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Gene |

Product(s) |

Expression|

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Standard Name	puuB
Gene Synonym(s)	ECK1296, b1301, JW1294, ycjA, ordL^[1], ordL
Product Desc.	γ-glutamylputrescine oxidase^[2]^[3] gamma-Glutamylputrescine oxidase, putrescine utilization pathway^[4]
Product Synonyms(s)	gamma-Glu-putrescine oxidase, FAD/NAD(P)-binding^[1], B1301^[2]^[1], YcjA^[2]^[1], OrdL^[2]^[1], PuuB^[2]^[1] , ECK1296, JW1294, ordL, ycjA, b1301
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): puuC^[2]
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	puuB
Mnemonic	PUtrescine Utilization
Synonyms	ECK1296, b1301, JW1294, ycjA, ordL^[1], ordL
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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	29.36 minutes	MG1655: 1362256..1363536 <gbrowseImage> name=NC_000913:1362256..1363536 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1362600..1363880 <gbrowseImage> name=NC_012967:1362600..1363880 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1253105..1254385 <gbrowseImage> name=NC_012759:1253105..1254385 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1365946..1367226 <gbrowseImage> name=NC_007779:1365946..1367226 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1451652..1452932 <gbrowseImage> name=NC_010473:1451652..1452932 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)	Reference	Availability	Comments
ΔpuuB (Keio:JW1294)	deletion	deletion	PMID:16738554	Shigen
ordL::Tn5KAN-2 (FB20287)	Insertion at nt 291 in Plus orientation		PMID:15262929	E. coli Genome Project:FB20287	does not contain pKD46
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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
JW1294	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCACCGAACATACCAGCAGTTA Primer 2:CCAACGCCCAGACGATCGCGCAG
1C2	Kohara Phage	Genobase	PMID:3038334
trpC83::Tn10	Linked marker	CAG18455 = CGSC7371^[5]	est. P1 cotransduction: 14% ^[6] Synonyms:trpB83::Tn10
zcj-233::Tn10	Linked marker	CAG12028 = CGSC7373^[5]	est. P1 cotransduction: 81% ^[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:EG11822	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11822	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001754	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945072	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1769	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004378	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	PuuB
Synonyms	gamma-Glu-putrescine oxidase, FAD/NAD(P)-binding^[1], B1301^[2]^[1], YcjA^[2]^[1], OrdL^[2]^[1], PuuB^[2]^[1] , ECK1296, JW1294, ordL, ycjA, b1301
Product description	γ-glutamylputrescine oxidase^[2]^[3] gamma-Glutamylputrescine oxidase, putrescine utilization pathway^[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:0016491	oxidoreductase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006076	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0560	F	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0560	P	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	References	Evidence
Protein	yleA	PMID:16606699	Experiment(s):EBI-1139510
Protein	narX	PMID:16606699	Experiment(s):EBI-1139510
Protein	ahpF	PMID:16606699	Experiment(s):EBI-1139510
Protein	fusA	PMID:16606699	Experiment(s):EBI-1139510
Protein	nadE	PMID:16606699	Experiment(s):EBI-1139510
Protein	rpsI	PMID:16606699	Experiment(s):EBI-1139510
Protein	groL	PMID:16606699	Experiment(s):EBI-1139510
Protein	aceE	PMID:16606699	Experiment(s):EBI-1139510
Protein	lacZ	PMID:16606699	Experiment(s):EBI-1139510
Protein	tpx	PMID:16606699	Experiment(s):EBI-1139510
Protein	acnB	PMID:16606699	Experiment(s):EBI-1139510
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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
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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 MTEHTSSYYA ASANKYAPFD TLNESITCDV CVVGGGYTGL SSALHLAEAG FDVVVLEASR IGFGASGRNG GQLVNSYSRD IDVIEKSYGM DTARMLGSMM FEGGEIIRER IKRYQIDCDY RPGGLFVAMN DKQLATLEEQ KENWERYGNK QLELLDANAI RREVASDRYT GALLDHSGGH IHPLNLAIGE ADAIRLNGGR VYELSAVTQI QHTTPAVVRT AKGQVTAKYV IVAGNAYLGD KVEPELAKRS MPCGTQVITT ERLSEDLARS LIPKNYCVED CNYLLDYYRL TADNRLLYGG GVVYGARDPD DVERLVVPKL LKTFPQLKGV KIDYRWTGNF LLTLSRMPQF GRLDTNIYYM QGYSGHGVTC THLAGRLIAE LLRGDAERFD AFANLPHYPF PGGRTLRVPF TAMGAAYYSL RDRLGV
Length	426
Mol. Wt	47.17 kDa
pI	6.9 (calculated)
Extinction coefficient	49,740 - 50,615 (calc based on 26 Y, 2 W, and 7 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	29..381	PF01266 FAD dependent oxidoreductase		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=puuB 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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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:16129262	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945072	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004378	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P37906	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11822	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11822	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945072	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001754	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1769	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	31	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	391	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	23^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)
puuC
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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_000913:1362236..1362276 source=MG1655 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:b1301 (EcoliWiki Page)	NCBI GEO profiles for puuB
microarray	GenExpDB:b1301 (EcoliWiki Page)	Summary of data for puuB 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 puuB Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11822	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1769	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1301
EcoGene	EcoGene:EG11822	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001754	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004378	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
Mus musculus	MGI:2446262 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000044899 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Shigella flexneri	ORDL	From SHIGELLACYC
E. coli O157	ORDL	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)	PF01266 FAD dependent oxidoreductase
Superfamily (EcoliWiki Page)	SUPERFAMILY:51905
Panther (EcoliWiki Page)	PTHR13847:SF20
EcoCyc	EcoCyc:EG11822	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11822	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001754	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1769	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004378	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 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 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 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).

puuB: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 puuB Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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