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Escherichia coli K-12 substr. MG1655 Polypeptide: YhdX



Gene: yhdX Accession Numbers: EG12835 (EcoCyc), b3269, ECK3256

Regulation Summary Diagram: ?

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

Summary:
YhdX is an ATP-binding component of a predicted amino acid ABC transporter.

Gene Citations: [Zimmer00]

Locations: inner membrane

Map Position: [3,418,156 -> 3,419,337] (73.67 centisomes)
Length: 1182 bp / 393 aa

Molecular Weight of Polypeptide: 43.261 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0010733 , EchoBASE:EB2684 , EcoGene:EG12835 , EcoliWiki:b3269 , OU-Microarray:b3269 , PortEco:yhdX , Protein Model Portal:P45767 , RefSeq:YP_026209 , RegulonDB:EG12835 , String:511145.b3269 , UniProt:P45767

Relationship Links: InterPro:IN-FAMILY:IPR000515 , InterPro:IN-FAMILY:IPR010065 , Pfam:IN-FAMILY:PF00528 , Prosite:IN-FAMILY:PS50928

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 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, GOA01]

MultiFun Terms: cell structure membrane
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, membrane component

Essentiality data for yhdX knockouts: ?

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

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.


Sequence Features

Feature Class Location Citations Comment
Transmembrane-Region 21 -> 41
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Conserved-Region 88 -> 381
[UniProt09]
UniProt: ABC transmembrane type-1;
Transmembrane-Region 92 -> 112
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 128 -> 148
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 180 -> 200
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 219 -> 239
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 256 -> 276
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 333 -> 353
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 363 -> 383
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b3269 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12835; 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

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

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

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

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."

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 Thu Nov 20, 2014, biocyc14.