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Product(s) |

Expression|

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Standard Name	ubiD
Gene Synonym(s)	ECK3835, b3843, JW3819, yigC, yigY^[1], yigY
Product Desc.	3-octaprenyl-4-hydroxybenzoate decarboxylase^[2]^[3]; Component of 3-octaprenyl-4-hydroxybenzoate decarboxylase^[3] 3-octaprenyl-4-hydroxybenzoate carboxylyase; ubiquinone biosynthesis, third step; UbiX isozyme^[4]
Product Synonyms(s)	3-octaprenyl-4-hydroxybenzoate decarboxylase^[1], YigY^[2]^[1], YigC^[2]^[1], UbiD^[2]^[1], B3843^[2]^[1] , ECK3835, JW3819, yigC, yigY, b3843
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ubiD^[2]
Regulation/Activity
Quick Links
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Notes

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AFMB Structural Genomics target No. 3 (http://afmb.cnrs-mrs.fr/article171.html)^[4]

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	ubiD
Mnemonic	Ubiquinone
Synonyms	ECK3835, b3843, JW3819, yigC, yigY^[1], yigY
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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	86.71 minutes	MG1655: 4023011..4024504 <gbrowseImage> name=NC_000913:4023011..4024504 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 4003459..4004952 <gbrowseImage> name=NC_012967:4003459..4004952 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3912680..3914173 <gbrowseImage> name=NC_012759:3912680..3914173 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3611693..3610200 <gbrowseImage> name=NC_007779:3610200..3611693 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4121931..4123424 <gbrowseImage> name=NC_010473:4121931..4123424 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)	Phenotype: Type	Phenotype: Description	Reference	Availability	Comments
ubiDG452R		G452R		(in AN66; inactive protein)			Strain variation; seeded from UniProt:P0AAB4
ubiD410						CGSC:9931
ubiD::Tn10dCam			Mutagenesis rate	Decreased stress-induced mutagenesis (SIM) phenotype.	PMID:23224554	Parental Strain: SMR4562 Experimental Strain: SMR12313	Mutation Rate was comparatively weak, to other strains, with decrease only happening in 33-67% of wild type population.
SMR4562 yiaG-yfp FRT ubiD::Tn10dCam	insertion		Sigma^S activity	Decrease in Sigma^S activity	PMID:23224554	Parental Strain: SMR10582 Experimental Strain: SMR13098	See table S8 for full experimental data.
CAG45114 ubiD::Tn10dCam	insertion		Sigma^E activity	Decrease in Sigma^E activity	PMID:23224554	Parental Strain: CAG45114 Experimental Strain: SMR15323	See table S11 for full experimental data.
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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
JW3819	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGACGCCATGAAATATAACGA Primer 2:CCGGCGCTTTTACCGTTGTTAAA
16G1	Kohara Phage	Genobase	PMID:3038334
metEo-3079::Tn10	Linked marker	CAG18491 = CGSC7464^[5]	est. P1 cotransduction: 60% ^[6] Synonyms:metE3079::Tn10 nnnThe Tn10 in CAG13491 is inserted in the metE regulatory region, but causes a Met- phenotype.
fad-751::Tn10	Linked marker	CAG18496 = CGSC7465^[5]	est. P1 cotransduction: 87% ^[6] Synonyms:fadAB101::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:EG11396	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11396	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001363	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948326	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1369	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012557	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	UbiD
Synonyms	3-octaprenyl-4-hydroxybenzoate decarboxylase^[1], YigY^[2]^[1], YigC^[2]^[1], UbiD^[2]^[1], B3843^[2]^[1] , ECK3835, JW3819, yigC, yigY, b3843
Product description	3-octaprenyl-4-hydroxybenzoate decarboxylase^[2]^[3]; Component of 3-octaprenyl-4-hydroxybenzoate decarboxylase^[3] 3-octaprenyl-4-hydroxybenzoate carboxylyase; ubiquinone biosynthesis, third step; UbiX isozyme^[4]
EC number (for enzymes)	4.1.1.-^[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:0008694	3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity	PMID:4897112	IMP: Inferred from Mutant Phenotype		F		complete
	GO:0005886	plasma membrane	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01636	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:0006744	ubiquinone biosynthetic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01636	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006744	ubiquinone biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0831	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008694	3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01636	F	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:0019898	extrinsic to membrane	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-9903	C	Seeded from EcoCyc (v14.0)	complete
	GO:0030145	manganese ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0464	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 3-octaprenyl-4-hydroxybenzoate decarboxylase	could be indirect
Protein	yiaG		PMID:16606699	Experiment(s):EBI-1146774
Protein	barA		PMID:16606699	Experiment(s):EBI-1146774
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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 MDAMKYNDLR DFLTLLEQQG ELKRITLPVD PHLEITEIAD RTLRAGGPAL LFENPKGYSM PVLCNLFGTP KRVAMGMGQE DVSALREVGK LLAFLKEPEP PKGFRDLFDK LPQFKQVLNM PTKRLRGAPC QQKIVSGDDV DLNRIPIMTC WPEDAAPLIT WGLTVTRGPH KERQNLGIYR QQLIGKNKLI MRWLSHRGGA LDYQEWCAAH PGERFPVSVA LGADPATILG AVTPVPDTLS EYAFAGLLRG TKTEVVKCIS NDLEVPASAE IVLEGYIEQG ETAPEGPYGD HTGYYNEVDS FPVFTVTHIT QREDAIYHST YTGRPPDEPA VLGVALNEVF VPILQKQFPE IVDFYLPPEG CSYRLAVVTI KKQYAGHAKR VMMGVWSFLR QFMYTKFVIV CDDDVNARDW NDVIWAITTR MDPARDTVLV ENTPIDYLDF ASPVSGLGSK MGLDATNKWP GETQREWGRP IKKDPDVVAH IDAIWDELAI FNNGKSA
Length	497
Mol. Wt	55.604 kDa
pI	5.3 (calculated)
Extinction coefficient	78,840 - 79,715 (calc based on 16 Y, 10 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	13..437	PF01977 3-octaprenyl-4-hydroxybenzoate carboxy-lyase		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=ubiD 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:16131689	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948326	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012557	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AAB4	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11396	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11396	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948326	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001363	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1369	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	2.60E+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	1216	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	295	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	922	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)
ubiD
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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_000913:4022991..4023031 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:b3843 (EcoliWiki Page)	NCBI GEO profiles for ubiD
microarray	GenExpDB:b3843 (EcoliWiki Page)	Summary of data for ubiD 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 ubiD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11396	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1369	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3843
EcoGene	EcoGene:EG11396	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001363	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012557	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
Saccharomyces cerevisiae	YDR539W (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	YIGC	From SHIGELLACYC
E. coli O157	YIGC	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
Superfamily (EcoliWiki Page)	SUPERFAMILY:50475
Superfamily (EcoliWiki Page)	SUPERFAMILY:143968
Pfam (EcoliWiki Page)	PF01977 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
EcoCyc	EcoCyc:EG11396	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11396	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001363	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1369	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012557	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 ^1.12 ^1.13 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 ^4.2 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).

ubiD: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 ubiD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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