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

Gene: alsB Accession Numbers: EG12458 (EcoCyc), b4088, ECK4081

Synonyms: yjcX

Regulation Summary Diagram

Regulation summary diagram for alsB

Component of: D-allose ABC transporter (extended summary available)

AlsB is the periplasmic substrate-binding component of the allose ABC transporter.

Gene Citations: [Kim97, Poulsen99]

Locations: inner membrane, periplasmic space

Map Position: [4,309,130 <- 4,310,065] (92.88 centisomes, 334°)
Length: 936 bp / 311 aa

Molecular Weight of Polypeptide: 32.91 kD (from nucleotide sequence)

pI: 6.45 [Han14]

Unification Links: ASAP:ABE-0013398, EchoBASE:EB2352, EcoGene:EG12458, EcoliWiki:b4088, ModBase:P39265, OU-Microarray:b4088, PortEco:alsB, PR:PRO_000022088, Pride:P39265, Protein Model Portal:P39265, RefSeq:NP_418512, RegulonDB:EG12458, SMR:P39265, String:511145.b4088, UniProt:P39265

Relationship Links: InterPro:IN-FAMILY:IPR025997, InterPro:IN-FAMILY:IPR028082, PDB:Structure:1GUB, PDB:Structure:1GUD, PDB:Structure:1RPJ, Pfam:IN-FAMILY:PF13407

In Paralogous Gene Group: 30 (25 members)

Gene-Reaction Schematic

Gene-Reaction Schematic

Genetic Regulation Schematic

Genetic regulation schematic for alsB

GO Terms:
Biological Process:
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 by computational analysisGO:0015145 - monosaccharide transmembrane transporter activity [Gaudet10]
Cellular Component:
Inferred from experimentGO:0016020 - membrane [Lasserre06]
Inferred from experimentInferred by computational analysisGO:0030288 - outer membrane-bounded periplasmic space [DiazMejia09, Han14]
Inferred by computational analysisGO:0005886 - plasma membrane [Gaudet10]
Inferred by computational analysisGO:0016021 - integral component of membrane [Gaudet10]
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 alsB 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: D-allose ABC transporter

Subunit composition of D-allose ABC transporter = [AlsA]2[AlsC]2[AlsB]
         D-allose ABC transporter - ATP binding subunit = AlsA (summary available)
         D-allose ABC transporter - membrane subunit = AlsC (summary available)
         D-allose ABC transporter - periplasmic binding protein = AlsB (summary available)

The AlsBAC transporter belongs to the ATP-binding Cassette (ABC) Superfamily [Saurin94]. It is responsible for the uptake of D-allose, an all-cis hexose that can be used by E. coli as a sole carbon source [Kim97]. Deletion of the als genes resulted in an inability to grow on D-allose [Kim97]. AlsB is a periplasmic protein that binds D-allose with a Kd of 0.33μM, as determined by fluorescence spectroscopy [Kim97]. Based on sequence similarity, AlsA is the ATP-binding component, and AlsC is the membrane component of the ABC transporter [Chaudhuri99]. The AlsBAC system also transports ribose at low affinity [Kim97]. Complementation analysis of als mutants showed that the cloned als genes could restore growth on ribose minimal media [Kim97]. Analysis of β-galactosidase transcriptional fusions suggest that AlsR is a negative regulator of alsABC, and transcription of alsR is regulated by allose [Kim97].

Enzymatic reaction of: D-allose ABC transporter

Inferred from experiment

Synonyms: Transport of D-allose

Transport reaction diagram for D-allose ABC transporter

Alternative Products for D-allose: β-D-ribopyranose [Kim97]

Sequence Features

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

Feature Class Location Citations Comment
Signal-Sequence 1 -> 23
Author statement[UniProt15]
Sequence-Conflict 16
Inferred by curator[Sorensen96, UniProt15]
UniProt: (in Ref. 4; CAA57686).
Chain 24 -> 311
Author statement[UniProt15]
UniProt: D-allose-binding periplasmic protein.
Pfam PF13407 28 -> 288
Inferred by computational analysis[Finn14]
Peripla_BP_4 : Periplasmic binding protein domain
Sequence-Conflict 125 -> 130
Inferred by curator[Sorensen96, UniProt15]
UniProt: (in Ref. 4; CAA57686).

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

Gene local context diagram

Transcription Units

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b4088 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12458; 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

Chaudhuri99: Chaudhuri BN, Ko J, Park C, Jones TA, Mowbray SL (1999). "Structure of D-allose binding protein from Escherichia coli bound to D-allose at 1.8 A resolution." J Mol Biol 1999;286(5);1519-31. PMID: 10064713

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

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

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

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

Kim97: Kim C, Song S, Park C (1997). "The D-allose operon of Escherichia coli K-12." J Bacteriol 1997;179(24);7631-7. PMID: 9401019

Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726

Poulsen99: Poulsen TS, Chang YY, Hove-Jensen B (1999). "D-Allose catabolism of Escherichia coli: involvement of alsI and regulation of als regulon expression by allose and ribose." J Bacteriol 1999;181(22);7126-30. PMID: 10559180

Saurin94: Saurin W, Dassa E (1994). "Sequence relationships between integral inner membrane proteins of binding protein-dependent transport systems: evolution by recurrent gene duplications." Protein Sci 1994;3(2);325-44. PMID: 8003968

Sorensen96: Sorensen KI, Hove-Jensen B (1996). "Ribose catabolism of Escherichia coli: characterization of the rpiB gene encoding ribose phosphate isomerase B and of the rpiR gene, which is involved in regulation of rpiB expression." J Bacteriol 1996;178(4);1003-11. PMID: 8576032

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

Bennik00: Bennik MH, Pomposiello PJ, Thorne DF, Demple B (2000). "Defining a rob regulon in Escherichia coli by using transposon mutagenesis." J Bacteriol 182(13);3794-801. PMID: 10850996

Zaslaver06: Zaslaver A, Bren A, Ronen M, Itzkovitz S, Kikoin I, Shavit S, Liebermeister W, Surette MG, Alon U (2006). "A comprehensive library of fluorescent transcriptional reporters for Escherichia coli." Nat Methods 3(8);623-8. PMID: 16862137

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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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