Escherichia coli K-12 substr. MG1655 Polypeptide: YddS

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

Synonyms: yddS

Regulation Summary Diagram

Regulation summary diagram for ddpA

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

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: inner membrane, periplasmic space

Map Position: [1,558,955 <- 1,560,505] (33.6 centisomes, 121°)
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, InterPro:IN-FAMILY:IPR030678, Pfam:IN-FAMILY:PF00496, Prosite:IN-FAMILY:PS01040

In Paralogous Gene Group: 25 (11 members)

Gene-Reaction Schematic

Gene-Reaction Schematic

Genetic Regulation Schematic

Genetic regulation schematic for ddpA

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

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

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)

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

Protein sequence of YddS with features indicated

Feature Class Location Citations Comment
Signal-Sequence 1 -> 25
Inferred by computational analysis[UniProt15]
Chain 26 -> 516
Author statement[UniProt15]
UniProt: Probable D,D-dipeptide-binding periplasmic protein DdpA.
Pfam PF00496 78 -> 432
Inferred by computational analysis[Finn14]
SBP_bac_5 : Bacterial extracellular solute-binding proteins, family 5 Middle

Gene Local Context (not to scale -- see Genome Browser for correct scale)

Gene local context diagram

Transcription Units

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


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


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

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

Finn14: Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M (2014). "Pfam: the protein families database." Nucleic Acids Res 42(Database issue);D222-30. PMID: 24288371

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

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

UniProt15: UniProt Consortium (2015). "UniProt version 2015-08 released on 2015-07-22." 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 Pathway Tools version 19.5 (software by SRI International) on Mon Nov 30, 2015, biocyc12.