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Escherichia coli K-12 substr. MG1655 Polypeptide: YddS



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

Synonyms: yddS

Regulation Summary Diagram: ?

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

Summary:
YddS is the periplasmic binding component of a predicted peptide ABC transporter.
ArcA appears to activate ddpA gene expression under anaerobiosis. A putative ArcA binding site was identified 103 bp upstream of this gene [Salmon05]; but no promoter upstream of it has been identified. Instead, ddpA is transcribed from a promoter that is located usptream of ddpX gene.

Gene Citations: [Lessard98, Zimmer00]

Locations: periplasmic space

Map Position: [1,558,955 <- 1,560,505] (33.6 centisomes)
Length: 1551 bp / 516 aa

Molecular Weight of Polypeptide: 57.641 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0004958 , DIP:DIP-11672N , EchoBASE:EB3551 , EcoGene:EG13790 , EcoliWiki:b1487 , ModBase:P76128 , OU-Microarray:b1487 , PortEco:ddpA , Pride:P76128 , Protein Model Portal:P76128 , RefSeq:NP_416004 , RegulonDB:G6781 , SMR:P76128 , String:511145.b1487 , UniProt:P76128

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

In Paralogous Gene Group: 25 (11 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]
Molecular Function: GO:0005215 - transporter activity Inferred by computational analysis [GOA01a]
Cellular Component: GO:0030288 - outer membrane-bounded periplasmic space Inferred by computational analysis [DiazMejia09]
GO:0042597 - periplasmic space Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]

MultiFun Terms: 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 ddpA knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes et al., 2003, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba et al., 2006, 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 [Baba et al., 2006, Comment 2]
Yes [Feist07, Comment 4]

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
Signal-Sequence 1 -> 25
[UniProt, 2010]
UniProt: Non-Experimental Qualifier: potential;
Chain 26 -> 516
[UniProt09]
UniProt: Probable D,D-dipeptide-binding periplasmic protein ddpA;


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

Baba et al., 2006: 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

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

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

Gerdes et al., 2003: 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

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

Salmon05: Salmon KA, Hung SP, Steffen NR, Krupp R, Baldi P, Hatfield GW, Gunsalus RP (2005). "Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA." J Biol Chem 280(15);15084-96. PMID: 15699038

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

UniProt, 2010: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

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

Zhao10a: 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


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 Tue Nov 25, 2014, BIOCYC14B.