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Expression|

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Standard Name	selU
Gene Synonym(s)	ECK0496, b0503, JW0491, ybbB^[1], JW0491, selE, ybbB
Product Desc.	EG11768^[2]^[3] tRNA 2-selenouridine synthase, selenophosphate-dependent; replaces a sulfur atom in 2-thiouridine in tRNA with selenium; required for 5-methylaminomethyl-2-selenouridine synthesis^[4]
Product Synonyms(s)	tRNA 2-selenouridine synthase, selenophosphate-dependent^[1], B0503^[2]^[1], YbbB^[2]^[1] , ECK0496, JW0491, selE, ybbB, b0503
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s):
Regulation/Activity
Quick Links
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Notes

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YbbB has a rhodanese domain.^[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	selU
Mnemonic	Selenium
Synonyms	ECK0496, b0503, JW0491, ybbB^[1], JW0491, selE, ybbB
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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	11.41 minutes	MG1655: 530450..529356 <gbrowseImage> name=NC_000913:529356..530450 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
BW2952		NC_012759: 432115..433209 <gbrowseImage> name=NC_012759:432115..433209 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 530450..529356 <gbrowseImage> name=NC_007779:529356..530450 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 469781..468687 <gbrowseImage> name=NC_010473:468687..469781 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
ΔybbB (Keio:JW0491)	deletion	deletion			PMID:16738554	Shigen CGSC8636^[5]
ybbB::Tn5KAN-I-SceI (FB20189)	Insertion at nt 1013 in Minus orientation				PMID:15262929	E. coli Genome Project:FB20190	does not contain pKD46
ybbB::Tn5KAN-I-SceI (FB20189)	Insertion at nt 1013 in Minus orientation				PMID:15262929	E. coli Genome Project:FB20191	contains pKD46
selUC96S		C96S		No change in activity			seeded from UniProt:P33667
selUC97S		C97S		In vivo, abolishes 2-selenouridine synthase activity. In vitro, reduces activity by only 50%			seeded from UniProt:P33667
ΔybbB::kan	deletion		Biolog:respiration	unable to respire a-Ketoglutarate	PMID:16095938
ΔybbB786::kan					PMID:16738554	CGSC:103658
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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
JW0491	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCAAGAGAGACACACGGAACA Primer 2:CCCCGCGCCTTAACCCATTCCGC
8E4	Kohara Phage	Genobase	PMID:3038334
9E5	Kohara Phage	Genobase	PMID:3038334
gsk-3055::Tn10	Linked marker	CAG12154 = CGSC7341^[5]	est. P1 cotransduction: 34% ^[6] Synonyms:zbb-30-55::TnlO, zba-3055::Tn10
purK79::Tn10	Linked marker	CAG12171 = CGSC7342^[5]	est. P1 cotransduction: 43% ^[6] Synonyms:purE79::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:EG11768	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1718	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0503
ECOL199310CYC (EcoliWiki Page)	ECOL199310CYC:C0618
EcoGene	EcoGene:EG11768	Escherichia coli str. K-12 substr. MG1655
ECOO157CYC (EcoliWiki Page)	ECOO157CYC:YBBB
ASAP	ASAP:ABE-0001740	Escherichia coli str. K-12 substr. MG1655
EcoCyc (EcoliWiki Page)	ECOCYC:EG11768	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947063	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001704	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	SelU
Synonyms	tRNA 2-selenouridine synthase, selenophosphate-dependent^[1], B0503^[2]^[1], YbbB^[2]^[1] , ECK0496, JW0491, selE, ybbB, b0503
Product description	EG11768^[2]^[3] tRNA 2-selenouridine synthase, selenophosphate-dependent; replaces a sulfur atom in 2-thiouridine in tRNA with selenium; required for 5-methylaminomethyl-2-selenouridine synthesis^[4]
EC number (for enzymes)
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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:0001887	selenium metabolic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01622	P	Seeded from EcoCyc (v14.0)	complete
	GO:0001887	selenium metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017582	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008430	selenium binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017582	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008430	selenium binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0711	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
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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 MQERHTEQDY RALLIADTPI IDVRAPIEFE HGAMPAAINL PLMNNDERAA VGTCYKQQGS DAALALGHKL VAGEIRQQRM DAWRAACLQN PQGILCCARG GQRSHIVQSW LHAAGIDYPL VEGGYKALRQ TAIQATIELA QKPIVLIGGC TGSGKTLLVQ QQPNGVDLEG LARHRGSAFG RTLQPQLSQA SFENLLAAEM LKTDARQNLR LWVLEDESRM IGSNHLPECL RERMTQAAIA VVEDPFEIRL ERLNEEYFLR MHHDFTHAYG DEQGWQEYCE YLHHGLSAIK RRLGLQRYNE LAARLDAALT TQLTTGSTDG HLAWLVPLLE EYYDPMYRYQ LEKKAEKVVF RGEWAEVAEW VKAR
Length	364
Mol. Wt	41.11 kDa
pI	6.3 (calculated)
Extinction coefficient	57,870 - 58,745 (calc based on 13 Y, 7 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	6..131	PF00581 Rhodanese-like 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=ybbB 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:16128487	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947063	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001740	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P33667	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11768	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11768	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947063	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001704	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1718	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	Ecoli K-12	6.821+/-0.118	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.009140768	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	266	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	32	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	95	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)
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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_000913:530430..530470 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:b0503 (EcoliWiki Page)	NCBI GEO profiles for ybbB
microarray	GenExpDB:b0503 (EcoliWiki Page)	Summary of data for ybbB 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 (530355..530595) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ18; Well:G12^[7]
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Notes

Accessions Related to selU Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11768	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1718	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0503
EcoGene	EcoGene:EG11768	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001704	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001740	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	YBBB	From SHIGELLACYC
E. coli O157	YBBB	From ECOO157CYC
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Notes

Families

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<protect> See Help:Evolution_families for help entering or editing information in this section of EcoliWiki.

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF00581 Rhodanese-like domain
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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 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 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 ^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

selU: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 selU Expression

Notes

Links

Evolution

Homologs in Other Organisms

Notes

Families

Notes

Links

References

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