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Escherichia coli K-12 substr. MG1655 Polypeptide: dipeptide ABC transporter - putative membrane subunit

Gene: dppB Accession Numbers: EG12625 (EcoCyc), b3543, ECK3530

Regulation Summary Diagram

Regulation summary diagram for dppB

Component of: dipeptide ABC transporter (extended summary available)

DppB is an integral membrane component of the dipeptide ABC transporter.

Gene Citations: [Abouhamad94]

Locations: inner membrane

Map Position: [3,702,794 <- 3,703,813] (79.81 centisomes, 287°)
Length: 1020 bp / 339 aa

Molecular Weight of Polypeptide: 37.497 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0011572, CGSC:33771, DIP:DIP-47927N, EchoBASE:EB2509, EcoGene:EG12625, EcoliWiki:b3543, Mint:MINT-1309644, OU-Microarray:b3543, PortEco:dppB, PR:PRO_000022474, Protein Model Portal:P0AEF8, RefSeq:NP_418000, RegulonDB:EG12625, String:511145.b3543, UniProt:P0AEF8

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

In Paralogous Gene Group: 24 (43 members)

Gene-Reaction Schematic

Gene-Reaction Schematic

Genetic Regulation Schematic

Genetic regulation schematic for dppB

GO Terms:
Biological Process:
Inferred from experimentGO:0042938 - dipeptide transport [Olson91]
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:0055085 - transmembrane transport [Gaudet10]
Molecular Function:
Inferred from experimentGO:0042936 - dipeptide transporter activity [Olson91]
Inferred by computational analysisGO:0015421 - oligopeptide-transporting ATPase activity [Abouhamad94]
Inferred by computational analysisGO:0022857 - transmembrane transporter activity [Gaudet10]
Cellular Component:
Inferred from experimentInferred by computational analysisGO:0005886 - plasma membrane [UniProtGOA11, UniProtGOA11a, DiazMejia09, Zhang07, 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, Abouhamad94]
Inferred by computational analysisGO:0043190 - ATP-binding cassette (ABC) transporter complex [Abouhamad94]

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

Essentiality data for dppB 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: dipeptide ABC transporter

Synonyms: DppABCDF

Subunit composition of dipeptide ABC transporter = [DppD][DppF][DppB][DppC][DppA]
         dipeptide ABC transporter - putative ATP binding subunit = DppD (summary available)
         dipeptide ABC transporter - putative ATP binding subunit = DppF (summary available)
         dipeptide ABC transporter - putative membrane subunit = DppB (summary available)
         dipeptide ABC transporter - putative membrane subunit = DppC (summary available)
         dipeptide ABC transporter - periplasmic binding protein = DppA (summary available)

The DppABCDF dipeptide transport system is a member of the ATP-Binding Cassette (ABC) Superfamily of transporters [Wu95]. Based on sequence similarity, DppA is the substrate-binding component, while DppB and DppC are the membrane components, and DppD and DppF are the ATP-binding components of the ABC transporter. DppABCDF is similar in sequence and subunit composition to the oligopeptide uptake system OppABCDF, suggesting similar subunit functions.

DppA's unbound structure has been resolved by x-ray crystallography to resolutions of 3.2 Å [Dunten93] and 2.0 Å, and shows two domains connected by two 'hinge' segments [Nickitenko95]. The structure of DppA has also been determined with bound glycyl-L-leucine has been determined to a resolution of 3.2 Å [Dunten95]. The structure reveals that the binding site recognizes the peptide backbone allowing for accommodation of various side chains [Dunten95]. There is also a requirement for an unsubstituted α-amino group for transport of a peptide [Gilvarg65].

Loss of DppA or DppBCDF resulted in pro mutants being unable to utilize Pro-Gly as a proline source [Olson91]. Pro-Gly transport was inhibited by His-Glu, suggesting His-Glu is an additional substrate for DppABCDF [Olson91]. Mutations in dpp displayed resistance to the toxic dipeptide Lys-aminoxyAla, the loss of ability to utilize Leu-Trp as a source of its required amino acids [Payne84], resistance to Gly-Val, Leu-Val, and Val-Leu, and reduced uptake of Gly-Gly [De73]. Substrate specificity of DppA was studied in a filter binding assay in which column fractions were monitored for binding activity towards radioactively labeled dipeptides and tripeptides. DppA was observed to mediate the ATP driven uptake of dipeptides and, to a lesser extent, tripeptides from the periplasm [Smith99]. When an outer membrane heme receptor is expressed in E. coli, the dipeptide ABC transporter is also capable of transporting heme and the heme precursor, δ aminolevulinic acid, from the periplasm into the cytoplasm [Letoffe06]. Binding of heme to purified DppA has been demonstrated [Letoffe06].

DppA accumulates to high levels when grown in minimal media, but levels of DppA are reduced when the medium is supplemented with casamino acids [Olson91]. DppA levels were decreased after 4 hours exposure to zinc stress [Easton06] and in response to glucose limitation [Wick01]. When grown in rich medium, gcvB deletion mutants had high constitutive expression of dppA compared to the parent strain [Urbanowski00]. dppA expression is also repressed by PhoB during phosphate limitation [Smith92].

Citations: [Rinas04, Payne79, Marshall03, Payne01]

Enzymatic reaction of: Transport of a dipeptide (dipeptide ABC transporter)

Inferred from experimentInferred by computational analysis

Transport reaction diagram for Transport of a dipeptide

Alternative Products for a dipeptide: 5-aminolevulinate [Letoffe06, Verkamp93], heme [Letoffe06], L-Tyr-FMDP [Marshall03], nva-FMDB [Marshall03], FMDP-Val [Marshall03], FMDP-L-Phe [Marshall03], norvalyl-FMDP [Marshall03], L-met-FMDP [Marshall03], L-Lys-FMDP [Marshall03], FMDP-Leu [Marshall03], L-alanyl-L-α-thiophenylglycine [Perry84] , lys-aminoxyAla [Smith99 ], glycylsarcosine [Payne01]

Sequence Features

Protein sequence of dipeptide ABC transporter - putative membrane subunit with features indicated

Feature Class Location Citations Comment
Transmembrane-Region 10 -> 30
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Conserved-Region 96 -> 328
Inferred by computational analysis[UniProt15]
UniProt: ABC transmembrane type-1.
Transmembrane-Region 103 -> 123
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Pfam PF00528 114 -> 336
Inferred by computational analysis[Finn14]
BPD_transp_1 : Binding-protein-dependent transport system inner membrane component
Transmembrane-Region 136 -> 156
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Transmembrane-Region 172 -> 192
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Transmembrane-Region 201 -> 221
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Transmembrane-Region 260 -> 280
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Transmembrane-Region 310 -> 330
Inferred by computational analysis[UniProt15]
UniProt: Helical.

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

Gene local context diagram

Transcription Unit

Transcription-unit diagram


10/20/97 Gene b3543 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12625; confirmed by SwissProt match.


Abouhamad94: Abouhamad WN, Manson MD (1994). "The dipeptide permease of Escherichia coli closely resembles other bacterial transport systems and shows growth-phase-dependent expression." Mol Microbiol 1994;14(5);1077-92. PMID: 7536291

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

De73: De Felice M, Guardiola J, Lamberti A, Iaccarino M (1973). "Escherichia coli K-12 mutants altered in the transport systems for oligo- and dipeptides." J Bacteriol 116(2);751-6. PMID: 4126826

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

Dunten93: Dunten PW, Harris JH, Feiz V, Mowbray SL (1993). "Crystallization and preliminary X-ray analysis of the periplasmic dipeptide binding protein from Escherichia coli." J Mol Biol 231(1);145-7. PMID: 8496961

Dunten95: Dunten P, Mowbray SL (1995). "Crystal structure of the dipeptide binding protein from Escherichia coli involved in active transport and chemotaxis." Protein Sci 4(11);2327-34. PMID: 8563629

Easton06: Easton JA, Thompson P, Crowder MW (2006). "Time-dependent translational response of E. coli to excess Zn(II)." J Biomol Tech 17(5);303-7. PMID: 17122063

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

Gilvarg65: Gilvarg C, Katchalski E (1965). "Peptide utilization in Escherichia coli." J Biol Chem 240;3093-8. PMID: 14342337

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

Letoffe06: Letoffe S, Delepelaire P, Wandersman C (2006). "The housekeeping dipeptide permease is the Escherichia coli heme transporter and functions with two optional peptide binding proteins." Proc Natl Acad Sci U S A 103(34);12891-6. PMID: 16905647

Marshall03: Marshall NJ, Andruszkiewicz R, Gupta S, Milewski S, Payne JW (2003). "Structure-activity relationships for a series of peptidomimetic antimicrobial prodrugs containing glutamine analogues." J Antimicrob Chemother 51(4);821-31. PMID: 12654735

Nickitenko95: Nickitenko AV, Trakhanov S, Quiocho FA (1995). "2 A resolution structure of DppA, a periplasmic dipeptide transport/chemosensory receptor." Biochemistry 34(51);16585-95. PMID: 8527431

Olson91: Olson ER, Dunyak DS, Jurss LM, Poorman RA (1991). "Identification and characterization of dppA, an Escherichia coli gene encoding a periplasmic dipeptide transport protein." J Bacteriol 173(1);234-44. PMID: 1702779

Payne01: Payne JW, Payne GM, Gupta S, Marshall NJ, Grail BM (2001). "Conformational limitations of glycylsarcosine as a prototypic substrate for peptide transporters." Biochim Biophys Acta 1514(1);65-75. PMID: 11513805

Payne79: Payne JW, Bell G (1979). "Direct determination of the properties of peptide transport systems in Escherichia coli, using a fluorescent-labeling procedure." J Bacteriol 137(1);447-55. PMID: 368023

Payne84: Payne JW, Morley JS, Armitage P, Payne GM (1984). "Transport and hydrolysis of antibacterial peptide analogues in Escherichia coli: backbone-modified aminoxy peptides." J Gen Microbiol 1984;130 ( Pt 9);2253-65. PMID: 6389761

Perry84: Perry D, Gilvarg C (1984). "Spectrophotometric determination of affinities of peptides for their transport systems in Escherichia coli." J Bacteriol 160(3);943-8. PMID: 6389518

Rinas04: Rinas U, Hoffmann F (2004). "Selective leakage of host-cell proteins during high-cell-density cultivation of recombinant and non-recombinant Escherichia coli." Biotechnol Prog 20(3);679-87. PMID: 15176868

Smith92: Smith MW, Payne JW (1992). "Expression of periplasmic binding proteins for peptide transport is subject to negative regulation by phosphate limitation in Escherichia coli." FEMS Microbiol Lett 79(1-3);183-90. PMID: 1478454

Smith99: Smith MW, Tyreman DR, Payne GM, Marshall NJ, Payne JW (1999). "Substrate specificity of the periplasmic dipeptide-binding protein from Escherichia coli: experimental basis for the design of peptide prodrugs." Microbiology 1999;145 ( Pt 10);2891-901. PMID: 10537211

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."

Urbanowski00: Urbanowski ML, Stauffer LT, Stauffer GV (2000). "The gcvB gene encodes a small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli." Mol Microbiol 37(4);856-68. PMID: 10972807

Verkamp93: Verkamp E, Backman VM, Bjornsson JM, Soll D, Eggertsson G (1993). "The periplasmic dipeptide permease system transports 5-aminolevulinic acid in Escherichia coli." J Bacteriol 175(5);1452-6. PMID: 8444807

Wick01: Wick LM, Quadroni M, Egli T (2001). "Short- and long-term changes in proteome composition and kinetic properties in a culture of Escherichia coli during transition from glucose-excess to glucose-limited growth conditions in continuous culture and vice versa." Environ Microbiol 3(9);588-99. PMID: 11683869

Wu95: Wu LF, Mandrand-Berthelot MA (1995). "A family of homologous substrate-binding proteins with a broad range of substrate specificity and dissimilar biological functions." Biochimie 1995;77(9);744-50. PMID: 8789466

Zhang07: Zhang N, Chen R, Young N, Wishart D, Winter P, Weiner JH, Li L (2007). "Comparison of SDS- and methanol-assisted protein solubilization and digestion methods for Escherichia coli membrane proteome analysis by 2-D LC-MS/MS." Proteomics 7(4);484-93. PMID: 17309111

Other References Related to Gene Regulation

Beisel11: Beisel CL, Storz G (2011). "The base-pairing RNA spot 42 participates in a multioutput feedforward loop to help enact catabolite repression in Escherichia coli." Mol Cell 41(3);286-97. PMID: 21292161

Constantinidou06: Constantinidou C, Hobman JL, Griffiths L, Patel MD, Penn CW, Cole JA, Overton TW (2006). "A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth." J Biol Chem 281(8);4802-15. PMID: 16377617

Maciag11: Maciag A, Peano C, Pietrelli A, Egli T, De Bellis G, Landini P (2011). "In vitro transcription profiling of the {sigma}S subunit of bacterial RNA polymerase: re-definition of the {sigma}S regulon and identification of {sigma}S-specific promoter sequence elements." Nucleic Acids Res 39(13);5338-55. PMID: 21398637

Pulvermacher08: Pulvermacher SC, Stauffer LT, Stauffer GV (2008). "The role of the small regulatory RNA GcvB in GcvB/mRNA posttranscriptional regulation of oppA and dppA in Escherichia coli." FEMS Microbiol Lett 281(1);42-50. PMID: 18312576

Urban07: Urban JH, Vogel J (2007). "Translational control and target recognition by Escherichia coli small RNAs in vivo." Nucleic Acids Res 35(3);1018-37. PMID: 17264113

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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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