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On One Page

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Gene |

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Expression|

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Standard Name	yedY
Gene Synonym(s)	ECK1967, b1971, JW1954^[1], JW1954
Product Desc.	reductase^[2]^[3] Membrane-anchored, periplasmic TMAO, DMSO reductase; activity shown in vitro; Mo-MPT form of the molybdenum cofactor; tungsten cofactor^[4]
Product Synonyms(s)	predicted reductase^[1], B1971^[2]^[1], YedY^[2]^[1] , ECK1967, JW1954, b1971
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yedY^[2]
Regulation/Activity
Quick Links
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Notes

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YedZY has other in vitro substrates, physiological role unknown; mutant had no growth defect. Verified Tat substrate: YedY has a Tat/Sec (Class II) 44 aa signal peptide (Tullman-Ercek, 2007). YedY is attached to membrane by the YedZ subunit. DmsD and TorD can act as REMPs for YedY.^[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	yedY
Mnemonic	Systematic nomenclature
Synonyms	ECK1967, b1971, JW1954^[1], JW1954
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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	43.91 minutes, 43.91 minutes	MG1655: 2037502..2038506 <gbrowseImage> name=NC_000913:2037502..2038506 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1977477..1978481 <gbrowseImage> name=NC_012967:1977477..1978481 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1929985..1930989 <gbrowseImage> name=NC_012759:1929985..1930989 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2041615..2042619 <gbrowseImage> name=NC_007779:2041615..2042619 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	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	2037634	Edman degradation	PMID:15355966
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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: Description	Reference	Availability	Comments
Strain DH10B		A319D	Nonsynonomous mutation	PMID:18245285	ASAP	This is a SNP in E. coli K-12 Strain DH10B
ΔyedY (Keio:JW1954)	deletion	deletion		PMID:16738554	Shigen
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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
JW1954	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAAAAGAATCAATTTTTAAA Primer 2:CCGAAATTCTCCCGCAAATCCAG
9G6	Kohara Phage	Genobase	PMID:3038334
zed-3069::Tn10	Linked marker	CAG18451 = CGSC7395^[5]	est. P1 cotransduction: 98% ^[6]
zef-3129::Tn10	Linked marker	CAG12099 = CGSC7397^[5]	est. P1 cotransduction: 13% ^[6] Synonyms:zee-3129::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:G7059	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG14047	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003645	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946484	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3800	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006540	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	YedY
Synonyms	predicted reductase^[1], B1971^[2]^[1], YedY^[2]^[1] , ECK1967, JW1954, b1971
Product description	reductase^[2]^[3] Membrane-anchored, periplasmic TMAO, DMSO reductase; activity shown in vitro; Mo-MPT form of the molybdenum cofactor; tungsten cofactor^[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:0009055	electron carrier activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000572	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	References	Evidence
Protein	groL	PMID:16606699	Experiment(s):EBI-1141527
Protein	dnaK	PMID:16606699	Experiment(s):EBI-1141527
Protein	groS	PMID:19402753	LCMS(ID Probability):99.6 MALDI(Z-score):7.990848
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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment	Evidence	Reference/Source
Periplasm	PMID:15355966	EchoLocation:yedY
periplasm
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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 MKKNQFLKES DVTAESVFFM KRRQVLKALG ISATALSLPH AAHADLLSWF KGNDRPPAPA GKALEFSKPA AWQNNLPLTP ADKVSGYNNF YEFGLDKADP AANAGSLKTD PWTLKISGEV AKPLTLDHDD LTRRFPLEER IYRMRCVEAW SMVVPWIGFP LHKLLALAEP TSNAKYVAFE TIYAPEQMPG QQDRFIGGGL KYPYVEGLRL DEAMHPLTLM TVGVYGKALP PQNGAPVRLI VPWKYGFKGI KSIVSIKLTR ERPPTTWNLA APDEYGFYAN VNPYVDHPRW SQATERFIGS GGILDVQRQP TLLFNGYAAQ VASLYRGLDL RENF
Length	334
Mol. Wt	37.369 kDa
pI	9.5 (calculated)
Extinction coefficient	64,860 - 64,985 (calc based on 14 Y, 8 W, and 1 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
motif	1-44	UniProt Manual:Signal Peptides	UniProt:P76342
Domain	97..269	PF00174 Oxidoreductase molybdopterin binding 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=yedY 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:16129917	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946484	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006540	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P76342	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7059	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG14047	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946484	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003645	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3800	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 MG1655	23	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	85	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	6^a	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	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)
yedY
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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_000913:2037482..2037522 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:b1971 (EcoliWiki Page)	NCBI GEO profiles for yedY
microarray	GenExpDB:b1971 (EcoliWiki Page)	Summary of data for yedY 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 (2037291..2037530) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ05; Well:A6^[7]
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Notes

Accessions Related to yedY Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7059	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3800	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1971
EcoGene	EcoGene:EG14047	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003645	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006540	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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<protect> See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
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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)	PF00174 Oxidoreductase molybdopterin binding domain
Panther (EcoliWiki Page)	PTHR19372:SF0
Superfamily (EcoliWiki Page)	SUPERFAMILY:56524
EcoCyc	EcoCyc:G7059	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG14047	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003645	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3800	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006540	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 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 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

yedY:On One Page

Quickview

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 yedY Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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