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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
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for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
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Escherichia coli K-12 substr. MG1655 Polypeptide: YhdW



Gene: yhdW Accession Numbers: EG12834 (EcoCyc), b3268, ECK3255

Regulation Summary Diagram: ?

Component of: YhdW/YhdX/YhdY/YhdZ ABC transporter (summary available)

Summary:
YhdW is a membrane component of a predicted amino acid ABC transporter.

Gene Citations: [Zimmer00]

Locations: periplasmic space, inner membrane

Map Position: [3,417,171 -> 3,418,088] (73.65 centisomes)
Length: 918 bp / 305 aa

Molecular Weight of Polypeptide: 33.425 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0010731 , EchoBASE:EB2683 , EcoGene:EG12834 , EcoliWiki:b3268 , ModBase:P45766 , OU-Microarray:b3268 , PortEco:yhdW , Protein Model Portal:P45766 , RefSeq:NP_417734 , RegulonDB:EG12834 , SMR:P45766 , String:316407.yhdW , UniProt:P45766

Relationship Links: InterPro:IN-FAMILY:IPR001638 , InterPro:IN-FAMILY:IPR018313 , Pfam:IN-FAMILY:PF00497 , Prosite:IN-FAMILY:PS01039 , Smart:IN-FAMILY:SM00062

In Paralogous Gene Group: 172 (5 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006810 - transport Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0006865 - amino acid transport Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0005215 - transporter activity Inferred by computational analysis [GOA01]
Cellular Component: GO:0005886 - plasma membrane
GO:0030288 - outer membrane-bounded periplasmic space Inferred by computational analysis [GOA01]
GO:0042597 - periplasmic space Inferred by computational analysis [UniProtGOA11a, UniProtGOA11]

MultiFun Terms: cell structure membrane
metabolism carbon utilization amino acids
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 yhdW 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]

Subunit of: YhdW/YhdX/YhdY/YhdZ ABC transporter

Subunit composition of YhdW/YhdX/YhdY/YhdZ ABC transporter = [YhdZ]2[YhdY][YhdX][YhdW]

Summary:
YhdZ, YhdY, YhdX and YhdW are uncharacterized members of the ABC superfamily of transporters [Saurin99]. YhdZ is the putative ATP binding component, YhdY and YhdX are membrane components, and YhdW is the putative binding protein. Based on sequence similarity they probably function together as an ATP-dependent amino acid transporter. The genes yhdZ, yhdY, yhdX, and yhdW probably constitute a single operon.


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b3268 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12834; 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

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

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

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."

Zimmer00: Zimmer DP, Soupene E, Lee HL, Wendisch VF, Khodursky AB, Peter BJ, Bender RA, Kustu S (2000). "Nitrogen regulatory protein C-controlled genes of Escherichia coli: scavenging as a defense against nitrogen limitation." Proc Natl Acad Sci U S A 97(26);14674-9. PMID: 11121068

Other References Related to Gene Regulation

Barrios99: Barrios H, Valderrama B, Morett E (1999). "Compilation and analysis of sigma(54)-dependent promoter sequences." Nucleic Acids Res 27(22);4305-13. PMID: 10536136

MedinaRivera11: Medina-Rivera A, Abreu-Goodger C, Thomas-Chollier M, Salgado H, Collado-Vides J, van Helden J (2011). "Theoretical and empirical quality assessment of transcription factor-binding motifs." Nucleic Acids Res 39(3);808-24. PMID: 20923783

Reitzer01: Reitzer L, Schneider BL (2001). "Metabolic context and possible physiological themes of sigma(54)-dependent genes in Escherichia coli." Microbiol Mol Biol Rev 65(3);422-44, table of contents. PMID: 11528004


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 Sun Dec 21, 2014, BIOCYC13B.