RegulonDB RegulonDB 11.1: Gene Form
   

rbsB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rbsC rbsK rbsB rbsZ RybB terminator anti-terminator TSS_4366 (cluster) TSS_4366 (cluster) TSS_4365 TSS_4365 TSS_4364 (cluster) TSS_4364 (cluster) TSS_4363 (cluster) TSS_4363 (cluster) TSS_4362 TSS_4362 TSS_4361 TSS_4361 TSS_4360 TSS_4360

Gene      
Name: rbsB    Texpresso search in the literature
Synonym(s): ECK3745, EG10815, b3751, prlB, rbsP
Genome position(nucleotides): 3936278 --> 3937168
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 52.86
External database links:  
ASAP:
 ABE-0012264
CGSC:
 12092
ECHOBASE:
 EB0808
ECOLIHUB:
 rbsB
OU-MICROARRAY:
 b3751
STRING:
 511145.b3751
COLOMBOS: rbsB


Product      
Name: ribose ABC transporter periplasmic binding protein
Synonym(s): PrlB, RbsB, RbsP
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane,periplasmic space
Molecular weight: 30.95
Isoelectric point: 7.761
Motif(s):
 
Type Positions Sequence Comment
1 -> 25 MNMKKLATLVSAVALSATVSANAMA
26 -> 296 KDTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDSQNNPAKELANVQDLTVRGTKILLINPTDSDAVGNAVKMANQANIPVITLDRQATKGEVVSHIASDNVLGGKIAGDYIAKKAGEGAKVIELQGIAGTSAARERGEGFQQAVAAHKFNVLASQPADFDRIKGLNVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAGKSDVMVVGFDGTPDGEKAVNDGKLAATIAQLPDQIGAKGVETADKVLKGEKVQAKYPVDLKLVVKQ UniProt: Ribose import binding protein RbsB.
29 -> 281 IALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDSQNNPAKELANVQDLTVRGTKILLINPTDSDAVGNAVKMANQANIPVITLDRQATKGEVVSHIASDNVLGGKIAGDYIAKKAGEGAKVIELQGIAGTSAARERGEGFQQAVAAHKFNVLASQPADFDRIKGLNVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAGKSDVMVVGFDGTPDGEKAVNDGKLAATIAQLPDQIGAKGVETADKVLKGEK
36 -> 36 L L→D/G: Class II mutation; severe effect on transport but not on chemotaxis
37 -> 37 N N→R: Class II mutation; severe effect on transport but not on chemotaxis

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.1 - carbon utilization --> 1.1.1 - carbon compounds
  4 - transport --> 4.3 - Primary Active Transporters --> 4.3.A - Pyrophosphate Bond (ATP; GTP; P2) Hydrolysis-driven Active Transporters --> 4.3.A.1 - The ATP-binding Cassette (ABC) Superfamily + ABC-type Uptake Permeases --> 4.3.A.1.p - ABC superfamily, periplasmic binding component
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0030288 - outer membrane-bounded periplasmic space
GO:0042597 - periplasmic space
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing
molecular_function GO:0005515 - protein binding
GO:0048029 - monosaccharide binding
biological_process GO:0008643 - carbohydrate transport
GO:0015752 - D-ribose transmembrane transport
GO:0006935 - chemotaxis
GO:0050918 - positive chemotaxis
Note(s): Note(s): ...[more].
Reference(s): [1] Bjorkman AJ., et al., 1994
[2] Bjorkman AJ., et al., 1994
[3] Collier DN., et al., 1990
[4] Eym Y., et al., 1996
[5] Francetic O., et al., 1996
[6] Iida A., et al., 1985
[7] Jindal S., et al., 2019
[8] Kim J., et al., 1992
[9] Li H., et al., 2021
[10] Li HY., et al., 2013
[11] Mahendroo M., et al., 1990
[12] Mowbray SL. 1992
[13] Ravindranathan KP., et al., 2005
[14] Rosemond MJ., et al., 1994
[15] Song T., et al., 1995
[16] Tavares D., et al., 2019
[17] Vyas NK., et al., 1991
External database links:  
ALPHAFOLD:
 P02925
DIP:
 DIP-10641N
ECOCYC:
 RBSB-MONOMER
ECOLIWIKI:
 b3751
INTERPRO:
 IPR025997
INTERPRO:
 IPR028082
MINT:
 P02925
MODBASE:
 P02925
PDB:
 1DRJ
PDB:
 1DRK
PDB:
 2GX6
PDB:
 1DBP
PDB:
 2DRI
PDB:
 1BA2
PDB:
 1URP
PFAM:
 PF13407
PRIDE:
 P02925
PRODB:
 PRO_000023683
REFSEQ:
 NP_418207
SMR:
 P02925
UNIPROT:
 P02925


Operon      
Name: rbsDACBKR         
Operon arrangement:
Transcription unit        Promoter
rbsDACBKR


Transcriptional Regulation      
Display Regulation             
Activated by: CRP
Repressed by: RbsR


Regulation by small RNA    
  Display Regulation
small RNA rybB


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_4360 3935432 forward nd [RS-EPT-CBR] [18]
  promoter TSS_4361 3936137 forward nd [RS-EPT-CBR] [18]
  promoter TSS_4362 3936145 forward nd [RS-EPT-CBR] [18]
  promoter TSS_4363 (cluster) 3936163 forward nd [RS-EPT-CBR] [18]
  promoter TSS_4364 (cluster) 3936177 forward nd [RS-EPT-CBR] [18]
  promoter TSS_4365 3936260 forward nd [RS-EPT-CBR] [18]
  promoter TSS_4366 (cluster) 3937237 forward nd [RS-EPT-CBR] [18]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates


Reference(s)    

 [1] Bjorkman AJ., Binnie RA., Cole LB., Zhang H., Hermodson MA., Mowbray SL., 1994, Identical mutations at corresponding positions in two homologous proteins with nonidentical effects., J Biol Chem 269(15):11196-200

 [2] Bjorkman AJ., Binnie RA., Zhang H., Cole LB., Hermodson MA., Mowbray SL., 1994, Probing protein-protein interactions. The ribose-binding protein in bacterial transport and chemotaxis., J Biol Chem 269(48):30206-11

 [3] Collier DN., Strobel SM., Bassford PJ., 1990, SecB-independent export of Escherichia coli ribose-binding protein (RBP): some comparisons with export of maltose-binding protein (MBP) and studies with RBP-MBP hybrid proteins., J Bacteriol 172(12):6875-84

 [4] Eym Y., Park Y., Park C., 1996, Genetically probing the regions of ribose-binding protein involved in permease interaction., Mol Microbiol 21(4):695-702

 [5] Francetic O., Kumamoto CA., 1996, Escherichia coli SecB stimulates export without maintaining export competence of ribose-binding protein signal sequence mutants., J Bacteriol 178(20):5954-9

 [6] Iida A., Groarke JM., Park S., Thom J., Zabicky JH., Hazelbauer GL., Randall LL., 1985, A signal sequence mutant defective in export of ribose-binding protein and a corresponding pseudorevertant isolated without imposed selection., EMBO J 4(7):1875-80

 [7] Jindal S., Yang L., Day PJ., Kell DB., 2019, Involvement of multiple influx and efflux transporters in the accumulation of cationic fluorescent dyes by Escherichia coli., BMC Microbiol 19(1):195

 [8] Kim J., Lee Y., Kim C., Park C., 1992, Involvement of SecB, a chaperone, in the export of ribose-binding protein., J Bacteriol 174(16):5219-27

 [9] Li H., Cao Z., Hu G., Zhao L., Wang C., Wang J., 2021, Ligand-induced structural changes analysis of ribose-binding protein as studied by molecular dynamics simulations., Technol Health Care 29(S1):103-114

 [10] Li HY., Cao ZX., Zhao LL., Wang JH., 2013, Analysis of conformational motions and residue fluctuations for Escherichia coli ribose-binding protein revealed with elastic network models., Int J Mol Sci 14(5):10552-69

 [11] Mahendroo M., Cole LB., Mowbray SL., 1990, Preliminary X-ray data for the periplasmic ribose receptor from Escherichia coli., J Mol Biol 211(4):689-90

 [12] Mowbray SL., 1992, Ribose and glucose-galactose receptors. Competitors in bacterial chemotaxis., J Mol Biol 227(2):418-40

 [13] Ravindranathan KP., Gallicchio E., Levy RM., 2005, Conformational equilibria and free energy profiles for the allosteric transition of the ribose-binding protein., J Mol Biol 353(1):196-210

 [14] Rosemond MJ., Strobel SM., Ray PH., Bassford PJ., 1994, Ability of MBP or RBP signal peptides to influence folding and in vitro translocation of wild-type and hybrid precursors., FEBS Lett 349(2):281-5

 [15] Song T., Park C., 1995, Effect of folding on the export of ribose-binding protein studied with the genetically isolated suppressors for the signal sequence mutation., J Mol Biol 253(2):304-12

 [16] Tavares D., Reimer A., Roy S., Joublin A., Sentchilo V., van der Meer JR., 2019, Computational redesign of the Escherichia coli ribose-binding protein ligand binding pocket for 1,3-cyclohexanediol and cyclohexanol., Sci Rep 9(1):16940

 [17] Vyas NK., Vyas MN., Quiocho FA., 1991, Comparison of the periplasmic receptors for L-arabinose, D-glucose/D-galactose, and D-ribose. Structural and Functional Similarity., J Biol Chem 266(8):5226-37

 [18] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

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