Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
twitter

Escherichia coli K-12 substr. MG1655 Polypeptide: galactofuranose / galactopyranose ABC transporter - periplasmic binding protein



Gene: ytfQ Accession Numbers: EG12517 (EcoCyc), b4227, ECK4223

Regulation Summary Diagram: ?

Component of: galactofuranose / galactopyranose ABC transporter (summary available)

Summary:
YtfQ is the periplasmic binding component of a galactose ABC transporter. Purified YtfQ binds galactose with a Kd of 1.7μM and arabinose with a Kd of 1.3μM [Horler09]. YtfQ exhibits selective binding of galactofuranose over galactopyranose [Horler09]. YtfQ is able to recognise both α and β forms of galactofuranose [Horler09]. The crystal structure of YtfQ with a single molecule of galactofuranose in its ligand binding pocket has been resolved at 1.2Å [Horler09].

YtfQ is upregulated under glucose-limited fed-batch conditions [Raman05].

Gene Citations: [Maciag11]

Locations: periplasmic space, inner membrane

Map Position: [4,447,985 -> 4,448,941] (95.87 centisomes)
Length: 957 bp / 318 aa

Molecular Weight of Polypeptide: 34.345 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0013829 , EchoBASE:EB2409 , EcoGene:EG12517 , EcoliWiki:b4227 , ModBase:P39325 , OU-Microarray:b4227 , PortEco:ytfQ , Pride:P39325 , Protein Model Portal:P39325 , RefSeq:NP_418648 , RegulonDB:EG12517 , SMR:P39325 , String:511145.b4227 , UniProt:P39325

Relationship Links: InterPro:IN-FAMILY:IPR025997 , InterPro:IN-FAMILY:IPR028082 , PDB:Structure:2VK2 , Pfam:IN-FAMILY:PF13407

In Paralogous Gene Group: 30 (25 members) , 581 (2 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0015757 - galactose transport Inferred from experiment [Horler09]
GO:0006810 - transport Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0005534 - galactose binding Inferred from experiment [Horler09]
Cellular Component: GO:0030288 - outer membrane-bounded periplasmic space Inferred from experiment Inferred by computational analysis [DiazMejia09, Han13, LopezCampistrou05]
GO:0042597 - periplasmic space Inferred by curator Inferred by computational analysis [UniProtGOA11a, UniProtGOA11]
GO:0043190 - ATP-binding cassette (ABC) transporter complex Inferred by computational analysis [Saurin99]

MultiFun Terms: transport Channel-type Transporters Pyrophosphate Bond (ATP; GTP; P2) Hydrolysis-driven Active Transporters The ATP-binding Cassette (ABC) Superfamily + ABC-type Uptake Permeases ABC superfamily, periplasmic binding component

Essentiality data for ytfQ 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]

Subunit of: galactofuranose / galactopyranose ABC transporter

Subunit composition of galactofuranose / galactopyranose ABC transporter = [YjfF][YtfR][YtfT]2[YtfQ]
         galactofuranose / galactospyranose ABC transporter - putative membrane subunit = YjfF (summary available)
         galactofuranose / galactopyranose ABC transporter - putative ATP binding subunit = YtfR (summary available)
         galactofuranose / galactopyranose ABC transporter - putative membrane subunit = YtfT (summary available)
         galactofuranose / galactopyranose ABC transporter - periplasmic binding protein = YtfQ (summary available)

Summary:
YtfQRT/YjfF is a galactofuranose and galactopyranose transporter that is a member of the ATP-Binding Cassette (ABC) superfamily of transporters. YtfR is the putative ATP-binding component. YtfT and YjfF are the putative membrane components. YtfQ is the periplasmic binding protein [Horler09].

Locations: inner membrane

GO Terms:

Biological Process: GO:0015757 - galactose transport Inferred from experiment [Horler09]
Molecular Function: GO:0005354 - galactose transmembrane transporter activity Inferred from experiment [Horler09]
GO:0015407 - monosaccharide-transporting ATPase activity Inferred by computational analysis [Saurin99]
Cellular Component: GO:0043190 - ATP-binding cassette (ABC) transporter complex Inferred by computational analysis [Saurin99]


Enzymatic reaction of: transport of β-D-galactofuranose (galactofuranose / galactopyranose ABC transporter)


Enzymatic reaction of: transport of α-D-galactofuranose (galactofuranose / galactopyranose ABC transporter)

EC Number: 3.6.3.-


Enzymatic reaction of: transport of β-D-galactose (galactofuranose / galactopyranose ABC transporter)

EC Number: 3.6.3.17


Sequence Features

Feature Class Location Citations Comment
Signal-Sequence 1 -> 21
[Link97, UniProt11]
.
Chain 22 -> 318
[UniProt09]
UniProt: ABC transporter periplasmic-binding protein ytfQ;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b4227 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12517; confirmed by SwissProt match.


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

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

Han13: Han MJ, Kim JY, Kim JA (2013). "Comparison of the large-scale periplasmic proteomes of the Escherichia coli K-12 and B strains." J Biosci Bioeng. PMID: 24140104

Horler09: Horler RS, Muller A, Williamson DC, Potts JR, Wilson KS, Thomas GH (2009). "Furanose-specific sugar transport: characterization of a bacterial galactofuranose-binding protein." J Biol Chem 284(45);31156-63. PMID: 19744923

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

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

Raman05: Raman B, Nandakumar MP, Muthuvijayan V, Marten MR (2005). "Proteome analysis to assess physiological changes in Escherichia coli grown under glucose-limited fed-batch conditions." Biotechnol Bioeng 92(3);384-92. PMID: 16180237

Saurin99: Saurin W, Hofnung M, Dassa E (1999). "Getting in or out: early segregation between importers and exporters in the evolution of ATP-binding cassette (ABC) transporters." J Mol Evol 1999;48(1);22-41. PMID: 9873074

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 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

Stringer14: Stringer AM, Currenti S, Bonocora RP, Baranowski C, Petrone BL, Palumbo MJ, Reilly AA, Zhang Z, Erill I, Wade JT (2014). "Genome-scale analyses of Escherichia coli and Salmonella enterica AraC reveal noncanonical targets and an expanded core regulon." J Bacteriol 196(3);660-71. PMID: 24272778


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 Mon Dec 22, 2014, biocyc14.