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Standard Name	ubiE
Gene Synonym(s)	ECK3827, b3833, JW5581, yigO^[1], menG, menH, yigO
Product Desc.	2-OCTAPRENYL-METHOXY-BENZOQ-METH^[2]; bifunctional 2-octaprenyl-6-methoxy-1,4-benzoquinone methylase and S-adenosylmethionine:2-DMK methyltransferase^[3] Ubiquinone/menaquinone biosynthesis methyltransferase; SAM-dependent; (1) Ubiqinone synthesis, 2-octaprenyl-6-methoxy-1,4-benzoquinone methyltransferase; (2) Menaquinone synthesis, 2-demethylmenaquinone (DMK) methyltransferase^[4]
Product Synonyms(s)	bifunctional 2-octaprenyl-6-methoxy-1,4-benzoquinone methylase and S-adenosylmethionine:2-DMK methyltransferase^[1], B3833^[2]^[1], YigO^[2]^[1], UbiE^[2]^[1] , ECK3827, JW5581, menG, menH, yigO, b3833
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ubiE-yigP-ubiB^[2]
Regulation/Activity
Quick Links
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Notes

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UbiE is the closest E. coli homolog to B. stearothermophilus MenG (MenH, SP O86169). ubiE mutants accumulate DMK, not MK. rraA (menG) does not encode a methyltransferase. Binds TrxA (Kumar, 2004).^[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	ubiE
Mnemonic	Ubiquinone
Synonyms	ECK3827, b3833, JW5581, yigO^[1], menG, menH, yigO
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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	86.58 minutes	MG1655: 4016878..4017633 <gbrowseImage> name=NC_000913:4016878..4017633 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3997326..3998081 <gbrowseImage> name=NC_012967:3997326..3998081 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3906547..3907302 <gbrowseImage> name=NC_012759:3906547..3907302 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3617826..3617071 <gbrowseImage> name=NC_007779:3617071..3617826 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4115798..4116553 <gbrowseImage> name=NC_010473:4115798..4116553 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
ubiE(del) (Keio:JW5581)	deletion	deletion			PMID:16738554	Shigen
ubiEG142D		G142D		In ubiE401; defective			seeded from UniProt:P0A887
ubiE778(del)::FRT	deletion		Mutagenesis rate	Decrease of Stress Induced Mutagenesis (SIM).	PMID:23224554	Parent Strain: SMR4562 Experimental Strain: SMR12242	The Mutation conferred a strong decrease in SIM, with a decrease in mutant frequency by over 90 percent of the wild type levels. See table S3 for full experimental data.
ubiE778(del)::FRT	deletion		Sensitivity to	Increased Sensitivity toward SDS-EDTA	PMID:23224554	Parent Strain: SMR4562 Experimental Strain: SMR12242	The mutation conferred an increase SDS-EDTA sensitivity. See tables S7 and S11 for experimental results.
SMR4562 ubiE778(del)::FRT yiaG-yfp FRTcatFRT	deletion		Sigma^S activity	Decrease in Sigma^S activity	PMID:23224554	Parental Strain: SMR10582 Experimental Strain: SMR12657	See table S8 for full experimental results.
CAG45114 ubiE778(del)::FRTKanFRT	deletion		Sigma^E activity	Decrease in sigma^E activity	PMID:23224554	Parental Strain: CAG45114 Experimental Strain: SMR15257	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
JW5581	Plasmid clone	Shigen	PMID:16769691 Status:cloned as old JW Primer 1:GCCGTGGATAAGTCACAAGAAAC Primer 2:CCGAACTTATAACCACGATGCAG
16G1	Kohara Phage	Genobase	PMID:3038334
1C10	Kohara Phage	Genobase	PMID:3038334
metEo-3079::Tn10	Linked marker	CAG18491 = CGSC7464^[5]	est. P1 cotransduction: 76% ^[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: 70% ^[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:EG11473	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11473	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001435	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948926	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1441	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012534	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	UbiE
Synonyms	bifunctional 2-octaprenyl-6-methoxy-1,4-benzoquinone methylase and S-adenosylmethionine:2-DMK methyltransferase^[1], B3833^[2]^[1], YigO^[2]^[1], UbiE^[2]^[1] , ECK3827, JW5581, menG, menH, yigO, b3833
Product description	2-OCTAPRENYL-METHOXY-BENZOQ-METH^[2]; bifunctional 2-octaprenyl-6-methoxy-1,4-benzoquinone methylase and S-adenosylmethionine:2-DMK methyltransferase^[3] Ubiquinone/menaquinone biosynthesis methyltransferase; SAM-dependent; (1) Ubiqinone synthesis, 2-octaprenyl-6-methoxy-1,4-benzoquinone methyltransferase; (2) Menaquinone synthesis, 2-demethylmenaquinone (DMK) methyltransferase^[4]
EC number (for enzymes)	2.1.1.-^[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: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:0009234	menaquinone biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0474	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	References	Evidence
Protein	lpdA	PMID:15690043	Experiment(s):EBI-883201
Protein	tufA	PMID:15690043	Experiment(s):EBI-883201
Protein	tufB	PMID:19402753	MALDI(Z-score):21.309723
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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 MVDKSQETTH FGFQTVAKEQ KADMVAHVFH SVASKYDVMN DLMSFGIHRL WKRFTIDCSG VRRGQTVLDL AGGTGDLTAK FSRLVGETGK VVLADINESM LKMGREKLRN IGVIGNVEYV QANAEALPFP DNTFDCITIS FGLRNVTDKD KALRSMYRVL KPGGRLLVLE FSKPIIEPLS KAYDAYSFHV LPRIGSLVAN DADSYRYLAE SIRMHPDQDT LKAMMQDAGF ESVDYYNLTA GVVALHRGYK F
Length	251
Mol. Wt	28.073 kDa
pI	8.2 (calculated)
Extinction coefficient	20,400 - 20,650 (calc based on 10 Y, 1 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
Domain	14..250	PF01209 ubiE/COQ5 methyltransferase 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=ubiE taxon=562,83333 </beststructure>

Models

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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:49176426	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948926	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012534	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A887	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11473	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11473	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948926	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001435	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1441	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	6.13E+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	Ecoli K-12	0.356+/-0.098	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.10794702	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by RNA_Seq	PMID:20671182
Protein	E. coli K-12 MG1655	3618	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	1229	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	2767	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)
ubiE-yigP-ubiB
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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_000913:4016858..4016898 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:b3833 (EcoliWiki Page)	NCBI GEO profiles for ubiE
microarray	GenExpDB:b3833 (EcoliWiki Page)	Summary of data for ubiE 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 (4016247..4016510) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ07; Well:F6^[7]
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Notes

Accessions Related to ubiE Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11473	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1441	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3833
EcoGene	EcoGene:EG11473	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001435	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012534	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
Shigella flexneri	UBIE	From SHIGELLACYC
E. coli O157	UBIE	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
Panther (EcoliWiki Page)	PTHR10108:SF24
Superfamily (EcoliWiki Page)	SUPERFAMILY:53335
Pfam (EcoliWiki Page)	PF01209 ubiE/COQ5 methyltransferase family
EcoCyc	EcoCyc:EG11473	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11473	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001435	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1441	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012534	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)
↑ ^2.0 ^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 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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

ubiE: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

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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 ubiE Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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