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Protein

Probable D,D-dipeptide transport system permease protein DdpB

Gene

ddpB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Part of the ABC transporter complex DdpABCDF, which is probably involved in D,D-dipeptide transport. Probably responsible for the translocation of the substrate across the membrane.

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Peptide transport, Protein transport, Transport

Enzyme and pathway databases

BioCyciEcoCyc:YDDR-MONOMER.
ECOL316407:JW1481-MONOMER.

Protein family/group databases

TCDBi3.A.1.5.38. the atp-binding cassette (abc) superfamily.

Names & Taxonomyi

Protein namesi
Recommended name:
Probable D,D-dipeptide transport system permease protein DdpB
Gene namesi
Name:ddpB
Synonyms:yddR
Ordered Locus Names:b1486, JW1481
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13789. ddpB.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 1111PeriplasmicSequence analysisAdd
BLAST
Transmembranei12 – 3221HelicalPROSITE-ProRule annotationAdd
BLAST
Topological domaini33 – 10472CytoplasmicSequence analysisAdd
BLAST
Transmembranei105 – 12521HelicalPROSITE-ProRule annotationAdd
BLAST
Topological domaini126 – 13510PeriplasmicSequence analysis
Transmembranei136 – 15621HelicalPROSITE-ProRule annotationAdd
BLAST
Topological domaini157 – 19943CytoplasmicSequence analysisAdd
BLAST
Transmembranei200 – 22021HelicalPROSITE-ProRule annotationAdd
BLAST
Topological domaini221 – 24626PeriplasmicSequence analysisAdd
BLAST
Transmembranei247 – 26923HelicalPROSITE-ProRule annotationAdd
BLAST
Topological domaini270 – 27910CytoplasmicSequence analysis
Transmembranei280 – 30021HelicalPROSITE-ProRule annotationAdd
BLAST
Topological domaini301 – 3011PeriplasmicSequence analysis
Transmembranei302 – 32221HelicalPROSITE-ProRule annotationAdd
BLAST
Topological domaini323 – 34018CytoplasmicSequence analysisAdd
BLAST

GO - Cellular componenti

  • integral component of plasma membrane Source: GO_Central
  • plasma membrane Source: EcoCyc
Complete GO annotation...

Keywords - Cellular componenti

Cell inner membrane, Cell membrane, Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 340340Probable D,D-dipeptide transport system permease protein DdpBPRO_0000060246Add
BLAST

Proteomic databases

PaxDbiP77308.

Expressioni

Inductioni

Induced by RpoS in stationary phase.1 Publication

Interactioni

Subunit structurei

The complex is composed of two ATP-binding proteins (DdpD and DdpF), two transmembrane proteins (DdpB and DdpC) and a solute-binding protein (DdpA).Curated

Protein-protein interaction databases

BioGridi4260211. 201 interactions.
DIPiDIP-11671N.
IntActiP77308. 2 interactions.
STRINGi511145.b1486.

Structurei

3D structure databases

ProteinModelPortaliP77308.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini97 – 327231ABC transmembrane type-1PROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 1 ABC transmembrane type-1 domain.PROSITE-ProRule annotation

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG4105CJM. Bacteria.
COG0601. LUCA.
HOGENOMiHOG000170242.
InParanoidiP77308.
KOiK02033.
OMAiAIPVMGV.
OrthoDBiEOG66F098.
PhylomeDBiP77308.

Family and domain databases

Gene3Di1.10.3720.10. 2 hits.
InterProiIPR000515. MetI-like.
[Graphical view]
PfamiPF00528. BPD_transp_1. 1 hit.
[Graphical view]
SUPFAMiSSF161098. SSF161098. 2 hits.
PROSITEiPS50928. ABC_TM1. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P77308-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTFWSILRQR CWGLVLVVAG VCVITFIISH LIPGDPARLL AGDRASDAIV
60 70 80 90 100
ENIRQQLGLD QPLYVQFYRY VSDLFHGDLG TSIRTGRPVL EELRIFFPAT
110 120 130 140 150
LELAFGALLL ALLIGIPLGI LSAVWRNRWL DHLVRIMAIT GISTPAFWLG
160 170 180 190 200
LGVIVLFYGH LQILPGGGRL DDWLDPPTHV TGFYLLDALL EGNGEVFFNA
210 220 230 240 250
LQHLILPALT LAFVHLGIVA RQIRSAMLEQ LSEDYIRTAR ASGLPGWYIV
260 270 280 290 300
LCYALPNALI PSITVLGLAL GDLLYGAVLT ETVFAWPGMG AWVVTSIQAL
310 320 330 340
DFPAVMGFAV VVSFAYVLVN LVVDLLYLWI DPRIGRGGGE
Length:340
Mass (Da):37,345
Last modified:February 1, 1997 - v1
Checksum:i5E684D9B0400487A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC74559.1.
AP009048 Genomic DNA. Translation: BAA15141.1.
PIRiA64902.
RefSeqiNP_416003.1. NC_000913.3.
WP_000145123.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC74559; AAC74559; b1486.
BAA15141; BAA15141; BAA15141.
GeneIDi946044.
KEGGiecj:JW1481.
eco:b1486.
PATRICi32118266. VBIEscCol129921_1553.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC74559.1.
AP009048 Genomic DNA. Translation: BAA15141.1.
PIRiA64902.
RefSeqiNP_416003.1. NC_000913.3.
WP_000145123.1. NZ_LN832404.1.

3D structure databases

ProteinModelPortaliP77308.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260211. 201 interactions.
DIPiDIP-11671N.
IntActiP77308. 2 interactions.
STRINGi511145.b1486.

Protein family/group databases

TCDBi3.A.1.5.38. the atp-binding cassette (abc) superfamily.

Proteomic databases

PaxDbiP77308.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74559; AAC74559; b1486.
BAA15141; BAA15141; BAA15141.
GeneIDi946044.
KEGGiecj:JW1481.
eco:b1486.
PATRICi32118266. VBIEscCol129921_1553.

Organism-specific databases

EchoBASEiEB3550.
EcoGeneiEG13789. ddpB.

Phylogenomic databases

eggNOGiENOG4105CJM. Bacteria.
COG0601. LUCA.
HOGENOMiHOG000170242.
InParanoidiP77308.
KOiK02033.
OMAiAIPVMGV.
OrthoDBiEOG66F098.
PhylomeDBiP77308.

Enzyme and pathway databases

BioCyciEcoCyc:YDDR-MONOMER.
ECOL316407:JW1481-MONOMER.

Miscellaneous databases

PROiP77308.

Family and domain databases

Gene3Di1.10.3720.10. 2 hits.
InterProiIPR000515. MetI-like.
[Graphical view]
PfamiPF00528. BPD_transp_1. 1 hit.
[Graphical view]
SUPFAMiSSF161098. SSF161098. 2 hits.
PROSITEiPS50928. ABC_TM1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. "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."
    Lessard I.A.D., Pratt S.D., McCafferty D.G., Bussiere D.E., Hutchins C., Wanner B.L., Katz L., Walsh C.T.
    Chem. Biol. 5:489-504(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION.
  5. "VanX, a bacterial D-alanyl-D-alanine dipeptidase: resistance, immunity, or survival function?"
    Lessard I.A.D., Walsh C.T.
    Proc. Natl. Acad. Sci. U.S.A. 96:11028-11032(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENE NAME.
  6. "Global topology analysis of the Escherichia coli inner membrane proteome."
    Daley D.O., Rapp M., Granseth E., Melen K., Drew D., von Heijne G.
    Science 308:1321-1323(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: TOPOLOGY [LARGE SCALE ANALYSIS].
    Strain: K12 / MG1655 / ATCC 47076.

Entry informationi

Entry nameiDDPB_ECOLI
AccessioniPrimary (citable) accession number: P77308
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: February 1, 1997
Last modified: February 17, 2016
This is version 122 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.