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Escherichia coli K-12 substr. MG1655 Protein: putative transport complex, ABC superfamily
Inferred by computational analysis

Subunit composition of putative transport complex, ABC superfamily = [YhdZ][YhdY][YhdX][YhdW]
         putative transport protein, ABC superfamily - periplasmic binding protein = YhdZ (summary available)
         putative transport protein, ABC superfamily - membrane component = YhdY (summary available)
         putative transport protein, ABC superfamily - ATP-binding component = YhdX (summary available)
         putative transport protein, ABC superfamily - membrane component = YhdW (summary available)

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-Reaction Schematic

Gene-Reaction Schematic


Subunit of putative transport complex, ABC superfamily: putative transport protein, ABC superfamily - periplasmic binding protein

Synonyms: YhdZ

Gene: yhdZ Accession Numbers: EG12837 (EcoCyc), b3271, ECK3258

Locations: cytosol, periplasmic space, inner membrane

Sequence Length: 252 AAs

Molecular Weight: 28.574 kD (from nucleotide sequence)


GO Terms:
Biological Process:
Inferred by computational analysisGO:0003333 - amino acid transmembrane transport [GOA01a]
Inferred by computational analysisGO:0006810 - transport [UniProtGOA11a]
Inferred by computational analysisGO:0006865 - amino acid transport [UniProtGOA11a]
Inferred by computational analysisGO:0008152 - metabolic process [GOA01a]
Molecular Function:
Inferred by computational analysisGO:0000166 - nucleotide binding [UniProtGOA11a]
Inferred by computational analysisGO:0005524 - ATP binding [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0015424 - amino acid-transporting ATPase activity [GOA01a]
Inferred by computational analysisGO:0016887 - ATPase activity [GOA01a]
Cellular Component:
Inferred by computational analysisGO:0005829 - cytosol [DiazMejia09]
Inferred by computational analysisGO:0005886 - plasma membrane [UniProtGOA11, UniProtGOA11a]
Inferred by computational analysisGO:0016020 - membrane [UniProtGOA11a]
GO:0030288 - outer membrane-bounded periplasmic space []

MultiFun Terms: transportChannel-type TransportersPyrophosphate Bond (ATP; GTP; P2) Hydrolysis-driven Active TransportersThe ATP-binding Cassette (ABC) Superfamily + ABC-type Uptake PermeasesABC superfamily ATP binding cytoplasmic component

Unification Links: EcoliWiki:b3271, ModBase:P45769, Protein Model Portal:P45769, RefSeq:NP_417737, SMR:P45769, Swiss-Model:P45769, UniProt:P45769

Relationship Links: InterPro:IN-FAMILY:IPR003439, InterPro:IN-FAMILY:IPR003593, InterPro:IN-FAMILY:IPR017871, InterPro:IN-FAMILY:IPR027417, InterPro:IN-FAMILY:IPR030679, Pfam:IN-FAMILY:PF00005, Prosite:IN-FAMILY:PS00211, Prosite:IN-FAMILY:PS50893, Smart:IN-FAMILY:SM00382

Summary:
Yhdz is a periplasmic binding component of a predicted amino acid ABC transporter.

Essentiality data for yhdZ knockouts:

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enrichedYes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB LennoxYes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerolYes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucoseYes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Subunit of putative transport complex, ABC superfamily: putative transport protein, ABC superfamily - membrane component

Synonyms: YhdY

Gene: yhdY Accession Numbers: EG12836 (EcoCyc), b3270, ECK3257

Locations: inner membrane

Sequence Length: 367 AAs

Molecular Weight: 41.484 kD (from nucleotide sequence)


GO Terms:
Biological Process:
Inferred by computational analysisGO:0006810 - transport [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0006865 - amino acid transport [UniProtGOA11a]
Molecular Function:
Inferred by computational analysisGO:0005215 - transporter activity [GOA01a]
Cellular Component:
Inferred from experimentInferred by computational analysisGO:0005886 - plasma membrane [UniProtGOA11, UniProtGOA11a, DiazMejia09, Daley05]
Inferred by computational analysisGO:0016020 - membrane [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0016021 - integral component of membrane [UniProtGOA11a, GOA01a]

MultiFun Terms: cell structuremembrane
transportChannel-type TransportersPyrophosphate Bond (ATP; GTP; P2) Hydrolysis-driven Active TransportersThe ATP-binding Cassette (ABC) Superfamily + ABC-type Uptake PermeasesABC superfamily, membrane component

Unification Links: DIP:DIP-12306N, EcoliWiki:b3270, Mint:MINT-1309860, Pride:P45768, Protein Model Portal:P45768, RefSeq:NP_417736, UniProt:P45768

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

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

Essentiality data for yhdY knockouts:

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enrichedYes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB LennoxYes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerolYes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucoseYes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Subunit of putative transport complex, ABC superfamily: putative transport protein, ABC superfamily - ATP-binding component

Synonyms: YhdX

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

Locations: inner membrane

Sequence Length: 393 AAs

Molecular Weight: 43.261 kD (from nucleotide sequence)


GO Terms:
Biological Process:
Inferred by computational analysisGO:0006810 - transport [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0006865 - amino acid transport [UniProtGOA11a]
Molecular Function:
Inferred by computational analysisGO:0005215 - transporter activity [GOA01a]
Cellular Component:
Inferred from experimentInferred by computational analysisGO:0005886 - plasma membrane [UniProtGOA11, UniProtGOA11a, DiazMejia09, Daley05]
Inferred by computational analysisGO:0016020 - membrane [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0016021 - integral component of membrane [UniProtGOA11a, GOA01a]

MultiFun Terms: cell structuremembrane
transportChannel-type TransportersPyrophosphate Bond (ATP; GTP; P2) Hydrolysis-driven Active TransportersThe ATP-binding Cassette (ABC) Superfamily + ABC-type Uptake PermeasesABC superfamily, membrane component

Unification Links: EcoliWiki:b3269, Protein Model Portal:P45767, RefSeq:YP_026209, UniProt:P45767

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

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

Essentiality data for yhdX knockouts:

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB LennoxYes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerolYes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucoseYes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Subunit of putative transport complex, ABC superfamily: putative transport protein, ABC superfamily - membrane component

Synonyms: YhdW

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

Locations: inner membrane, periplasmic space

Sequence Length: 305 AAs

Molecular Weight: 33.425 kD (from nucleotide sequence)


GO Terms:
Biological Process:
Inferred by computational analysisGO:0006810 - transport [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0006865 - amino acid transport [UniProtGOA11a]
Molecular Function:
Inferred by computational analysisGO:0005215 - transporter activity [GOA01a]
Cellular Component:
GO:0005886 - plasma membrane []
Inferred by computational analysisGO:0042597 - periplasmic space [UniProtGOA11, UniProtGOA11a]

MultiFun Terms: cell structuremembrane
metabolismcarbon utilizationamino acids
transportChannel-type TransportersPyrophosphate Bond (ATP; GTP; P2) Hydrolysis-driven Active TransportersThe ATP-binding Cassette (ABC) Superfamily + ABC-type Uptake PermeasesABC superfamily, periplasmic binding component

Unification Links: EcoliWiki:b3268, ModBase:P45766, Protein Model Portal:P45766, RefSeq:NP_417734, SMR:P45766, UniProt:P45766

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

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

Essentiality data for yhdW knockouts:

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enrichedYes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB LennoxYes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerolYes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucoseYes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

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

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

GOA01a: 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 the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

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


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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