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On One Page

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Gene |

Product(s) |

Expression|

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References |

Quickview

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Standard Name	csdE
Gene Synonym(s)	ygdK, ECK2807, b2811, JW2782^[1]^[2], JW2782
Product Desc.	CsdE^[2]^[3]; Component of cysteine sulfinate desulfinase^[3] Binds and stimulates CsdA activity^[4]
Product Synonyms(s)	predicted Fe-S metabolism protein^[1], B2811^[2]^[1], YgdK^[2]^[1] , ECK2807, JW2782, ygdK, b2811
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): csdA^[2]
Regulation/Activity
Quick Links
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</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

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CdsE is homologous to SufE. csdAE are a multicopy suppressor of iscS.^[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	csdE
Mnemonic	Cysteine, selenocysteine decomposition
Synonyms	ygdK, ECK2807, b2811, JW2782^[1]^[2], JW2782
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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	63.42 minutes	MG1655: 2942564..2943007 <gbrowseImage> name=NC_000913:2942564..2943007 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2839161..2839604 <gbrowseImage> name=NC_012967:2839161..2839604 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2829712..2830155 <gbrowseImage> name=NC_012759:2829712..2830155 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2943198..2943641 <gbrowseImage> name=NC_007779:2943198..2943641 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
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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
ΔcsdE739::kan					PMID:16738554	CGSC:106150
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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
	Plasmid clone	Shigen	PMID:16769691 Status: Primer 1: Primer 2:
9A12	Kohara Phage	Genobase	PMID:3038334
10B6	Kohara Phage	Genobase	PMID:3038334
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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:G7455	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13083	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004018	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947274	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2892	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009220	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	YgdK
Synonyms	predicted Fe-S metabolism protein^[1], B2811^[2]^[1], YgdK^[2]^[1] , ECK2807, JW2782, ygdK, b2811
Product description	CsdE^[2]^[3]; Component of cysteine sulfinate desulfinase^[3] Binds and stimulates CsdA activity^[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:0005515	protein binding	PMID:15901727	IPI: Inferred from Physical Interaction	UniProtKB:Q46925	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005515	protein binding	PMID:16606699	IPI: Inferred from Physical Interaction	UniProtKB:P18843	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005515	protein binding	PMID:20054882	IPI: Inferred from Physical Interaction	UniProtKB:Q46927	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 cysteine sulfinate desulfinase	could be indirect
Protein	nadE		PMID:16606699	Experiment(s):EBI-1144036
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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 MTNPQFAGHP FGTTVTAETL RNTFAPLTQW EDKYRQLIML GKQLPALPDE LKAQAKEIAG CENRVWLGYT VAENGKMHFF GDSEGRIVRG LLAVLLTAVE GKTAAELQAQ SPLALFDELG LRAQLSASRS QGLNALSEAI IAATKQV
Length	147
Mol. Wt	15.94 kDa
pI	6.3 (calculated)
Extinction coefficient	13,980 - 14,105 (calc based on 2 Y, 2 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
Domain	20..145	PF02657 Fe-S metabolism associated 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=csdE 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:16130718	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947274	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009220	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AGF2	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7455	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13083	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947274	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004018	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2892	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 MG1655	813	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	181	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	370	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)
csdA
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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_000913:2942544..2942584 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:b2811 (EcoliWiki Page)	NCBI GEO profiles for csdE
microarray	GenExpDB:b2811 (EcoliWiki Page)	Summary of data for csdE 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 csdE Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7455	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2892	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2811
EcoGene	EcoGene:EG13083	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004018	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009220	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	ENSANGP00000000033 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Oryza gramene	Q6K258 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	YGDK	From SHIGELLACYC
E. coli O157	YGDK	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:82649
Pfam (EcoliWiki Page)	PF02657 Fe-S metabolism associated domain
EcoCyc	EcoCyc:G7455	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13083	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004018	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2892	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009220	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 ^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 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.

csdE: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 csdE Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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