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Escherichia coli K-12 substr. MG1655 Polypeptide: YbbW NCS1 Transporter



Gene: ybbW Accession Numbers: G6280 (EcoCyc), b0511, ECK0504

Synonyms: allP, glxB2

Regulation Summary Diagram: ?

Summary:
The YbbW protein is an uncharacterized member of the NCS1 family of purine and pyrimidine transporters [Saier99]. Based on sequence similarity, YbbW may function as a proton-driven allantoin uptake system [Cusa99]. Supporting this notion, the downstream gene from ybbW encodes a putative allantoinase enzyme.

Locations: inner membrane

Map Position: [536,857 -> 538,311] (11.57 centisomes)
Length: 1455 bp / 484 aa

Molecular Weight of Polypeptide: 52.456 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0001764 , EchoBASE:EB3383 , EcoGene:EG13618 , EcoliWiki:b0511 , OU-Microarray:b0511 , PortEco:ybbW , Protein Model Portal:P75712 , RefSeq:NP_415044 , RegulonDB:G6280 , SMR:P75712 , String:511145.b0511 , UniProt:P75712

Relationship Links: InterPro:IN-FAMILY:IPR001248 , InterPro:IN-FAMILY:IPR012681 , Pfam:IN-FAMILY:PF02133

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006144 - purine nucleobase metabolic process Inferred by computational analysis [UniProtGOA11]
GO:0006810 - transport Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0015720 - allantoin transport Inferred by computational analysis [Cusa99]
GO:0015851 - nucleobase transport Inferred by computational analysis [GOA01]
Molecular Function: GO:0005215 - transporter activity Inferred by computational analysis [GOA01]
GO:0005274 - allantoin uptake transmembrane transporter activity Inferred by computational analysis [Cusa99]
GO:0015205 - nucleobase transmembrane transporter activity Inferred by computational analysis [GOA01]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, DiazMejia09, Daley05]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure membrane
transport Electrochemical potential driven transporters Porters (Uni-, Sym- and Antiporters)

Essentiality data for ybbW knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Sequence Features

Feature Class Location Citations Comment
Transmembrane-Region 35 -> 55
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 59 -> 79
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 115 -> 135
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 156 -> 176
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 191 -> 211
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 225 -> 245
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 266 -> 286
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 307 -> 327
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 347 -> 367
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 373 -> 393
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 426 -> 446
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 448 -> 468
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
Peter D. Karp on Wed Jan 18, 2006:
Gene left-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


References

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

Cusa99: Cusa E, Obradors N, Baldoma L, Badia J, Aguilar J (1999). "Genetic analysis of a chromosomal region containing genes required for assimilation of allantoin nitrogen and linked glyoxylate metabolism in Escherichia coli." J Bacteriol 1999;181(24);7479-84. PMID: 10601204

Daley05: Daley DO, Rapp M, Granseth E, Melen K, Drew D, von Heijne G (2005). "Global topology analysis of the Escherichia coli inner membrane proteome." Science 308(5726);1321-3. PMID: 15919996

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

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

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

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

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

Saier99: Saier MH, Eng BH, Fard S, Garg J, Haggerty DA, Hutchinson WJ, Jack DL, Lai EC, Liu HJ, Nusinew DP, Omar AM, Pao SS, Paulsen IT, Quan JA, Sliwinski M, Tseng TT, Wachi S, Young GB (1999). "Phylogenetic characterization of novel transport protein families revealed by genome analyses." Biochim Biophys Acta 1999;1422(1);1-56. PMID: 10082980

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

Other References Related to Gene Regulation

Hasegawa08: Hasegawa A, Ogasawara H, Kori A, Teramoto J, Ishihama A (2008). "The transcription regulator AllR senses both allantoin and glyoxylate and controls a set of genes for degradation and reutilization of purines." Microbiology 154(Pt 11);3366-78. PMID: 18957590

Huerta03: Huerta AM, Collado-Vides J (2003). "Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals." J Mol Biol 333(2);261-78. PMID: 14529615

Rintoul02: Rintoul MR, Cusa E, Baldoma L, Badia J, Reitzer L, Aguilar J (2002). "Regulation of the Escherichia coli allantoin regulon: coordinated function of the repressor AllR and the activator AllS." J Mol Biol 324(4);599-610. PMID: 12460564

Teramoto10a: Teramoto J, Yamanishi Y, Magdy el-SH, Hasegawa A, Kori A, Nakajima M, Arai F, Fukuda T, Ishihama A (2010). "Single live-bacterial cell assay of promoter activity and regulation." Genes Cells 15(11);1111-22. PMID: 20964794


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Wed Nov 26, 2014, biocyc13.