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On One Page

Quickview |

Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

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Standard Name	pyrE
Gene Synonym(s)	ECK3632, b3642, JW3617^[1], JW3617
Product Desc.	PyrE^[2]^[3]; Component of orotate phosphoribosyltransferase^[2]^[3] Orotate phosphoribosyltransferase^[4]
Product Synonyms(s)	orotate phosphoribosyltransferase^[1], B3642^[2]^[1], PyrE^[2]^[1] , ECK3632, JW3617, b3642
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): rph-pyrE^[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	pyrE
Mnemonic	Pyrimidine
Synonyms	ECK3632, b3642, JW3617^[1], JW3617
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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	82.19 minutes	MG1655: 3813791..3813150 <gbrowseImage> name=NC_000913:3813150..3813791 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3754123..3753482 <gbrowseImage> name=NC_012967:3753482..3754123 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3701476..3702117 <gbrowseImage> name=NC_012759:3701476..3702117 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3824647..3825288 <gbrowseImage> name=NC_007779:3824647..3825288 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3911368..3910727 <gbrowseImage> name=NC_010473:3910727..3911368 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	3813150	Edman degradation	PMID:6349999
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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
ΔpyrE (Keio:JW3617)	deletion	deletion	PMID:16738554	Shigen CGSC10658^[5]
pyrE::Tn5KAN-I-SceI (FB21359)	Insertion at nt 349 in Plus orientation		PMID:15262929	E. coli Genome Project:FB21359	contains pKD46
pyrE60				CGSC:6249
pyrE41				CGSC:6254
pyrE70				CGSC:6888
pyrE69				CGSC:6945
ΔpyrE748::kan			PMID:16738554	CGSC:102572
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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
JW3617	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAACCATATCAGCGCCAGTT Primer 2:CCAACGCCAAACTCTTCGCGATA
2A6	Kohara Phage	Genobase	PMID:3038334
4D2	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: 60% ^[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:EG10808	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10808	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000799	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948157	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0801	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011904	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	PyrE
Synonyms	orotate phosphoribosyltransferase^[1], B3642^[2]^[1], PyrE^[2]^[1] , ECK3632, JW3617, b3642
Product description	PyrE^[2]^[3]; Component of orotate phosphoribosyltransferase^[2]^[3] Orotate phosphoribosyltransferase^[4]
EC number (for enzymes)	2.4.2.10^[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:0000287	magnesium ion binding	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01208	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:0004588	orotate phosphoribosyltransferase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01208	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004588	orotate phosphoribosyltransferase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004467	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004588	orotate phosphoribosyltransferase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:2.4.2.10	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	PMID:9222315	IDA: Inferred from Direct Assay		C		complete
	GO:0006221	pyrimidine nucleotide biosynthetic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01208	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006221	pyrimidine nucleotide biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004467	P	Seeded from EcoCyc (v14.0)	complete
	GO:0004588	orotate phosphoribosyltransferase activity	PMID:9222315	IDA: Inferred from Direct Assay		F		complete
	GO:0000287	magnesium ion binding	PMID:7050303	IDA: Inferred from Direct Assay		F		complete
	GO:0006221	pyrimidine nucleotide biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0665	P	Seeded from EcoCyc (v14.0)	complete
	GO:0000287	magnesium ion binding	PMID:8620002	IDA: Inferred from Direct Assay		F		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:0006221	pyrimidine nucleotide biosynthetic process	PMID:8501045	IMP: Inferred from Mutant Phenotype		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
Protein	Subunits of orotate phosphoribosyltransferase	could be indirect
Protein	iscS		PMID:16606699	Experiment(s):EBI-1146389
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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 MKPYQRQFIE FALSKQVLKF GEFTLKSGRK SPYFFNAGLF NTGRDLALLG RFYAEALVDS GIEFDLLFGP AYKGIPIATT TAVALAEHHD LDLPYCFNRK EAKDHGEGGN LVGSALQGRV MLVDDVITAG TAIRESMEII QANGATLAGV LISLDRQERG RGEISAIQEV ERDYNCKVIS IITLKDLIAY LEEKPEMAEH LAAVKAYREE FGV
Length	213
Mol. Wt	23.567 kDa
pI	5.3 (calculated)
Extinction coefficient	11,920 - 12,170 (calc based on 8 Y, 0 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
Initiator Methionine	1	Removed	UniProt:P0A7E3
Domain	37..154	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=pyrE 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:16131513	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948157	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011904	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A7E3	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10808	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10808	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948157	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000799	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0801	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	Reference(s)
Protein	E. coli K-12 MC4100	9.05E+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	E. coli K-12 MG1655	823	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	119	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	323	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)
rph-pyrE
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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_000913:3813771..3813811 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:b3642 (EcoliWiki Page)	NCBI GEO profiles for pyrE
microarray	GenExpDB:b3642 (EcoliWiki Page)	Summary of data for pyrE 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 pyrE Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10808	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0801	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3642
EcoGene	EcoGene:EG10808	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000799	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011904	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
Apis mellifera	ENSAPMP00000008680 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT3G54470 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000018248 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00033092 (score: 1.000; bootstrap: 100%) WBGene00042643 (score: 0.187)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00020036 (score: 1.000; bootstrap: 100%) WBGene00011559 (score: 0.203)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000018290 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000018708 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Danio rerio	ZDB-CDNA-040425-1712 (score: 1.000; bootstrap: 100%) ZDB-GENE-040426-785 (score: 1.000; bootstrap: 100%) ZDB-CDNA-040425-1711 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0214958 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0003257 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila pseudoobscura	GA17544-PA (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000019192 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Homo sapiens	ENSP00000232607 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000022885 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Mus musculus	MGI:1298388 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Oryza gramene	Q9LDN2 (score: 1.000; bootstrap: 100%) Q7FZ76 (score: 1.000; bootstrap: 100%) Q9LKI4 (score: 0.867) Q8RZA1 (score: 0.836) Q9M666 (score: 0.648) Q9M665 (score: 0.644) Q9LRF0 (score: 0.538)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000026399 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000002450 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YML106W (score: 1.000; bootstrap: 100%) YMR271C (score: 0.575)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPBC7255 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000155998 (score: 1.000; bootstrap: 100%) NEWSINFRUP00000172271 (score: 0.873)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00031620001 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	PYRE	From SHIGELLACYC
E. coli O157	PYRE	From ECOO157CYC
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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
Panther (EcoliWiki Page)	PTHR19278:SF30
Superfamily (EcoliWiki Page)	SUPERFAMILY:53271
EcoCyc	EcoCyc:EG10808	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10808	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000799	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0801	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011904	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 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 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).

pyrE: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 pyrE Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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