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Standard Name	potD
Gene Synonym(s)	ECK1109, b1123, JW1109^[1], JW1109
Product Desc.	PotD^[2]^[3]; Component of putrescine/spermidine ABC transporter^[2]^[3] Spermidine ABC transporter periplasmic binding protein; also binds putrescine^[4]
Product Synonyms(s)	polyamine transporter subunit^[1], periplasmic-binding component of ABC superfamily^[1], B1123^[2]^[1], PotD^[2]^[1] , ECK1109, JW1109, b1123
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): potABCD^[2]
Regulation/Activity
Quick Links
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Notes

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PotBCAD spermidine/putrescine ABC transport system.^[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	potD
Mnemonic	Putrescine-ornithine transporter
Synonyms	ECK1109, b1123, JW1109^[1], JW1109
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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	25.45 minutes	MG1655: 1182052..1181006 <gbrowseImage> name=NC_000913:1181006..1182052 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1198199..1197153 <gbrowseImage> name=NC_012967:1197153..1198199 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1084931..1085977 <gbrowseImage> name=NC_012759:1084931..1085977 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1184406..1183360 <gbrowseImage> name=NC_007779:1183360..1184406 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1237497..1236451 <gbrowseImage> name=NC_010473:1236451..1237497 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	1181009	Edman degradation	PMID:1939142 PMID:8740179 PMID:9298646
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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
potD(del) (Keio:JW1109)	deletion	deletion			PMID:16738554	Shigen CGSC9040^[5]
potD::Tn5KAN-2 (FB20257)	Insertion at nt 632 in Minus orientation				PMID:15262929	E. coli Genome Project:FB20257	does not contain pKD46
potD783(del)::kan					PMID:16738554	CGSC:102404
yeeF(del) speA(del) speB(del) speC(del) potA(del) potB(del) potC(del) potD(del)	deletion	deletion	Motility	Deletion of yeeF in a speA(del) speB(del) speC(del) potA(del) potB(del) potC(del) potD(del) genetic background resulted in severe inhibition of surface motility under the same conditions, fig 2.	PMID:21266585
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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
JW1109	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAAAAATGGTCACGCCACCT Primer 2:CCACGTCCTGCTTTCAGCTTCTG
E4C2	Kohara Phage	Genobase	PMID:3038334
zce-726::Tn10	Linked marker	CAG12078 = CGSC7361^[5]	est. P1 cotransduction: 38% ^[6]
zcf-117::Tn10	Linked marker	CAG18463 = CGSC7363^[5]	est. P1 cotransduction: 31% ^[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:EG10752	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10752	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000743	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945682	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0745	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003789	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	PotD
Synonyms	polyamine transporter subunit^[1], periplasmic-binding component of ABC superfamily^[1], B1123^[2]^[1], PotD^[2]^[1] , ECK1109, JW1109, b1123
Product description	PotD^[2]^[3]; Component of putrescine/spermidine ABC transporter^[2]^[3] Spermidine ABC transporter periplasmic binding protein; also binds putrescine^[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:0015417	polyamine-transporting ATPase activity	PMID:8366082	IMP: Inferred from Mutant Phenotype		F	Seeded from EcoCyc (v14.0)	complete
	GO:0015846	polyamine transport	PMID:1939142	IMP: Inferred from Mutant Phenotype		P	Seeded from EcoCyc (v14.0)	complete
	GO:0030288	outer membrane-bounded periplasmic space	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001188	C	Seeded from EcoCyc (v14.0)	complete
	GO:0030288	outer membrane-bounded periplasmic space	PMID:1939142	IEP: Inferred from Expression Pattern		C	Seeded from EcoCyc (v14.0)	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 putrescine/spermidine ABC transporter	could be indirect
Protein	ydfK		PMID:16606699	Experiment(s):EBI-1138932
Protein	stpA		PMID:16606699	Experiment(s):EBI-1138932
Protein	ymfG		PMID:16606699	Experiment(s):EBI-1138932
Protein	dtd		PMID:16606699	Experiment(s):EBI-1138932
Protein	tatE		PMID:16606699	Experiment(s):EBI-1138932
Protein	ynaE		PMID:16606699	Experiment(s):EBI-1138932
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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:1939142	EchoLocation:potD
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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 MKKWSRHLLA AGALALGMSA AHADDNNTLY FYNWTEYVPP GLLEQFTKET GIKVIYSTYE SNETMYAKLK TYKDGAYDLV VPSTYYVDKM RKEGMIQKID KSKLTNFSNL DPDMLNKPFD PNNDYSIPYI WGATAIGVNG DAVDPKSVTS WADLWKPEYK GSLLLTDDAR EVFQMALRKL GYSGNTTDPK EIEAAYNELK KLMPNVAAFN SDNPANPYME GEVNLGMIWN GSAFVARQAG TPIDVVWPKE GGIFWMDSLA IPANAKNKEG ALKLINFLLR PDVAKQVAET IGYPTPNLAA RKLLSPEVAN DKTLYPDAET IKNGEWQNDV GAASSIYEEY YQKLKAGR
Length	348
Mol. Wt	38.868 kDa
pI	5.1 (calculated)
Extinction coefficient	80,790 (calc based on 21 Y, 9 W, and 0 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	1-23	UniProt Manual:Signal Peptides	UniProt:P0AFK9
Domain	31..285	PF01547 Bacterial extracellular solute-binding protein		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=potD taxon=562,83333 </beststructure>

Models

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Structure figures

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Notes

Gene Product Resources

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Resource type	Source	Notes/Reference
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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:16129086	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945682	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003789	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AFK9	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10752	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10752	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945682	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000743	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0745	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	2.57E+03	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	E. coli K-12 EMG2	1040	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: M47	PMID: 9298646
Protein	E. coli K-12 EMG2	260	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: Ml49	PMID: 9298646
Protein	E. coli K-12 MG1655	9151	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	3262	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	4414	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)
potABCD
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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_000913:1182032..1182072 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:b1123 (EcoliWiki Page)	NCBI GEO profiles for potD
microarray	GenExpDB:b1123 (EcoliWiki Page)	Summary of data for potD 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 potD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10752	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0745	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1123
EcoGene	EcoGene:EG10752	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000743	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003789	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
Arabidopsis thaliana	AT1G31410 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	POTD	From SHIGELLACYC
E. coli O157	POTD	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
Pfam (EcoliWiki Page)	PF01547 Bacterial extracellular solute-binding protein
Superfamily (EcoliWiki Page)	SUPERFAMILY:53850
EcoCyc	EcoCyc:EG10752	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10752	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000743	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0745	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003789	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.

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 ^1.8 ^1.9 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 ^2.3 ^2.4 ^2.5 ^2.6 ^2.7 ^2.8 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).

potD:On One Page

Quickview

Notes

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 potD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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