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



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

Synonyms: yddQ

Regulation Summary Diagram: ?

Component of: YddO/YddP/YddQ/YddR/YddS ABC transporter (summary available)

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

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

Gene Citations: [Lessard98, Zimmer00]

Locations: inner membrane

Map Position: [1,557,038 <- 1,557,934] (33.56 centisomes)
Length: 897 bp / 298 aa

Molecular Weight of Polypeptide: 31.971 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0004953 , EchoBASE:EB3549 , EcoGene:EG13788 , EcoliWiki:b1485 , OU-Microarray:b1485 , PortEco:ddpC , Pride:P77463 , Protein Model Portal:P77463 , RefSeq:NP_416002 , RegulonDB:G6779 , String:511145.b1485 , UniProt:P77463

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

In Paralogous Gene Group: 24 (43 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006810 - transport Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0015031 - protein transport Inferred by computational analysis [UniProtGOA11a]
GO:0015833 - peptide transport Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, DiazMejia09, Daley05]
GO:0005887 - integral component of plasma membrane Inferred from experiment [Drew02]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11a]

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 ddpC 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]
Yes [Feist07, Comment 3]

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

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.


Sequence Features

Feature Class Location Citations Comment
Transmembrane-Region 34 -> 54
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 97 -> 117
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Conserved-Region 97 -> 282
[UniProt09]
UniProt: ABC transmembrane type-1;
Transmembrane-Region 125 -> 145
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 146 -> 166
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 218 -> 238
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 261 -> 281
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


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

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

Lessard98: Lessard IA, Pratt SD, McCafferty DG, Bussiere DE, Hutchins C, Wanner BL, Katz L, Walsh CT (1998). "Homologs of the vancomycin resistance D-Ala-D-Ala dipeptidase VanX in Streptomyces toyocaensis, Escherichia coli and Synechocystis: attributes of catalytic efficiency, stereoselectivity and regulation with implications for function." Chem Biol 5(9);489-504. PMID: 9751644

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 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."

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

Zhao10: Zhao K, Liu M, Burgess RR (2010). "Promoter and regulon analysis of nitrogen assimilation factor, sigma54, reveal alternative strategy for E. coli MG1655 flagellar biosynthesis." Nucleic Acids Res 38(4);1273-83. PMID: 19969540


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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 Sat Dec 20, 2014, biocyc11.