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Escherichia coli K-12 substr. MG1655 Protein: YddO/YddP/YddQ/YddR/YddS ABC transporter
Inferred by computational analysis

Subunit composition of YddO/YddP/YddQ/YddR/YddS ABC transporter = [DdpB][DdpC][DdpA][DdpD][DdpF]
         YddR = DdpB (summary available)
         YddQ = DdpC (summary available)
         YddS = DdpA (summary available)
         YddP = DdpD (summary available)
         YddO = DdpF (summary available)

Summary:
YddO, YddP, YddQ, YddR and YddS are uncharacterized members of the ABC superfamily of transporters [Saurin99]. YddO and YddP are the putative ATP-binding proteins. YddQ and YddR are the putative membrane components. YddS is the putativeperiplasmic binding protein. Based on sequence similarity, these proteins probably function together as an ATP-dependent peptide transporter. The genes yddO, yddP, yddQ, yddR, and yddS are probably located within a single operon.

Gene-Reaction Schematic

Gene-Reaction Schematic


Subunit of YddO/YddP/YddQ/YddR/YddS ABC transporter: YddR

Synonyms: DdpB

Gene: ddpB Accession Numbers: G6780 (EcoCyc), b1486, ECK1480

Locations: inner membrane

Sequence Length: 340 AAs

Molecular Weight: 37.345 kD (from nucleotide sequence)


GO Terms:
Biological Process:
Inferred by computational analysisGO:0006810 - transport [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0015031 - protein transport [UniProtGOA11a]
Inferred by computational analysisGO:0015833 - peptide transport [UniProtGOA11a]
Inferred by computational analysisGO:0042938 - dipeptide transport [Gaudet10]
Inferred by computational analysisGO:0055085 - transmembrane transport [Gaudet10]
Molecular Function:
Inferred by computational analysisGO:0022857 - transmembrane transporter activity [Gaudet10]
Inferred by computational analysisGO:0042936 - dipeptide transporter activity [Gaudet10]
Cellular Component:
Inferred from experimentInferred by computational analysisGO:0005886 - plasma membrane [UniProtGOA11, UniProtGOA11a, DiazMejia09, Daley05]
Inferred by computational analysisGO:0005887 - integral component of plasma membrane [Gaudet10]
Inferred by computational analysisGO:0016020 - membrane [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0016021 - integral component of membrane [UniProtGOA11a]

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-11671N, EcoliWiki:b1486, Protein Model Portal:P77308, RefSeq:NP_416003, UniProt:P77308

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

Summary:
YddR is a membrane component of a predicted peptide ABC transporter.

Essentiality data for ddpB 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]
Yes [Feist07, Comment 4]

Subunit of YddO/YddP/YddQ/YddR/YddS ABC transporter: YddQ

Synonyms: DdpC

Gene: ddpC Accession Numbers: G6779 (EcoCyc), b1485, ECK1479

Locations: inner membrane

Sequence Length: 298 AAs

Molecular Weight: 31.971 kD (from nucleotide sequence)


GO Terms:
Biological Process:
Inferred by computational analysisGO:0006810 - transport [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0015031 - protein transport [UniProtGOA11a]
Inferred by computational analysisGO:0015833 - peptide transport [UniProtGOA11a]
Inferred by computational analysisGO:0042938 - dipeptide transport [Gaudet10]
Inferred by computational analysisGO:0055085 - transmembrane transport [Gaudet10]
Molecular Function:
Inferred by computational analysisGO:0022857 - transmembrane transporter activity [Gaudet10]
Inferred by computational analysisGO:0042936 - dipeptide transporter activity [Gaudet10]
Cellular Component:
Inferred from experimentInferred by computational analysisGO:0005886 - plasma membrane [UniProtGOA11, UniProtGOA11a, DiazMejia09, Daley05]
Inferred from experimentGO:0005887 - integral component of plasma membrane [Drew02]
Inferred by computational analysisGO:0016020 - membrane [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0016021 - integral component of membrane [UniProtGOA11a]

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:b1485, Pride:P77463, Protein Model Portal:P77463, RefSeq:NP_416002, UniProt:P77463

Relationship Links: InterPro:IN-FAMILY:IPR000515, InterPro:IN-FAMILY:IPR025966, Pfam:IN-FAMILY:PF00528, Pfam:IN-FAMILY:PF12911, Prosite:IN-FAMILY:PS50928

Summary:
YddQ is a membrane component of a predicted peptide ABC transporter.

Protein topology in the inner membrane has been determined [Drew02].

Essentiality data for ddpC 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]
Yes [Feist07, Comment 4]

Subunit of YddO/YddP/YddQ/YddR/YddS ABC transporter: YddS

Synonyms: DdpA

Gene: ddpA Accession Numbers: G6781 (EcoCyc), b1487, ECK1481

Locations: inner membrane, periplasmic space

Sequence Length: 516 AAs

Molecular Weight: 57.641 kD (from nucleotide sequence)


GO Terms:
Biological Process:
Inferred by computational analysisGO:0006810 - transport [UniProtGOA11a]
Inferred by computational analysisGO:0015031 - protein transport [UniProtGOA11a]
Inferred by computational analysisGO:0015833 - peptide transport [UniProtGOA11a]
Inferred by computational analysisGO:0042938 - dipeptide transport [Gaudet10]
Inferred by computational analysisGO:0055085 - transmembrane transport [GOA01a]
Molecular Function:
Inferred by computational analysisGO:0015197 - peptide transporter activity [Gaudet10]
Cellular Component:
Inferred by computational analysisGO:0030288 - outer membrane-bounded periplasmic space [Gaudet10, DiazMejia09]
Inferred by computational analysisGO:0042597 - periplasmic space [UniProtGOA11, UniProtGOA11a]
Inferred by computational analysisGO:0043190 - ATP-binding cassette (ABC) transporter complex [GOA01a]

MultiFun Terms: 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: DIP:DIP-11672N, EcoliWiki:b1487, ModBase:P76128, Pride:P76128, Protein Model Portal:P76128, RefSeq:NP_416004, SMR:P76128, UniProt:P76128

Relationship Links: InterPro:IN-FAMILY:IPR000914, InterPro:IN-FAMILY:IPR023765, InterPro:IN-FAMILY:IPR030678, Pfam:IN-FAMILY:PF00496, Prosite:IN-FAMILY:PS01040

Summary:
YddS is the periplasmic binding component of a predicted peptide ABC transporter.

Essentiality data for ddpA 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]
Yes [Feist07, Comment 4]

Subunit of YddO/YddP/YddQ/YddR/YddS ABC transporter: YddP

Synonyms: DdpD

Gene: ddpD Accession Numbers: G6778 (EcoCyc), b1484, ECK1478

Locations: inner membrane, cytosol

Sequence Length: 328 AAs

Molecular Weight: 36.1 kD (from nucleotide sequence)


GO Terms:
Biological Process:
Inferred by computational analysisGO:0006810 - transport [UniProtGOA11a]
Inferred by computational analysisGO:0008152 - metabolic process [GOA01a]
Inferred by computational analysisGO:0015031 - protein transport [UniProtGOA11a]
Inferred by computational analysisGO:0015833 - peptide transport [UniProtGOA11a, GOA01a]
Molecular Function:
Inferred by computational analysisGO:0000166 - nucleotide binding [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0005524 - ATP binding [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0016887 - ATPase activity [GOA01a]
Cellular Component:
GO:0005737 - cytoplasm []
GO:0005829 - cytosol []
Inferred by computational analysisGO:0005886 - plasma membrane [UniProtGOA11, UniProtGOA11a]
Inferred by computational analysisGO:0016020 - membrane [UniProtGOA11a]

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: DIP:DIP-11669N, EcoliWiki:b1484, ModBase:P77268, Protein Model Portal:P77268, RefSeq:NP_416001, SMR:P77268, UniProt:P77268

Relationship Links: InterPro:IN-FAMILY:IPR003439, InterPro:IN-FAMILY:IPR003593, InterPro:IN-FAMILY:IPR010066, InterPro:IN-FAMILY:IPR013563, InterPro:IN-FAMILY:IPR017871, InterPro:IN-FAMILY:IPR027417, Pfam:IN-FAMILY:PF00005, Pfam:IN-FAMILY:PF08352, Prosite:IN-FAMILY:PS00211, Prosite:IN-FAMILY:PS50893, Smart:IN-FAMILY:SM00382

Summary:
YddP is an ATP-binding component of a predicted peptide ABC transporter.

Essentiality data for ddpD 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]
Yes [Feist07, Comment 4]

Subunit of YddO/YddP/YddQ/YddR/YddS ABC transporter: YddO

Synonyms: DdpF

Gene: ddpF Accession Numbers: G6777 (EcoCyc), b1483, ECK1477

Locations: cytosol, inner membrane

Sequence Length: 308 AAs

Molecular Weight: 34.621 kD (from nucleotide sequence)


GO Terms:
Biological Process:
Inferred by computational analysisGO:0006810 - transport [UniProtGOA11a]
Inferred by computational analysisGO:0008152 - metabolic process [GOA01a]
Inferred by computational analysisGO:0015031 - protein transport [UniProtGOA11a]
Inferred by computational analysisGO:0015833 - peptide transport [UniProtGOA11a, GOA01a]
Molecular Function:
Inferred by computational analysisGO:0000166 - nucleotide binding [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0005524 - ATP binding [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0016887 - ATPase activity [GOA01a]
Cellular Component:
GO:0005737 - cytoplasm []
Inferred by computational analysisGO:0005829 - cytosol [DiazMejia09]
Inferred by computational analysisGO:0005886 - plasma membrane [UniProtGOA11, UniProtGOA11a]
Inferred by computational analysisGO:0016020 - membrane [UniProtGOA11a]

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:b1483, ModBase:P77622, Protein Model Portal:P77622, RefSeq:NP_416000, SMR:P77622, UniProt:P77622

Relationship Links: InterPro:IN-FAMILY:IPR003439, InterPro:IN-FAMILY:IPR003593, InterPro:IN-FAMILY:IPR010066, InterPro:IN-FAMILY:IPR013563, InterPro:IN-FAMILY:IPR017871, InterPro:IN-FAMILY:IPR027417, Pfam:IN-FAMILY:PF00005, Pfam:IN-FAMILY:PF08352, Prosite:IN-FAMILY:PS00211, Prosite:IN-FAMILY:PS50893, Smart:IN-FAMILY:SM00382

Summary:
YddO is an ATP-binding component of a predicted peptide ABC transporter.

Essentiality data for ddpF 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]
Yes [Feist07, Comment 4]

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

Drew02: Drew D, Sjostrand D, Nilsson J, Urbig T, Chin CN, de Gier JW, von Heijne G (2002). "Rapid topology mapping of Escherichia coli inner-membrane proteins by prediction and PhoA/GFP fusion analysis." Proc Natl Acad Sci U S A 99(5);2690-5. PMID: 11867724

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

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

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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