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Standard Name	pyrC
Gene Synonym(s)	ECK1047, b1062, JW1049^[1], JW1049
Product Desc.	PyrC^[2]^[3]; Component of dihydroorotase^[2]^[3] Dihydroorotase, the third step in pyrimidine biosynthesis; dimeric; Zn(II) metalloenzyme, binuclear metal center^[4]
Product Synonyms(s)	dihydro-orotase^[1], B1062^[2]^[1], PyrC^[2]^[1] , ECK1047, JW1049, b1062
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): pyrC^[2], OP00083
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	pyrC
Mnemonic	Pyrimidine
Synonyms	ECK1047, b1062, JW1049^[1], JW1049
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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	24.16 minutes	MG1655: 1121830..1120784 <gbrowseImage> name=NC_000913:1120784..1121830 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1137179..1136133 <gbrowseImage> name=NC_012967:1136133..1137179 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1024709..1025755 <gbrowseImage> name=NC_012759:1024709..1025755 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1124184..1123138 <gbrowseImage> name=NC_007779:1123138..1124184 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1177275..1176229 <gbrowseImage> name=NC_010473:1176229..1177275 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	1120787	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)	Reference	Availability
ΔpyrC (Keio:JW1049)	deletion	deletion	PMID:16738554	Shigen CGSC9010^[5]
pyrC44				CGSC:5571
pyrC45				CGSC:5581
pyrC46				CGSC:5584
ΔpyrC732::kan			PMID:16738554	CGSC:102568
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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
JW1049	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCACTGCACCATCCCAGGTATT Primer 2:CCTTGTTTAACGGACCAGCGTAC
1H7	Kohara Phage	Genobase	PMID:3038334
E4H10S	Kohara Phage	Genobase	PMID:3038334
zcc-282::Tn10	Linked marker	CAG18466 = CGSC7359^[5]	est. P1 cotransduction: 5% ^[6]
zce-726::Tn10	Linked marker	CAG12078 = CGSC7361^[5]	est. P1 cotransduction: 25% ^[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:EG10806	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10806	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000797	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945787	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0799	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003607	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	PyrC
Synonyms	dihydro-orotase^[1], B1062^[2]^[1], PyrC^[2]^[1] , ECK1047, JW1049, b1062
Product description	PyrC^[2]^[3]; Component of dihydroorotase^[2]^[3] Dihydroorotase, the third step in pyrimidine biosynthesis; dimeric; Zn(II) metalloenzyme, binuclear metal center^[4]
EC number (for enzymes)	3.5.2.3^[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:0004151	dihydroorotase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00219	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004151	dihydroorotase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004721	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004151	dihydroorotase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:3.5.2.3	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006221	pyrimidine nucleotide biosynthetic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00219	P	Seeded from EcoCyc (v14.0)	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:0008270	zinc ion binding	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00219	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008270	zinc ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0862	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016787	hydrolase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006680	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016787	hydrolase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0378	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016812	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002195	F	Seeded from EcoCyc (v14.0)	complete
	GO:0019856	pyrimidine base biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004721	P	Seeded from EcoCyc (v14.0)	complete
	GO:0046872	metal ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0479	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 dihydroorotase	could be indirect
Protein	nadE		PMID:16606699	Experiment(s):EBI-1138734
Protein	solA		PMID:16606699	Experiment(s):EBI-1138734
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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 MTAPSQVLKI RRPDDWHLHL RDGDMLKTVV PYTSEIYGRA IVMPNLAPPV TTVEAAVAYR QRILDAVPAG HDFTPLMTCY LTDSLDPNEL ERGFNEGVFT AAKLYPANAT TNSSHGVTSI DAIMPVLERM EKIGMPLLVH GEVTHADIDI FDREARFIES VMEPLRQRLT ALKVVFEHIT TKDAADYVRD GNERLAATIT PQHLMFNRNH MLVGGVRPHL YCLPILKRNI HQQALRELVA SGFNRVFLGT DSAPHARHRK ESSCGCAGCF NAPTALGSYA TVFEEMNALQ HFEAFCSVNG PQFYGLPVND TFIELVREEQ QVAESIALTD DTLVPFLAGE TVRWSVKQ
Length	348
Mol. Wt	38.826 kDa
pI	6.2 (calculated)
Extinction coefficient	24,410 - 25,160 (calc based on 9 Y, 2 W, and 6 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:P05020
Domain	10..323	PF01979 Amidohydrolase family		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=pyrC 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:16129025	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945787	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003607	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P05020	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10806	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10806	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945787	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000797	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0799	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	6.64E+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 EMG2	340	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: M95	PMID: 9298646
Protein	E. coli K-12 MG1655	4309	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	5040	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	1634	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)
pyrC
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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_000913:1121810..1121850 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:b1062 (EcoliWiki Page)	NCBI GEO profiles for pyrC
microarray	GenExpDB:b1062 (EcoliWiki Page)	Summary of data for pyrC 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 (1121763..1121960) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ09; Well:G10^[7]
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Notes

Accessions Related to pyrC Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10806	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0799	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1062
EcoGene	EcoGene:EG10806	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000797	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003607	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	AT4G22930 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YLR420W (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAC163c (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000000410 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	PYRC	From SHIGELLACYC
E. coli O157	PYRC	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)	PF01979 Amidohydrolase family
Superfamily (EcoliWiki Page)	SUPERFAMILY:51556
EcoCyc	EcoCyc:EG10806	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10806	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000797	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0799	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003607	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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

pyrC:On One Page

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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 pyrC Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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