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Gene |

Product(s) |

Expression|

Evolution |

References |

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Standard Name	upp
Gene Synonym(s)	ECK2494, b2498, JW2483, uraP^[1], uraP
Product Desc.	Upp^[2]^[3]; Component of uracil phosphoribosyltransferase^[2]^[3] Uracil phosphoribosyltransferase^[4]
Product Synonyms(s)	uracil phosphoribosyltransferase^[1], B2498^[2]^[1], UraP^[2]^[1], Upp^[2]^[1] , ECK2494, JW2483, uraP, b2498
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): upp-uraA^[2]
Regulation/Activity
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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	upp
Mnemonic	Uracil PRTase
Synonyms	ECK2494, b2498, JW2483, uraP^[1], uraP
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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	56.43 minutes	MG1655: 2618894..2618268 <gbrowseImage> name=NC_000913:2618268..2618894 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2541692..2541066 <gbrowseImage> name=NC_012967:2541066..2541692 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2504073..2504699 <gbrowseImage> name=NC_012759:2504073..2504699 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2619528..2618902 <gbrowseImage> name=NC_007779:2618902..2619528 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2710659..2710033 <gbrowseImage> name=NC_010473:2710033..2710659 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	2618268	Edman degradation	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: Description	Reference	Availability	Comments
Δupp (Keio:JW2483)	deletion	deletion		PMID:16738554	Shigen CGSC9982^[5]
upp::Tn5KAN-2 (FB20828)	Insertion at nt 334 in Plus orientation			PMID:15262929	E. coli Genome Project:FB20828	contains pKD46
upp::Tn5KAN-2 (FB20829)	Insertion at nt 334 in Plus orientation			PMID:15262929	E. coli Genome Project:FB20829	does not contain pKD46
uppP131D		P131D	60-fold reduction of the catalytic rate, and large decrease in uracil- binding affinity			seeded from UniProt:P0A8F0
upp-1					CGSC:5955
upp-11					CGSC:7317
upp-33					CGSC:7421
upp-12					CGSC:9798
upp-31					CGSC:11199
upp-30					CGSC:16948
upp-32					CGSC:16979
Δupp-746::kan				PMID:16738554	CGSC:103326
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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
JW2483	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAGATCGTGGAAGTCAAACA Primer 2:CCTTTCGTACCAAAGATTTTGTC
10H6	Kohara Phage	Genobase	PMID:3038334
5A11	Kohara Phage	Genobase	PMID:3038334
purC80::Tn10	Linked marker	CAG18470 = CGSC7413^[5]	est. P1 cotransduction: 40% ^[6]
zfh-208::Tn10	Linked marker	CAG18481 = CGSC7417^[5]	est. P1 cotransduction: 14% ^[6] Synonyms:zff-208::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:EG11332	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11332	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001303	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946979	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1308	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008224	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	Upp
Synonyms	uracil phosphoribosyltransferase^[1], B2498^[2]^[1], UraP^[2]^[1], Upp^[2]^[1] , ECK2494, JW2483, uraP, b2498
Product description	Upp^[2]^[3]; Component of uracil phosphoribosyltransferase^[2]^[3] Uracil phosphoribosyltransferase^[4]
EC number (for enzymes)	2.4.2.9^[1]
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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:0005737	cytoplasm				C	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	GO:0000287	magnesium ion binding	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01218	F	Seeded from EcoCyc (v14.0)	complete
	GO:0000287	magnesium ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0460	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004845	uracil phosphoribosyltransferase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01218	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004845	uracil phosphoribosyltransferase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005765	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004845	uracil phosphoribosyltransferase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:2.4.2.9	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005829	cytosol	PMID:16858726	IDA: Inferred from Direct Assay		C	Seeded from EcoCyc (v14.0)	complete
	GO:0006223	uracil salvage	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005765	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008655	pyrimidine salvage	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01218	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009116	nucleoside metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000836	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016020	membrane	PMID:16858726	IDA: Inferred from Direct Assay		C	Seeded from EcoCyc (v14.0)	complete
	GO:0016740	transferase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0808	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016757	transferase activity, transferring glycosyl groups	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0328	F	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 uracil phosphoribosyltransferase	could be indirect
Protein	rplQ		PMID:16606699	Experiment(s):EBI-1143039
Protein	lrp		PMID:16606699	Experiment(s):EBI-1143039
Protein	pepD		PMID:16606699	Experiment(s):EBI-1143039
Protein	purN		PMID:16606699	Experiment(s):EBI-1143039
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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 MAAPQRRKSM KIVEVKHPLV KHKLGLMREQ DISTKRFREL ASEVGSLLTY EATADLETEK VTIEGWNGPV EIDQIKGKKI TVVPILRAGL GMMDGVLENV PSARISVVGM YRNEETLEPV PYFQKLVSNI DERMALIVDP MLATGGSVIA TIDLLKKAGC SSIKVLVLVA APEGIAALEK AHPDVELYTA SIDQGLNEHG YIIPGLGDAG DKIFGTK
Length	217
Mol. Wt	23.559 kDa
pI	6.2 (calculated)
Extinction coefficient	12,950 - 13,075 (calc based on 5 Y, 1 W, and 1 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	41..160	PF00156 Phosphoribosyl transferase domain		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=upp 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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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:90111448	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946979	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008224	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A8F0	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11332	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11332	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946979	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001303	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1308	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	2.78E+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	2580	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: Ml7	PMID: 9298646
Protein	E. coli K-12 MG1655	18345	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	9464	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	6246	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)
upp-uraA
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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_000913:2618874..2618914 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

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:b2498 (EcoliWiki Page)	NCBI GEO profiles for upp
microarray	GenExpDB:b2498 (EcoliWiki Page)	Summary of data for upp 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 (2618830..2619265) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ05; Well:E12^[7]
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Notes

Accessions Related to upp Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11332	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1308	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2498
EcoGene	EcoGene:EG11332	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001303	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008224	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	ENSANGP00000014631 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT3G53900 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000025365 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0230206 (score: 1.000; bootstrap: 100%) DDB0216233 (score: 0.276)	From Inparanoid:20070104
Oryza gramene	Q60EM2 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000046353 (score: 1.000; bootstrap: 100%) ENSPTRP00000037904 (score: 0.121)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000038431 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YHR128W (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAC1B31c (score: 1.000; bootstrap: 48%) SPAC13994c (score: 0.266)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000009951 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	UPP	From SHIGELLACYC
E. coli O157	UPP	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)	PF00156 Phosphoribosyl transferase domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:53271
EcoCyc	EcoCyc:EG11332	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11332	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001303	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1308	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008224	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 ^3.2 ^3.3 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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

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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 upp Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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