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Escherichia coli K-12 substr. MG1655 Polypeptide: arabinose ABC transporter - periplasmic binding protein

Gene: araF Accession Numbers: EG10057 (EcoCyc), b1901, ECK1899

Regulation Summary Diagram

Regulation summary diagram for araF

Component of: arabinose ABC transporter (summary available)

araF encodes the periplasmic binding protein of the high-affinity arabinose transport system. Purified AraF binds L-arabinose [Hogg77]

Citations: [Clark81]

Gene Citations: [Maciag11, Scripture87]

Locations: inner membrane, periplasmic space

Map Position: [1,983,163 <- 1,984,152] (42.74 centisomes, 154°)
Length: 990 bp / 329 aa

Molecular Weight of Polypeptide: 35.541 kD (from nucleotide sequence), 33.0 kD (experimental) [Hogg77]

Unification Links: ASAP:ABE-0006330, CGSC:1023, EchoBASE:EB0055, EcoGene:EG10057, EcoliWiki:b1901, ModBase:P02924, OU-Microarray:b1901, PortEco:araF, PR:PRO_000022119, Pride:P02924, Protein Model Portal:P02924, RefSeq:NP_416414, RegulonDB:EG10057, SMR:P02924, String:511145.b1901, UniProt:P02924

Relationship Links: InterPro:IN-FAMILY:IPR001761, InterPro:IN-FAMILY:IPR026266, InterPro:IN-FAMILY:IPR028082, PDB:Structure:1ABE, PDB:Structure:1ABF, PDB:Structure:1APB, PDB:Structure:1BAP, PDB:Structure:2WRZ, PDB:Structure:5ABP, PDB:Structure:6ABP, PDB:Structure:7ABP, PDB:Structure:8ABP, PDB:Structure:9ABP, Pfam:IN-FAMILY:PF00532

In Paralogous Gene Group: 30 (25 members)

Gene-Reaction Schematic

Gene-Reaction Schematic

Genetic Regulation Schematic

Genetic regulation schematic for araF

GO Terms:
Biological Process:
Inferred from experimentInferred by computational analysisGO:0042882 - L-arabinose transport [GOA01a, Horazdovsky89]
Inferred by computational analysisGO:0006810 - transport [UniProtGOA11a]
Inferred by computational analysisGO:0008643 - carbohydrate transport [UniProtGOA11a]
Inferred by computational analysisGO:0015749 - monosaccharide transport [Gaudet10]
Molecular Function:
Inferred from experimentGO:0015407 - monosaccharide-transporting ATPase activity [Daruwalla81]
Inferred from experimentGO:0048029 - monosaccharide binding [Hogg77]
Cellular Component:
Inferred by computational analysisInferred from experimentGO:0030288 - outer membrane-bounded periplasmic space [Horazdovsky87, Hogg77, DiazMejia09, LopezCampistrou05, Han14]
Inferred from experimentGO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Horazdovsky89]
Inferred by computational analysisGO:0042597 - periplasmic space [UniProtGOA11, UniProtGOA11a]

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

Essentiality data for araF knockouts:

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

Last-Curated 03-Jul-2014 by Mackie A, Macquarie University

Subunit of: arabinose ABC transporter

Subunit composition of arabinose ABC transporter = [AraG]2[AraH]2[AraF]
         arabinose ABC transporter - ATP binding subunit = AraG (summary available)
         arabinose ABC transporter - membrane subunit = AraH (summary available)
         arabinose ABC transporter - periplasmic binding protein = AraF (summary available)

E. coli K-12 contains two kinetically distinguishable systems for L-arabinose import - the low affinity AraE L-arabinose:H+ symporter and the high affinity ATP-driven system encoded by the araFGH genes [Schleif69, Kolodrubetz81, Daruwalla81].

The AraFGH arabinose transporter is a member of the ATP Binding Cassette (ABC) transporter superfamily [Saier14]. Expression of all three components is necessary to complement high-affinity arabinose transport in an araFGH knockout strain [Horazdovsky89]. The AraF periplasmic binding protein has been experimentally characterised [Hogg77]. Based on sequence similarity, AraH is the membrane component and AraG is the ATP-binding component of this ABC transporter [Horazdovsky87, Scripture87].

Transcription of the araFGH operon is positively regulated by the AraC protein in the presence of arabinose and cAMP-CRP [Kolodrubetz81a, Hendrickson90, Johnson00].

Locations: inner membrane

GO Terms:
Biological Process:
Inferred from experimentGO:0042882 - L-arabinose transport [Horazdovsky89]
Molecular Function:
Inferred from experimentGO:0015147 - L-arabinose transmembrane transporter activity [Horazdovsky89]
Cellular Component:
Inferred from experimentGO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Horazdovsky89, Daruwalla81]

Last-Curated 03-Jul-2014 by Mackie A, Macquarie University

Enzymatic reaction of: transport of arabinose (arabinose ABC transporter)

Inferred from experiment

EC Number:

Transport reaction diagram for transport of arabinose

Kinetic Parameters:
Substrate Km (μM) Citations
L-arabinose 4.0 [Daruwalla81]

Sequence Features

Protein sequence of arabinose ABC transporter - periplasmic binding protein with features indicated

Feature Class Location Citations Comment
Signal-Sequence 1 -> 23
Inferred from experiment[Link97, Hogg77a]
Chain 24 -> 329
Author statement[UniProt15]
UniProt: L-arabinose-binding periplasmic protein.
Pfam PF00532 26 -> 319
Inferred by computational analysis[Finn14]
Peripla_BP_1 : Periplasmic binding proteins and sugar binding domain of LacI family
Amino-Acid-Site 87
Author statement[UniProt15]
UniProt: The binding site for the sugar molecule has not yet been established, but C-87 may be involved; Sequence Annotation Type: site.
Sequence-Conflict 194
Inferred by curator[Scripture87, UniProt15]
UniProt: (in Ref. 1; CAA29476).
Mutagenesis-Variant 277
Author statement[UniProt15]
UniProt: Improves binding to galactose.
Sequence-Conflict 281
Inferred by curator[Scripture87, UniProt15]
UniProt: (in Ref. 1; CAA29476).

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

Gene local context diagram

Transcription Units

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b1901 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10057; 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

Clark81: Clark AF, Hogg RW (1981). "High-affinity arabinose transport mutants of Escherichia coli: isolation and gene location." J Bacteriol 147(3);920-4. PMID: 7024251

Daruwalla81: Daruwalla KR, Paxton AT, Henderson PJ (1981). "Energization of the transport systems for arabinose and comparison with galactose transport in Escherichia coli." Biochem J 1981;200(3);611-27. PMID: 6282256

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

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

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

Han14: Han MJ, Kim JY, Kim JA (2014). "Comparison of the large-scale periplasmic proteomes of the Escherichia coli K-12 and B strains." J Biosci Bioeng 117(4);437-42. PMID: 24140104

Hendrickson90: Hendrickson W, Stoner C, Schleif R (1990). "Characterization of the Escherichia coli araFGH and araJ promoters." J Mol Biol 1990;215(4);497-510. PMID: 2231717

Hogg77: Hogg RW (1977). "L-Arabinose transport and the L-arabinose binding protein of Escherichia coli." J Supramol Struct 1977;6(3);411-7. PMID: 338992

Hogg77a: Hogg RW, Hermodson MA (1977). "Amino acid sequence of the L-arabinose-binding protein from Escherichia coli B/r." J Biol Chem 252(14);5135-41. PMID: 326784

Horazdovsky87: Horazdovsky BF, Hogg RW (1987). "High-affinity L-arabinose transport operon. Gene product expression and mRNAs." J Mol Biol 1987;197(1);27-35. PMID: 2445995

Horazdovsky89: Horazdovsky BF, Hogg RW (1989). "Genetic reconstitution of the high-affinity L-arabinose transport system." J Bacteriol 1989;171(6);3053-9. PMID: 2656640

Johnson00: Johnson CM, Schleif RF (2000). "Cooperative action of the catabolite activator protein and AraC in vitro at the araFGH promoter." J Bacteriol 182(7);1995-2000. PMID: 10715008

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

Kolodrubetz81: Kolodrubetz D, Schleif R (1981). "L-arabinose transport systems in Escherichia coli K-12." J Bacteriol 148(2);472-9. PMID: 7028715

Kolodrubetz81a: Kolodrubetz D, Schleif R (1981). "Regulation of the L-arabinose transport operons in Escherichia coli." J Mol Biol 151(2);215-27. PMID: 6461771

Link97: Link AJ, Robison K, Church GM (1997). "Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12." Electrophoresis 18(8);1259-313. PMID: 9298646

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

Maciag11: Maciag A, Peano C, Pietrelli A, Egli T, De Bellis G, Landini P (2011). "In vitro transcription profiling of the {sigma}S subunit of bacterial RNA polymerase: re-definition of the {sigma}S regulon and identification of {sigma}S-specific promoter sequence elements." Nucleic Acids Res 39(13);5338-55. PMID: 21398637

Saier14: Saier MH, Reddy VS, Tamang DG, Vastermark A (2014). "The transporter classification database." Nucleic Acids Res 42(1);D251-8. PMID: 24225317

Schleif69: Schleif R (1969). "An L-arabinose binding protein and arabinose permeation in Escherichia coli." J Mol Biol 46(1);185-96. PMID: 4902208

Scripture87: Scripture JB, Voelker C, Miller S, O'Donnell RT, Polgar L, Rade J, Horazdovsky BF, Hogg RW (1987). "High-affinity L-arabinose transport operon. Nucleotide sequence and analysis of gene products." J Mol Biol 1987;197(1);37-46. PMID: 2445996

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."

Other References Related to Gene Regulation

Gallegos97: Gallegos MT, Schleif R, Bairoch A, Hofmann K, Ramos JL (1997). "Arac/XylS family of transcriptional regulators." Microbiol Mol Biol Rev 61(4);393-410. PMID: 9409145

Hendrickson92: Hendrickson W, Flaherty C, Molz L (1992). "Sequence elements in the Escherichia coli araFGH promoter." J Bacteriol 174(21);6862-71. PMID: 1400237

Johnson95: Johnson CM, Schleif RF (1995). "In vivo induction kinetics of the arabinose promoters in Escherichia coli." J Bacteriol 177(12);3438-42. PMID: 7768852

Lu92: Lu Y, Flaherty C, Hendrickson W (1992). "AraC protein contacts asymmetric sites in the Escherichia coli araFGH promoter." J Biol Chem 1992;267(34);24848-57. PMID: 1447222

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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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