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Expression|

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Standard Name	dppA
Gene Synonym(s)	ECK3531, b3544, JW3513, alu, dpp, fpp^[1], fpp
Product Desc.	DppA^[2]^[3]; Component of dipeptide ABC transporter^[2]^[3] Dipeptide/heme transport, periplasmic binding protein; recognition for transport and chemotaxis^[4]
Product Synonyms(s)	dipeptide transporter^[1], periplasmic-binding component of ABC superfamily^[1], B3544^[2]^[1], Fpp^[2]^[1], Dpp^[2]^[1], Alu^[2]^[1], DppA^[2]^[1] , alu, dpp, ECK3531, fpp, JW3513, b3544
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): dppABCDF^[2], dpp, dppABCDE
Regulation/Activity
Quick Links
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Notes

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DppA binds dipeptides and heme, and mediates chemotaxis to dipeptides through the Tap chemoreceptor. E. coli does not normally use exogeneous heme, but heme can be utilized if a foreign OM heme receptor is expressed in E. coli; heme and dipeptides compete for the same binding site; MppA is an alternative heme periplasmic binding protein; MppA or DppA is required for the uptake of 5-aminolevulinic acid (Letoffe, 2006). After four hours of Zn(II) stress, DppA protein levels decreased (Easton, 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	dppA
Mnemonic	Dipeptide permease system
Synonyms	ECK3531, b3544, JW3513, alu, dpp, fpp^[1], fpp
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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	79.84 minutes	MG1655: 3705728..3704121 <gbrowseImage> name=NC_000913:3704121..3705728 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3638163..3636556 <gbrowseImage> name=NC_012967:3636556..3638163 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3592615..3594222 <gbrowseImage> name=NC_012759:3592615..3594222 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3932710..3934317 <gbrowseImage> name=NC_007779:3932710..3934317 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3803473..3801866 <gbrowseImage> name=NC_010473:3801866..3803473 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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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
Coding Start (SO:0000323)	MG1655	3704124	Edman degradation	PMID:1956284 PMID:9298646 PMID:9600841 PMID:9740056 PMID:10972807
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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
dppA(del) (Keio:JW3513)	deletion	deletion			PMID:16738554	Shigen CGSC10599^[5]
dppA::Tn5KAN-I-SceI (FB21271)	Insertion at nt 837 in Minus orientation				PMID:15262929	E. coli Genome Project:FB21271	does not contain pKD46
dppA728(del)::kan					PMID:16738554	CGSC:100636
dppA in strain PA0113			Resistant to	Lysyl-2-aminooxypronate resistance	PMID:6389761	PA0113
dppA::Kan mppA::Cm			Auxotrophies	Abolished heme utilization.	PMID:16905647		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
JW3513	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCGTATTTCCTTGAAAAAGTC Primer 2:CCTTCGATAGAGACGTTTTCGAA
9F6	Kohara Phage	Genobase	PMID:3038334
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:EG10248	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10248	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000242	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948062	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0244	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011576	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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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	DppA
Synonyms	dipeptide transporter^[1], periplasmic-binding component of ABC superfamily^[1], B3544^[2]^[1], Fpp^[2]^[1], Dpp^[2]^[1], Alu^[2]^[1], DppA^[2]^[1] , alu, dpp, ECK3531, fpp, JW3513, b3544
Product description	DppA^[2]^[3]; Component of dipeptide ABC transporter^[2]^[3] Dipeptide/heme transport, periplasmic binding protein; recognition for transport and chemotaxis^[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
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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	ydhK		PMID:16606699	Experiment(s):EBI-1146107
Protein	yhjG		PMID:16606699	Experiment(s):EBI-1146107
Protein	fliF		PMID:16606699	Experiment(s):EBI-1146107
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Notes

Localization

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

Compartment	Evidence	Reference/Source
periplasm		From EcoCyc^[3]
Periplasm	PMID:9298646	EchoLocation:dppA
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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 MRISLKKSGM LKLGLSLVAM TVAASVQAKT LVYCSEGSPE GFNPQLFTSG TTYDASSVPL YNRLVEFKIG TTEVIPGLAE KWEVSEDGKT YTFHLRKGVK WHDNKEFKPT RELNADDVVF SFDRQKNAQN PYHKVSGGSY EYFEGMGLPE LISEVKKVDD NTVQFVLTRP EAPFLADLAM DFASILSKEY ADAMMKAGTP EKLDLNPIGT GPFQLQQYQK DSRIRYKAFD GYWGTKPQID TLVFSITPDA SVRYAKLQKN ECQVMPYPNP ADIARMKQDK SINLMEMPGL NVGYLSYNVQ KKPLDDVKVR QALTYAVNKD AIIKAVYQGA GVSAKNLIPP TMWGYNDDVQ DYTYDPEKAK ALLKEAGLEK GFSIDLWAMP VQRPYNPNAR RMAEMIQADW AKVGVQAKIV TYEWGEYLKR AKDGEHQTVM MGWTGDNGDP DNFFATLFSC AASEQGSNYS KWCYKPFEDL IQPARATDDH NKRVELYKQA QVVMHDQAPA LIIAHSTVFE PVRKEVKGYV VDPLGKHHFE NVSIE
Length	535
Mol. Wt	60.294 kDa
pI	6.6 (calculated)
Extinction coefficient	89,730 - 90,230 (calc based on 27 Y, 9 W, and 4 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
motif	1-28	UniProt Manual:Signal Peptides	UniProt:P23847
Domain	73..455	PF00496 Bacterial extracellular solute-binding proteins, family 5 Middle		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=dppA taxon=562,83333 </beststructure>

Models

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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:16131416	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948062	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011576	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P23847	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10248	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10248	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948062	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000242	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0244	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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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 MC4100	5.65E+02	molecules/cell	Medium: median data from rich and minimal media Temperature (°C): 37 Doubling time (min): Growth Rate(min): Growth phase: other:	emPAI		PMID:18304323
Protein	Ecoli K-12	0.294+/-0.065	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.49502178	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by RNA_Seq	PMID:20671182
Protein	E. coli K-12 EMG2	660	molecules/cell	Medium: MOPS glucose minimal Temperature (°C): 37 Doubling time (min): Growth phase: Exponential OD: OD600 = 0.2 to 0.25 other: aerated	Quantitative protein sequencing	Spot ID: M8S	PMID: 9298646
Protein	E. coli K-12 MG1655	2460	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	5339	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	2510	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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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_000913:3705708..3705748 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:b3544 (EcoliWiki Page)	NCBI GEO profiles for dppA
microarray	GenExpDB:b3544 (EcoliWiki Page)	Summary of data for dppA 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
	GFP Fusion	Intergenic region (3705253..3706289) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ15; Well:A3^[7]
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Notes

Accessions Related to dppA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10248	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0244	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3544
EcoGene	EcoGene:EG10248	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000242	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011576	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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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	ENSANGP00000026819 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000030908 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	DPPA	From SHIGELLACYC
E. coli O157	DPPA	From ECOO157CYC
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Do-It-Yourself Web Tools

Notes

Families

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

Database	Accession	Notes
Superfamily (EcoliWiki Page)	SUPERFAMILY:53850
Pfam (EcoliWiki Page)	PF00496 Bacterial extracellular solute-binding proteins, family 5 Middle
PFAM (EcoliWiki Page)	PFAM:PF00496
EcoCyc	EcoCyc:EG10248	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10248	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000242	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0244	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011576	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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

↑ ^1.00 ^1.01 ^1.02 ^1.03 ^1.04 ^1.05 ^1.06 ^1.07 ^1.08 ^1.09 ^1.10 ^1.11 ^1.12 ^1.13 ^1.14 ^1.15 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.00 ^2.01 ^2.02 ^2.03 ^2.04 ^2.05 ^2.06 ^2.07 ^2.08 ^2.09 ^2.10 ^2.11 ^2.12 ^2.13 ^2.14 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^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
↑ ^4.0 ^4.1 ^4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 ^5.2 CGSC: The Coli Genetics Stock Center
↑ ^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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

dppA:On One Page

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Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to dppA Expression

Notes

Links

Evolution

Homologs in Other Organisms

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Notes

Families

Notes

Links

References

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