dppF:On One Page

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

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Standard Name

dppF

Gene Synonym(s)

ECK3527, b3540, JW3509, dppE[1]

Product Desc.

DppF[2][3];

Component of dipeptide ABC transporter[2][3]

Dipeptide/heme transport, ATP-binding protein; also transports 5-aminolevulinic acid[4]

Product Synonyms(s)

dipeptide transporter[1], ATP-binding component of ABC superfamily[1], B3540[2][1], DppE[2][1], DppF[2][1] , ECK3527, JW3509, b3540

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): dppABCDF[2], dpp, dppABCDE

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

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Notes

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E. coli does not normally use exogeneous heme, but heme can be utilized if a foreign OM heme receptor is expressed in E. coli (Letoffe, 2006).[4]



Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

dppF

Mnemonic

Dipeptide permease system

Synonyms

ECK3527, b3540, JW3509, dppE[1]

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Notes

Location(s) and DNA Sequence

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<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain Map location Genome coordinates Genome browsers Sequence links

MG1655

79.74 minutes 

MG1655: 3700891..3699887
<gbrowseImage> name=NC_000913:3699887..3700891 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3633326..3632322
<gbrowseImage> name=NC_012967:3632322..3633326 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3588381..3589385
<gbrowseImage> name=NC_012759:3588381..3589385 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3937547..3938551
<gbrowseImage> name=NC_007779:3937547..3938551 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3798636..3797632
<gbrowseImage> name=NC_010473:3797632..3798636 source=DH10B preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type Strain Genomic Location Evidence Reference Notes
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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele Nt change(s) AA change(s) Phenotype: Type Phenotype: Description Reference Availability Comments

ΔdppF (Keio:JW3509)

deletion

deletion

PMID:16738554

Shigen
CGSC10595[5]

dppF::Tn5KAN-I-SceI (FB21266)

Insertion at nt 329 in Plus orientation

PMID:15262929

E. coli Genome Project:FB21266

contains pKD46

ΔdppF723::kan

PMID:16738554

CGSC:100644

dppF::Kan

Auxotrophies

Abolished heme utilization.

PMID:16905647

Experimental Strain: JWN3509-2

See table 1.

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Notes

Genetic Interactions

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Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW3509

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAGTACGCAAGAGGCCACCCT

Primer 2:CCACGCTGCGGATTTTCATCCTG

1D1

Kohara Phage

Genobase

PMID:3038334

zhg-50::Tn10

Linked marker

CAG18450 = CGSC7450[5]

est. P1 cotransduction: % [6]
Synonyms:zhf-50::Tn10, zhf-5::Tn10

zic-4901::Tn10

Linked marker

CAG18492 = CGSC7457[5]

est. P1 cotransduction: % [6]

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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:EG12628

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12628

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002340

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948056

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2512

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011564

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Product(s)

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Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name

DppF

Synonyms

dipeptide transporter[1], ATP-binding component of ABC superfamily[1], B3540[2][1], DppE[2][1], DppF[2][1] , ECK3527, JW3509, b3540

Product description

DppF[2][3];

Component of dipeptide ABC transporter[2][3]

Dipeptide/heme transport, ATP-binding protein; also transports 5-aminolevulinic acid[4]

EC number (for enzymes)


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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status

GO:0000166

nucleotide binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003593

F

Seeded from EcoCyc (v14.0)

complete

GO:0000166

nucleotide binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013563

F

Seeded from EcoCyc (v14.0)

complete

GO:0000166

nucleotide binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0547

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003439

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010066

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013563

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR017871

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0067

F

Seeded from EcoCyc (v14.0)

complete

GO:0005886

plasma membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0997

C

Seeded from EcoCyc (v14.0)

complete

GO:0005886

plasma membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-1003

C

Seeded from EcoCyc (v14.0)

complete

GO:0015031

protein transport

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0653

P

Seeded from EcoCyc (v14.0)

complete

GO:0016020

membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0472

C

Seeded from EcoCyc (v14.0)

complete

GO:0016887

ATPase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003439

F

Seeded from EcoCyc (v14.0)

complete

GO:0016887

ATPase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR017871

F

Seeded from EcoCyc (v14.0)

complete

GO:0017111

nucleoside-triphosphatase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003593

F

Seeded from EcoCyc (v14.0)

complete

GO:0019898

extrinsic to membrane

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-9903

C

Seeded from EcoCyc (v14.0)

complete

GO:0015232

heme transporter activity

PMID:16905647

IMP: Inferred from Mutant Phenotype

F

complete

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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type Partner Notes References Evidence

Protein

Subunits of dipeptide ABC transporter

could be indirect

Protein

rplB

PMID:16606699

Experiment(s):EBI-1146094

Protein

groL

PMID:16606699

Experiment(s):EBI-1146094

Protein

metH

PMID:16606699

Experiment(s):EBI-1146094

Protein

eutT

PMID:16606699

Experiment(s):EBI-1146094

Protein

dnaK

PMID:16606699

Experiment(s):EBI-1146094

Protein

rplA

PMID:16606699

Experiment(s):EBI-1146094

Protein

kdgR

PMID:16606699

Experiment(s):EBI-1146094

Protein

dnaE

PMID:16606699

Experiment(s):EBI-1146094

Protein

ydiJ

PMID:16606699

Experiment(s):EBI-1146094

Protein

rpoB

PMID:16606699

Experiment(s):EBI-1146094

Protein

lacZ

PMID:16606699

Experiment(s):EBI-1146094
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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes

cytoplasm

From EcoCyc[3]


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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence

at EcoCyc 

MSTQEATLQQ PLLQAIDLKK HYPVKKGMFA PERLVKALDG VSFNLERGKT LAVVGESGCG
KSTLGRLLTM IEMPTGGELY YQGQDLLKHD PQAQKLRRQK IQIVFQNPYG SLNPRKKVGQ
ILEEPLLINT SLSKEQRREK ALSMMAKVGL KTEHYDRYPH MFSGGQRQRI AIARGLMLDP
DVVIADEPVS ALDVSVRAQV LNLMMDLQQE LGLSYVFISH DLSVVEHIAD EVMVMYLGRC
VEKGTKDQIF NNPRHPYTQA LLSATPRLNP DDRRERIKLS GELPSPLNPP PGCAFNARCR
RRFGPCTQLQ PQLKDYGGQL VACFAVDQDE NPQR
Length

334

Mol. Wt

37.56 kDa

pI

9.1 (calculated)

Extinction coefficient

14,900 - 15,650 (calc based on 10 Y, 0 W, and 6 C residues)

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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type Residues Description Notes References

Domain

62..190

PF00005 ABC transporter

PMID:19920124

Domain

241..306

PF08352 Oligopeptide/dipeptide transporter, C-terminal region

PMID:19920124

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<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=dppF taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16131412

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948056

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011564

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P37313

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG12628

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12628

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948056

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002340

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2512

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.


Cellular Levels

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See Help:Cellular levels

Molecule Organism or Strain Value Units Experimental Conditions Assay used Notes Reference(s)

Protein

E. coli K-12 MG1655

552

molecules/cell/generation

  • Medium: MOPS Complete
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

413

molecules/cell/generation

  • Medium: MOPS Minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

336

molecules/cell/generation

  • Medium: MOPS Complete without Methionine
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

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Notes

Transcription and Transcriptional Regulation

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<protect>

See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)

dppABCDF

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Figure courtesy of RegulonDB

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Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:3700871..3700911 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

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Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name Mutation Phenotype Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type Reference Notes

microarray

GEO Profiles:b3540 (EcoliWiki Page)

NCBI GEO profiles for dppF

microarray

GenExpDB:b3540 (EcoliWiki Page)

Summary of data for dppF from multiple microarray studies

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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name Resource Type Description Source Notes
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Notes

Accessions Related to dppF Expression

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:EG12628

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2512

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3540

EcoGene

EcoGene:EG12628

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002340

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011564

Escherichia coli str. K-12 substr. MG1655

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Notes

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Evolution

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Homologs in Other Organisms

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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism Homologs (Statistics) Comments

Anopheles gambiae

  • ENSANGP00000000682 (score: 1.000; bootstrap: 99%)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00022364001 (score: 1.000; bootstrap: 56%)
  • GSTENP00030600001 (score: 0.153)
  • GSTENP00019589001 (score: 0.144)
  • GSTENP00022664001 (score: 0.133)
  • GSTENP00012322001 (score: 0.120)
  • GSTENP00012676001 (score: 0.120)
  • GSTENP00011937001 (score: 0.119)
  • GSTENP00008809001 (score: 0.087)
  • GSTENP00036523001 (score: 0.082)
  • GSTENP00029830001 (score: 0.064)
  • GSTENP00006944001 (score: 0.063)
  • GSTENP00019587001 (score: 0.058)
  • YP_025300 (score: 0.098)

From Inparanoid:20070104

Shigella flexneri

DPPF

From SHIGELLACYC

E. coli O157

DPPF

From ECOO157CYC

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Do-It-Yourself Web Tools

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Notes

Families

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Database Accession Notes

Pfam (EcoliWiki Page)

PF00005 ABC transporter

Superfamily (EcoliWiki Page)

SUPERFAMILY:52540

Pfam (EcoliWiki Page)

PF08352 Oligopeptide/dipeptide transporter, C-terminal region

EcoCyc

EcoCyc:EG12628

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12628

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002340

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2512

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011564

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 3.2 3.3 3.4 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  6. ↑ 6.0 6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).

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