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

Gene: rbsB Accession Numbers: EG10815 (EcoCyc), b3751, ECK3745

Synonyms: prlB, rbsP

Regulation Summary Diagram

Regulation summary diagram for rbsB

Component of: ribose ABC transporter (extended summary available)

Gene Citations: [Bell86, Burland93]

Locations: inner membrane, periplasmic space

Map Position: [3,934,301 -> 3,935,191] (84.8 centisomes, 305°)
Length: 891 bp / 296 aa

Molecular Weight of Polypeptide: 30.95 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0012264, CGSC:12092, DIP:DIP-10641N, EchoBASE:EB0808, EcoGene:EG10815, EcoliWiki:b3751, Mint:MINT-1244685, ModBase:P02925, OU-Microarray:b3751, PortEco:rbsB, PR:PRO_000023683, Pride:P02925, Protein Model Portal:P02925, RefSeq:NP_418207, RegulonDB:EG10815, SMR:P02925, String:511145.b3751, UniProt:P02925

Relationship Links: InterPro:IN-FAMILY:IPR025997, InterPro:IN-FAMILY:IPR028082, PDB:Structure:1BA2, PDB:Structure:1DBP, PDB:Structure:1DRJ, PDB:Structure:1DRK, PDB:Structure:1URP, PDB:Structure:2DRI, PDB:Structure:2GX6, Pfam:IN-FAMILY:PF13407

In Paralogous Gene Group: 30 (25 members)

Gene-Reaction Schematic

Gene-Reaction Schematic

Genetic Regulation Schematic

Genetic regulation schematic for rbsB

GO Terms:
Biological Process:
Inferred by computational analysisGO:0006810 - transport [UniProtGOA11a]
Inferred by computational analysisGO:0006935 - chemotaxis [UniProtGOA11a]
Inferred by computational analysisGO:0008643 - carbohydrate transport [UniProtGOA11a]
Inferred by computational analysisGO:0015749 - monosaccharide transport [Gaudet10]
Molecular Function:
Inferred from experimentGO:0005515 - protein binding [Zheng11]
Inferred by computational analysisGO:0015145 - monosaccharide transmembrane transporter activity [Gaudet10]
Inferred by computational analysisGO:0015407 - monosaccharide-transporting ATPase activity []
Cellular Component:
Inferred from experimentGO:0016020 - membrane [Lasserre06]
Inferred from experimentInferred by computational analysisGO:0030288 - outer membrane-bounded periplasmic space [DiazMejia09, Han14, LopezCampistrou05]
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 rbsB 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: ribose ABC transporter

Subunit composition of ribose ABC transporter = [RbsA]2[RbsC]2[RbsB]
         ribose ABC transporter - putative ATP binding subunit = RbsA
         ribose ABC transporter - membrane subunit = RbsC
         ribose ABC transporter - putative periplasmic binding protein = RbsB

RbsACB is an ATP-dependent ribose transporter that is a member of the ATP-Binding Cassette (ABC) Superfamily of transporters [Park99]. Based on sequence similarity, RbsA is the ATP-binding constituent, RbsB is the periplasmic substrate-binding protein, and RbsC form the transmembrane constituent of the transporter [Park99]. Mutations in each of the components eliminated transport of ribose at external concentration of 1 μM, indicating that the components make up a transport system that is responsible for high-affinity ribose transport. However, these mutants are able to grow normally on high concentrations of the sugar, suggesting that there is at least a second, low-affinity transport system for ribose in E. coli [Iida84]. Hydrophobicity analysis has shown that RbsC contains six transmembrane helices, while alkaline phosphatase fusions and the use of inside-out vesicles with proteolysis have shown that the C and N termini are both on the cytoplasmic side of the membrane.

Enzymatic reaction of: transport of D-ribose (ribose ABC transporter)

Inferred from experimentInferred by computational analysis

EC Number:

Transport reaction diagram for transport of D-ribose

Sequence Features

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

Feature Class Location Citations Comment
Signal-Sequence 1 -> 25
Inferred from experiment[Link97, GonzalezGil96]
Chain 26 -> 296
Author statement[UniProt15]
UniProt: D-ribose-binding periplasmic protein.
Pfam PF13407 29 -> 281
Inferred by computational analysis[Finn14]
Peripla_BP_4 : Periplasmic binding protein domain

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

Gene local context diagram

Transcription Unit

Transcription-unit diagram


10/20/97 Gene b3751 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10815; 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

Bell86: Bell AW, Buckel SD, Groarke JM, Hope JN, Kingsley DH, Hermodson MA (1986). "The nucleotide sequences of the rbsD, rbsA, and rbsC genes of Escherichia coli K12." J Biol Chem 261(17);7652-8. PMID: 3011793

Burland93: Burland V, Plunkett G, Daniels DL, Blattner FR (1993). "DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around the origin of replication." Genomics 1993;16(3);551-61. PMID: 7686882

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

GonzalezGil96: Gonzalez-Gil G, Bringmann P, Kahmann R (1996). "FIS is a regulator of metabolism in Escherichia coli." Mol Microbiol 22(1);21-9. PMID: 8899705

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

Iida84: Iida A, Harayama S, Iino T, Hazelbauer GL (1984). "Molecular cloning and characterization of genes required for ribose transport and utilization in Escherichia coli K-12." J Bacteriol 158(2);674-82. PMID: 6327617

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

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

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

Park99: Park Y, Park C (1999). "Topology of RbsC, a membrane component of the ribose transporter, belonging to the AraH superfamily." J Bacteriol 1999;181(3);1039-42. PMID: 9922273

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."

Zheng11: Zheng C, Yang L, Hoopmann MR, Eng JK, Tang X, Weisbrod CR, Bruce JE (2011). "Cross-linking measurements of in vivo protein complex topologies." Mol Cell Proteomics 10(10);M110.006841. PMID: 21697552

Other References Related to Gene Regulation

Mauzy92: Mauzy CA, Hermodson MA (1992). "Structural and functional analyses of the repressor, RbsR, of the ribose operon of Escherichia coli." Protein Sci 1992;1(7);831-42. PMID: 1304369

Shimada13: Shimada T, Kori A, Ishihama A (2013). "Involvement of the ribose operon repressor RbsR in regulation of purine nucleotide synthesis in Escherichia coli." FEMS Microbiol Lett 344(2);159-65. PMID: 23651393

Zheng04: Zheng D, Constantinidou C, Hobman JL, Minchin SD (2004). "Identification of the CRP regulon using in vitro and in vivo transcriptional profiling." Nucleic Acids Res 32(19);5874-93. PMID: 15520470

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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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