInferred by computational analysisGO:0015288 - porin activity [UniProtGOA11a, GOA01a, Nikaido85, Saint96]
Inferred from experimentGO:0042912 - colicin transmembrane transporter activity [Bourdineaud90]
Author statementGO:0015075 - ion transmembrane transporter activity [Nikaido85]
Cellular Component:
Inferred from experimentInferred by computational analysisGO:0009279 - cell outer membrane [UniProtGOA11, UniProtGOA11a, DiazMejia09, Han12a, Zhang07, Molloy00, LopezCampistrou05, Palva78]
Inferred from experimentInferred by computational analysisGO:0046930 - pore complex [UniProtGOA11a, Cowan92]
Inferred by computational analysisGO:0016020 - membrane [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0016021 - integral component of membrane [UniProtGOA11a]

MultiFun Terms: transportChannel-type TransportersBeta barrel porins (The Outer Membrane Porin (OMP) Functional Superfamily)

Unification Links: DIP:DIP-10398N, EcoliWiki:b0929, Mint:MINT-1511804, ModBase:P02931, PR:PRO_000023452, Pride:P02931, Protein Model Portal:P02931, RefSeq:NP_415449, SMR:P02931, UniProt:P02931

Relationship Links: InterPro:IN-FAMILY:IPR001702, InterPro:IN-FAMILY:IPR001897, InterPro:IN-FAMILY:IPR013793, InterPro:IN-FAMILY:IPR023614, PDB:Structure:1BT9, PDB:Structure:1GFM, PDB:Structure:1GFN, PDB:Structure:1GFO, PDB:Structure:1GFP, PDB:Structure:1GFQ, PDB:Structure:1HXT, PDB:Structure:1HXU, PDB:Structure:1HXX, PDB:Structure:1MPF, PDB:Structure:1OPF, PDB:Structure:2OMF, PDB:Structure:2ZFG, PDB:Structure:2ZLD, PDB:Structure:3FYX, PDB:Structure:3HW9, PDB:Structure:3HWB, PDB:Structure:3K19, PDB:Structure:3K1B, PDB:Structure:3POQ, PDB:Structure:3POU, PDB:Structure:3POX, PDB:Structure:4GCP, PDB:Structure:4GCQ, PDB:Structure:4GCS, PDB:Structure:4JFB, PDB:Structure:4LSE, PDB:Structure:4LSF, PDB:Structure:4LSH, PDB:Structure:4LSI, Pfam:IN-FAMILY:PF00267, Prints:IN-FAMILY:PR00182, Prints:IN-FAMILY:PR00183, Prosite:IN-FAMILY:PS00576

S-methyl-5-thio-D-ribose[periplasm]S-methyl-5-thio-D-ribose[extracellular space],
an inositol[periplasm] ↔ an inositol[extracellular space],
an amino acid[periplasm] ↔ an amino acid[extracellular space],
a nucleobase[periplasm] ↔ a nucleobase[extracellular space],
a sugar alcohol[periplasm] ↔ a sugar alcohol[extracellular space],
a short-chain alcohol[periplasm] ↔ a short-chain alcohol[extracellular space],
a short-chain carboxylate[periplasm] ↔ a short-chain carboxylate[extracellular space],
an organosulfur compound[periplasm] ↔ an organosulfur compound[extracellular space],
H2O[periplasm] ↔ H2O[extracellular space],
CO2[periplasm] ↔ CO2[extracellular space],
an ion[periplasm] ↔ an ion[extracellular space],
a monosaccharide[periplasm] ↔ a monosaccharide[extracellular space],
glycine betaine[extracellular space] ↔ glycine betaine[periplasm],
hydrophilic solute or ion < 600 Da[extracellular space] ↔ hydrophilic solute or ion < 600 Da[periplasm]

OmpF is a member of the General Bacterial Porin (GBP) family. X-ray crystallography has determined the three-dimensional structure of the OmpF porin to be a trimeric structure with each monomer consisting of 16 antiparallel β strands [Cowan92]. OmpF is tightly but noncovalently associated with the peptidoglycan layer [Lambert88]. Targeting of OmpF to the Sec-translocase for transport across the inner membrane is SecB-dependent [Baars06].

OmpF allows the passage of solutes such as sugars, ions, and amino acids which are less than 600 daltons, with a weak preference for cationic molecules [Cowan92]. Studies in which OmpF was chemically modified suggested OmpF has two separate ionic pathways preferential for either small, highly charged ions or large ions [Miedema06]. Double OmpC-OmpF mutants and OmpR mutants (incapable of synthesizing OmpC and OmpF) survive poorly in comparison to single mutants of OmpC or OmpF when suspended in filtered-autoclaved water or sea water. This suggests that these two porins are crucial for entry into survival mode [Darcan03]. OmpF is believed to be the main pathway for β-lactam antibiotics (reviewed in [Nikaido89]). OmpF has been implicated in the secretion of the extracellular protein YebF [Prehna12].

Expression of a mutant OmpF in the absence of DegP, which is normally lethal, was shown to be down-regulated post-transcriptionally in response to overexpression of ipeX, an RNA containing the 3' ends of ybcQ and nmpC [CastilloKeller06]. In E. coli K-12 the nmpC gene, encoding a qsr phage porin protein, is disrupted by an IS5 element.

OmpF imports the cytotoxic domains of group A colicins E1 and E3 after the colicins bind to the BtuB receptor [Zakharov04, Zakharov06]. The Colicin E9 (ColE9) translocon is a heptameric complex consisting of single copies of the ColE9-immunity protein complex, BtuB, the OmpF trimer and TolB [Housden13]. ColE9's unstructured N-terminal domain occupies two OmpF subunits and captures TolB on the other side of the membrane [Housden10, Housden13]. Colicin N uses only OmpF for entry [elKouhen93] - it does not require a separate receptor protein, rather it binds to lipopolysaccharide molecules adjacent to OmpF [Baboolal08, Johnson14].

OmpF production decreased in response to exogenous polyamines which are known to provide resistance to ColE7 [Pan06]. Polyamines have also been shown to inhibit antibiotic flux through polyliposome reconstituted OmpF [Kreir08, Iyer97].

Crystal structures of OmpF with and without bound N-terminal segment of colicin E3 have been solved to 3.0 Å and 1.6 Å resolution, respectively [Yamashita08].

Amounts of OmpF porin are reduced in mutants in which lon and ycgE are inactivated [Duval09]. The drug susceptibilities of the lon and ycgE mutants are associated with a decreased level of OmpF and not the result of overexpression of MarA or AcrAB [Duval09].

A description of outer membrane protein nomenclature, including early and recommended names can be found in [Osborn80].

Citations: [Nikaido85, Rosenbusch74, Schabert95, Miedema06a, Zhu09, Kumar10, Burgess08, Zakharov08, Zhao15]

Gene Citations: [Mizuno83]

Essentiality data for ompF 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]


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Baars06: Baars L, Ytterberg AJ, Drew D, Wagner S, Thilo C, van Wijk KJ, de Gier JW (2006). "Defining the role of the Escherichia coli chaperone SecB using comparative proteomics." J Biol Chem 281(15);10024-34. PMID: 16352602

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Benedetti91: Benedetti H, Frenette M, Baty D, Knibiehler M, Pattus F, Lazdunski C (1991). "Individual domains of colicins confer specificity in colicin uptake, in pore-properties and in immunity requirement." J Mol Biol 217(3);429-39. PMID: 1704440

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Bourdineaud90: Bourdineaud JP, Fierobe HP, Lazdunski C, Pages JM (1990). "Involvement of OmpF during reception and translocation steps of colicin N entry." Mol Microbiol 4(10);1737-43. PMID: 1706457

Bouveret95: Bouveret E, Derouiche R, Rigal A, Lloubes R, Lazdunski C, Benedetti H (1995). "Peptidoglycan-associated lipoprotein-TolB interaction. A possible key to explaining the formation of contact sites between the inner and outer membranes of Escherichia coli." J Biol Chem 270(19);11071-7. PMID: 7744736

Bouveret98: Bouveret E, Rigal A, Lazdunski C, Benedetti H (1998). "Distinct regions of the colicin A translocation domain are involved in the interaction with TolA and TolB proteins upon import into Escherichia coli." Mol Microbiol 27(1);143-57. PMID: 9466263

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Carr00: Carr S, Penfold CN, Bamford V, James R, Hemmings AM (2000). "The structure of TolB, an essential component of the tol-dependent translocation system, and its protein-protein interaction with the translocation domain of colicin E9." Structure 8(1);57-66. PMID: 10673426

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FogniniLefebvre87: Fognini-Lefebvre N, Lazzaroni JC, Portalier R (1987). "tolA, tolB and excC, three cistrons involved in the control of pleiotropic release of periplasmic proteins by Escherichia coli K12." Mol Gen Genet 209(2);391-5. PMID: 3312962

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

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

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

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Housden13: Housden NG, Hopper JT, Lukoyanova N, Rodriguez-Larrea D, Wojdyla JA, Klein A, Kaminska R, Bayley H, Saibil HR, Robinson CV, Kleanthous C (2013). "Intrinsically disordered protein threads through the bacterial outer-membrane porin OmpF." Science 340(6140);1570-4. PMID: 23812713

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Johnson14: Johnson CL, Ridley H, Marchetti R, Silipo A, Griffin DC, Crawford L, Bonev B, Molinaro A, Lakey JH (2014). "The antibacterial toxin colicin N binds to the inner core of lipopolysaccharide and close to its translocator protein." Mol Microbiol. PMID: 24589252

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Levengood89: Levengood SK, Webster RE (1989). "Nucleotide sequences of the tolA and tolB genes and localization of their products, components of a multistep translocation system in Escherichia coli." J Bacteriol 171(12);6600-9. PMID: 2687247

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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

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Mizuno83: Mizuno T, Chou MY, Inouye M (1983). "A comparative study on the genes for three porins of the Escherichia coli outer membrane. DNA sequence of the osmoregulated ompC gene." J Biol Chem 1983;258(11);6932-40. PMID: 6304064

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Palva78: Palva ET, Randall LL (1978). "Arrangement of protein I in Escherichia coli outer membrane: cross-linking study." J Bacteriol 133(1);279-86. PMID: 338582

Pan06: Pan YH, Liao CC, Kuo CC, Duan KJ, Liang PH, Yuan HS, Hu ST, Chak KF (2006). "The critical roles of polyamines in regulating ColE7 production and restricting ColE7 uptake of the colicin-producing Escherichia coli." J Biol Chem 281(19);13083-91. PMID: 16549429

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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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