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Product(s) |

Expression|

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Standard Name	csdA
Gene Synonym(s)	ECK2806, b2810, JW2781, ygdJ^[1], ygdJ
Product Desc.	G7454^[2]^[3]; Component of cysteine sulfinate desulfinase^[3] Cysteine desulfurase, stimulated by CsdE^[4]
Product Synonyms(s)	cysteine sulfinate desulfinase^[1], B2810^[2]^[1], YgdJ^[2]^[1], CsdA^[2]^[1] , ECK2806, JW2781, ygdJ, b2810
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): csdA^[2]
Regulation/Activity
Quick Links
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Notes

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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	csdA
Mnemonic	Cysteine, selenocysteine decomposition
Synonyms	ECK2806, b2810, JW2781, ygdJ^[1], ygdJ
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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	63.4 minutes	MG1655: 2941359..2942564 <gbrowseImage> name=NC_000913:2941359..2942564 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2837956..2839161 <gbrowseImage> name=NC_012967:2837956..2839161 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2828507..2829712 <gbrowseImage> name=NC_012759:2828507..2829712 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2941993..2943198 <gbrowseImage> name=NC_007779:2941993..2943198 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3035229..3036434 <gbrowseImage> name=NC_010473:3035229..3036434 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
Coding Start (SO:0000323)	MG1655	2941359	Edman degradation	PMID:9278392
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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
csdAC323A		C323A	No loss of activity			seeded from UniProt:Q46925
csdAC358A		C358A	Loss of cysteine desulfurization			seeded from UniProt:Q46925
csdAC100A		C100A	No loss of activity			seeded from UniProt:Q46925
csdAC176A		C176A	No loss of activity			seeded from UniProt:Q46925
ΔcsdA (Keio:JW2781)	deletion	deletion		PMID:16738554	Shigen CGSC10177^[5]
ΔcsdA738::kan				PMID:16738554	CGSC:100406
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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
JW2781	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAACGTTTTTAATCCCGCGCA Primer 2:CCATCCACCAATAATTCCAGCGC
9A12	Kohara Phage	Genobase	PMID:3038334
10B6	Kohara Phage	Genobase	PMID:3038334
fucP3072::Tn10	Linked marker	CAG12079 = CGSC7427^[5]	est. P1 cotransduction: 73% ^[6] Synonyms:fuc-3072::Tn10
recD1901::Tn10	Linked marker	CAG12135 = CGSC7429^[5]	est. P1 cotransduction: 72% ^[6]
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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:G7454	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13082	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004017	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947275	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2891	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009218	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	CsdA
Synonyms	cysteine sulfinate desulfinase^[1], B2810^[2]^[1], YgdJ^[2]^[1], CsdA^[2]^[1] , ECK2806, JW2781, ygdJ, b2810
Product description	G7454^[2]^[3]; Component of cysteine sulfinate desulfinase^[3] Cysteine desulfurase, stimulated by CsdE^[4]
EC number (for enzymes)	4.4.1.-^[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:0000096	sulfur amino acid metabolic process	PMID:9278392	IDA: Inferred from Direct Assay		P	Seeded from EcoCyc (v14.0)	complete
	GO:0005515	protein binding	PMID:15690043	IPI: Inferred from Physical Interaction	UniProtKB:P15877	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005515	protein binding	PMID:15901727	IPI: Inferred from Physical Interaction	UniProtKB:P0AGF2	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016783	sulfurtransferase activity	PMID:11290749	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0016829	lyase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0456	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030170	pyridoxal phosphate binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR015421	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030170	pyridoxal phosphate binding	PMID:9278392	IDA: Inferred from Direct Assay		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-1144031
Protein	groL		PMID:16606699	Experiment(s):EBI-1144031
Protein	dapE		PMID:16606699	Experiment(s):EBI-1144031
Protein	gcd		PMID:15690043	Experiment(s):EBI-894875
Protein	gcd		PMID:19402753	LCMS(ID Probability):99.6
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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 MNVFNPAQFR AQFPALQDAG VYLDSAATAL KPEAVVEATQ QFYSLSAGNV HRSQFAEAQR LTARYEAARE KVAQLLNAPD DKTIVWTRGT TESINMVAQC YARPRLQPGD EIIVSVAEHH ANLVPWLMVA QQTGAKVVKL PLNAQRLPDV DLLPELITPR SRILALGQMS NVTGGCPDLA RAITFAHSAG MVVMVDGAQG AVHFPADVQQ LDIDFYAFSG HKLYGPTGIG VLYGKSELLE AMSPWLGGGK MVHEVSFDGF TTQSAPWKLE AGTPNVAGVI GLSAALEWLA DYDINQAESW SRSLATLAED ALAKRPGFRS FRCQDSSLLA FDFAGVHHSD MVTLLAEYGI ALRAGQHCAQ PLLAELGVTG TLRASFAPYN TKSDVDALVN AVDRALELLV D
Length	401
Mol. Wt	43.233 kDa
pI	5.3 (calculated)
Extinction coefficient	47,900 - 48,400 (calc based on 10 Y, 6 W, and 4 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	21..388	PF00266 Aminotransferase class-V		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=csdA 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:16130717	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947275	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009218	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:Q46925	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7454	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13082	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947275	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004017	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2891	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	307	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	72	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	185	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_000913:2941339..2941379 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:b2810 (EcoliWiki Page)	NCBI GEO profiles for csdA
microarray	GenExpDB:b2810 (EcoliWiki Page)	Summary of data for csdA 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 (2941073..2941439) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ19; Well:E4^[7]
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Notes

Accessions Related to csdA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7454	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2891	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2810
EcoGene	EcoGene:EG13082	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004017	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009218	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
Danio rerio	YP_026169 (score: 0.053) ZDB-GENE-050327-94 (score: 1.000; bootstrap: 100%) ZDB-CDNA-050327-94 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAC11D30 (score: 1.000; bootstrap: 100%) SPCC7773c (score: 0.499)	From Inparanoid:20070104
Shigella flexneri	S3019	From SHIGELLACYC
E. coli O157	Z4127	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
Pfam (EcoliWiki Page)	PF00266 Aminotransferase class-V
Superfamily (EcoliWiki Page)	SUPERFAMILY:53383
EcoCyc	EcoCyc:G7454	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13082	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004017	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2891	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009218	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 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.
↑ ^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

csdA: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 csdA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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