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On One Page

Quickview |

Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

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Standard Name	pyrD
Gene Synonym(s)	ECK0936, b0945, JW0928^[1], JW0928
Product Desc.	PyrD^[2]^[3]; Component of dihydroorotate oxidase^[2]^[3] Dihydroorotate dehydrogenase, UMP biosynthesis^[4]
Product Synonyms(s)	dihydro-orotate oxidase, FMN-linked^[1], B0945^[2]^[1], PyrD^[2]^[1] , ECK0936, JW0928, b0945
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): pyrD^[2], OP00084
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	pyrD
Mnemonic	Pyrimidine
Synonyms	ECK0936, b0945, JW0928^[1], JW0928
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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	21.64 minutes	MG1655: 1003991..1005001 <gbrowseImage> name=NC_000913:1003991..1005001 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1021859..1022869 <gbrowseImage> name=NC_012967:1021859..1022869 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 906959..907969 <gbrowseImage> name=NC_012759:906959..907969 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1005190..1006200 <gbrowseImage> name=NC_007779:1005190..1006200 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1057919..1058929 <gbrowseImage> name=NC_010473:1057919..1058929 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	1003991	Edman degradation	PMID:2992959
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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
pyrD(del) (Keio:JW0928)	deletion	deletion	PMID:16738554	Shigen CGSC8935^[5]
pyrD34				CGSC:4745
pyrD36				CGSC:5772
pyrD67				CGSC:6940
pyrD68				CGSC:6942
pyrD0				CGSC:12983
pyrD761(del)::kan			PMID:16738554	CGSC:102570
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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
JW0928	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCTACTACCCCTTCGTTCGTAA Primer 2:CCGATATGGGTAACGATTTCTTT
9E9	Kohara Phage	Genobase	PMID:3038334
zcb-3059::Tn10	Linked marker	CAG12094 = CGSC7358^[5]	est. P1 cotransduction: 94% ^[6]
zcc-282::Tn10	Linked marker	CAG18466 = CGSC7359^[5]	est. P1 cotransduction: 5% ^[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:EG10807	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10807	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000798	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945556	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0800	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003201	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	PyrD
Synonyms	dihydro-orotate oxidase, FMN-linked^[1], B0945^[2]^[1], PyrD^[2]^[1] , ECK0936, JW0928, b0945
Product description	PyrD^[2]^[3]; Component of dihydroorotate oxidase^[2]^[3] Dihydroorotate dehydrogenase, UMP biosynthesis^[4]
EC number (for enzymes)	1.3.3.1^[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:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013785	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004152	dihydroorotate dehydrogenase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00225	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004152	dihydroorotate dehydrogenase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001295	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004152	dihydroorotate dehydrogenase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012135	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004158	dihydroorotate oxidase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005719	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005886	plasma membrane	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00225	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:0006207	'de novo' pyrimidine base biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001295	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006207	'de novo' pyrimidine base biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005719	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006221	pyrimidine nucleotide biosynthetic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00225	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:0006222	UMP biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012135	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013785	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016020	membrane	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005719	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: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:0019898	extrinsic to membrane	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-9903	C	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001295	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005719	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012135	P	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	Notes	References	Evidence
Protein	Subunits of dihydroorotate oxidase	could be indirect
Protein	hyaB		PMID:16606699	Experiment(s):EBI-1138439
Protein	groL		PMID:16606699	Experiment(s):EBI-1138439
Protein	uspG		PMID:16606699	Experiment(s):EBI-1138439
Protein	dld		PMID:16606699	Experiment(s):EBI-1138439
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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			From EcoCyc^[3]
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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 MYYPFVRKAL FQLDPERAHE FTFQQLRRIT GTPFEALVRQ KVPAKPVNCM GLTFKNPLGL AAGLDKDGEC IDALGAMGFG SIEIGTVTPR PQPGNDKPRL FRLVDAEGLI NRMGFNNLGV DNLVENVKKA HYDGVLGINI GKNKDTPVEQ GKDDYLICME KIYAYAGYIA INISSPNTPG LRTLQYGEAL DDLLTAIKNK QNDLQAMHHK YVPIAVKIAP DLSEEELIQV ADSLVRHNID GVIATNTTLD RSLVQGMKNC DQTGGLSGRP LQLKSTEIIR RLSLELNGRL PIIGVGGIDS VIAAREKIAA GASLVQIYSG FIFKGPPLIK EIVTHI
Length	336
Mol. Wt	36.775 kDa
pI	7.9 (calculated)
Extinction coefficient	14,900 - 15,400 (calc based on 10 Y, 0 W, and 4 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	45..336	PF01180 Dihydroorotate dehydrogenase		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=pyrD 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:16128912	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945556	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003201	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A7E1	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10807	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10807	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945556	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000798	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0800	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	1.73E+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	1798	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	1337	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	482	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)
pyrD
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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_000913:1003971..1004011 source=MG1655 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:b0945 (EcoliWiki Page)	NCBI GEO profiles for pyrD
microarray	GenExpDB:b0945 (EcoliWiki Page)	Summary of data for pyrD 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 pyrD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10807	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0800	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0945
EcoGene	EcoGene:EG10807	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000798	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003201	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	ENSANGP00000011275 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000019103 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT5G23300 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000026495 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00026793 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00020932 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000029990 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000019111 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-041212-32 (score: 1.000; bootstrap: 100%) ZDB-CDNA-041212-36 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0000447 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila pseudoobscura	GA22001-PA (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000001161 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Homo sapiens	ENSP00000219240 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000030689 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000003011 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Mus musculus	MGI:1928378 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Oryza gramene	Q7XKC8 (score: 1.000; bootstrap: 100%) Q9FZM9 (score: 0.865)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000014234 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000020302 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAC57A102c (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000132672 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00010523001 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000050631 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	PYRD	From SHIGELLACYC
E. coli O157	PYRD	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)	PF01180 Dihydroorotate dehydrogenase
Superfamily (EcoliWiki Page)	SUPERFAMILY:51395
Panther (EcoliWiki Page)	PTHR11938:SF32
EcoCyc	EcoCyc:EG10807	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10807	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000798	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0800	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003201	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 ^3.2 ^3.3 ^3.4 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).

pyrD: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 pyrD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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