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Gene |

Product(s) |

Expression|

Evolution |

References |

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Standard Name	puuP
Gene Synonym(s)	ECK1291, b1296, JW1289, ycjJ^[1], ycjJ
Product Desc.	putrescine importer^[2]^[3] Putrescine importer^[4]
Product Synonyms(s)	putrescine importer^[1], B1296^[2]^[1], YcjJ^[2]^[1], PuuP^[2]^[1] , ECK1291, JW1289, ycjJ, b1296
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): puuP^[2], ycjJ
Regulation/Activity
Quick Links
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Notes

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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	puuP
Mnemonic	PUtrescine Utilization
Synonyms	ECK1291, b1296, JW1289, ycjJ^[1], ycjJ
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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	29.22 minutes	MG1655: 1357211..1355826 <gbrowseImage> name=NC_000913:1355826..1357211 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1356170..1357555 <gbrowseImage> name=NC_012967:1356170..1357555 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1246675..1248060 <gbrowseImage> name=NC_012759:1246675..1248060 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1360901..1359516 <gbrowseImage> name=NC_007779:1359516..1360901 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1446607..1445222 <gbrowseImage> name=NC_010473:1445222..1446607 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
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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: Description	Reference	Availability	Comments
Strain DH10B		Y110C	Nonsynonomous mutation	PMID:18245285	ASAP	This is a SNP in E. coli K-12 Strain DH10B
puuP(del) (Keio:JW1289)	deletion	deletion		PMID:16738554	Shigen CGSC9158^[5]
puuP732(del)::kan				PMID:16738554	CGSC:102558
puuP(del)	deletion	deletion	Mutation decreases uptake of putrescine from medium, figure 2A.	PMID:19181795
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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
JW1289	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGCTATTAATTCACCACTGAA Primer 2:CCtGTTTCACTCACCGGCGTTCT
E14F6	Kohara Phage	Genobase	PMID:3038334
1C2	Kohara Phage	Genobase	PMID:3038334
trpC83::Tn10	Linked marker	CAG18455 = CGSC7371^[5]	est. P1 cotransduction: 20% ^[6] Synonyms:trpB83::Tn10
zcj-233::Tn10	Linked marker	CAG12028 = CGSC7373^[5]	est. P1 cotransduction: 64% ^[6] Synonyms:zci-233::Tn10
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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:G6643	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13907	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003238	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946287	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3666	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004362	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	PuuP
Synonyms	putrescine importer^[1], B1296^[2]^[1], YcjJ^[2]^[1], PuuP^[2]^[1] , ECK1291, JW1289, ycjJ, b1296
Product description	putrescine importer^[2]^[3] Putrescine importer^[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: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:0006865	amino acid transport	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002293	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006865	amino acid transport	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0029	P	Seeded from EcoCyc (v14.0)	complete
	GO:0015171	amino acid transmembrane transporter activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002293	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016020	membrane	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002293	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016020	membrane	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004841	C	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:0016021	integral to membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0812	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-9909	C	Seeded from EcoCyc (v14.0)	complete
	GO:0055085	transmembrane transport	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002293	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055085	transmembrane transport	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004841	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006974	response to DNA damage stimulus	PMID:11967071	IEP: Inferred from Expression Pattern		P		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
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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
plasma membrane	C-terminus localized in the cytoplasm with 12 predicted transmembrane domains	Daley et al. (2005) ^[7]
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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 MISGRHDRKP YYAGEAAIMA INSPLNIAAQ PGKTRLRKSL KLWQVVMMGL AYLTPMTVFD TFGIVSGISD GHVPASYLLA LAGVLFTAIS YGKLVRQFPE AGSAYTYAQK SINPHVGFMV GWSSLLDYLF LPMINVLLAK IYLSALFPEV PPWVWVVTFV AILTAANLKS VNLVANFNTL FVLVQISIMV VFIFLVVQGL HKGEGVGTVW SLQPFISENA HLIPIITGAT IVCFSFLGFD AVTTLSEETP DAARVIPKAI FLTAVYGGVI FIAASFFMQL FFPDISRFKD PDAALPEIAL YVGGKLFQSI FLCTTFVNTL ASGLASHASV SRLLYVMGRD NVFPERVFGY VHPKWRTPAL NVIMVGIVAL SALFFDLVTA TALINFGALV AFTFVNLSVF NHFWRRKGMN KSWKDHFHYL LMPLVGALTV GVLWVNLEST SLTLGLVWAS LGGAYLWYLI RRYRKVPLYD GDRTPVSET
Length	479
Mol. Wt	52.871 kDa
pI	9.7 (calculated)
Extinction coefficient	87,320 - 87,570 (calc based on 18 Y, 11 W, and 2 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	26..442	PF00324 Amino acid permease		PMID:19920124
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<motif_map/>

Click the image to view raw output from TMHMM.

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

Structures

<beststructure> gene=puuP 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:90111243	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946287	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004362	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P76037	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6643	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13907	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946287	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003238	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3666	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 MG1655	13	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	48	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	0^a	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	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)
puuP
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Figure courtesy of RegulonDB

</protect>

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_000913:1357191..1357231 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:b1296 (EcoliWiki Page)	NCBI GEO profiles for puuP
microarray	GenExpDB:b1296 (EcoliWiki Page)	Summary of data for puuP 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 puuP Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6643	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3666	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1296
EcoGene	EcoGene:EG13907	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003238	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004362	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	ENSANGP00000016290 (score: 1.000; bootstrap: 100%) ENSANGP00000016984 (score: 0.339)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000012050 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00016806 (score: 1.000; bootstrap: 100%) WBGene00017747 (score: 0.456) WBGene00015197 (score: 0.455)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000018906 (score: 1.000; bootstrap: 100%) ENSCINP00000016866 (score: 0.384) ENSCINP00000002795 (score: 0.277)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-030919-2 (score: 1.000; bootstrap: 86%) ZDB-CDNA-041114-206 (score: 0.303) ZDB-GENE-041114-206 (score: 0.303) ZDB-CDNA-041212-7 (score: 0.300) ZDB-GENE-041212-5 (score: 0.300)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0185190 (score: 1.000; bootstrap: 89%) DDB0189300 (score: 1.000; bootstrap: 82%) DDB0205912 (score: 0.262)	From Inparanoid:20070104
Mus musculus	MGI:2146512 (score: 1.000; bootstrap: 100%) MGI:88117 (score: 0.314) MGI:99828 (score: 0.295) MGI:1100521 (score: 0.294) MGI:3040688 (score: 0.229)	From Inparanoid:20070104
Oryza gramene	Q7X636 (score: 1.000; bootstrap: 87%) Q53QH5 (score: 0.448) Q9LD96 (score: 0.282) Q5Z6S8 (score: 0.266) Q6AST5 (score: 0.208)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPCC5843 (score: 1.000; bootstrap: 64%) SPCC744 (score: 0.493) SPAC10391 (score: 0.441) SPBC15C44c (score: 0.210) SPAC11D38c (score: 0.167) SPAPB24D32c (score: 0.148) SPAC90 (score: 0.068) SPCC7943 (score: 0.052)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000140033 (score: 1.000; bootstrap: 100%) NEWSINFRUP00000132890 (score: 0.503) NEWSINFRUP00000151033 (score: 0.502) NEWSINFRUP00000136276 (score: 0.311) NEWSINFRUP00000135371 (score: 0.302)	From Inparanoid:20070104
Shigella flexneri	YCJJ	From SHIGELLACYC
E. coli O157	YCJJ	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)	PF00324 Amino acid permease
Panther (EcoliWiki Page)	PTHR11785:SF55
EcoCyc	EcoCyc:G6643	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13907	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003238	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3666	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004362	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 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 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).
↑ Daley, DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 1321-3 PubMed

puuP:On One Page

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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 puuP Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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