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Standard Name	cyaY
Gene Synonym(s)	ECK3801, b3807, JW3779^[1], JW3779
Product Desc.	iron-binding frataxin homolog^[2]^[3] Iron donor during [Fe-S] cluster assembly on IscU; iron-binding and oxidizing protein^[4]
Product Synonyms(s)	frataxin, iron-binding and oxidizing protein^[1], B3807^[2]^[1], CyaY^[2]^[1] , ECK3801, JW3779, b3807
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): cyaY^[2]
Regulation/Activity
Quick Links
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Notes

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CyaY forms iron-promoted aggregates in vitro, but not at physiological salt concentrations. There is no iron accumulation or oxidative stress defect in cyaY mutant or overproducing strains. cyaY is expressed, as measured using LacZ fusions (Trotot, 1996). Frataxin-related. A dubious 116 codon ORF named cyaX on the opposite strand of cyaY was dropped (Aiba, 1984).^[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	cyaY
Mnemonic	Cyclase, adenylate
Synonyms	ECK3801, b3807, JW3779^[1], JW3779
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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	86.04 minutes	MG1655: 3992082..3991762 <gbrowseImage> name=NC_000913:3991762..3992082 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3955889..3955569 <gbrowseImage> name=NC_012967:3955569..3955889 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3881431..3881751 <gbrowseImage> name=NC_012759:3881431..3881751 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3642622..3642942 <gbrowseImage> name=NC_007779:3642622..3642942 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4091002..4090682 <gbrowseImage> name=NC_010473:4090682..4091002 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
ΔcyaY (Keio:JW3779)	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
JW3779	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAACGACAGTGAATTTCATCG Primer 2:CCGCGGAAACTGACTGTTTCACC
12G1	Kohara Phage	Genobase	PMID:3038334
ilvD500::Tn10	Linked marker	CAG18431 = CGSC7462^[5]	est. P1 cotransduction: 20% ^[6] Synonyms:ilv500::Tn10
metEo-3079::Tn10	Linked marker	CAG18491 = CGSC7464^[5]	est. P1 cotransduction: 55% ^[6] Synonyms:metE3079::Tn10 nnnThe Tn10 in CAG13491 is inserted in the metE regulatory region, but causes a Met- phenotype.
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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:EG11653	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11653	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001597	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947754	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1606	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012435	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	CyaY
Synonyms	frataxin, iron-binding and oxidizing protein^[1], B3807^[2]^[1], CyaY^[2]^[1] , ECK3801, JW3779, b3807
Product description	iron-binding frataxin homolog^[2]^[3] Iron donor during [Fe-S] cluster assembly on IscU; iron-binding and oxidizing protein^[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:0005737	cytoplasm	PMID:17650323	IDA: Inferred from Direct Assay		C	Fig. 5 and Fig. 6.	complete
	GO:0016226	iron-sulfur cluster assembly	PMID:16603772	IDA: Inferred from Direct Assay		P	In vitro iron donor to IscU in the presence of IscS and cysteine (Fig. 6).	complete
	GO:0016226	iron-sulfur cluster assembly	PMID:17727661	IGI: Inferred from Genetic Interaction	UniProtKB:Q07540	P	Complementation of a yeast strain depleted of the endogenous frataxin protein (yfh1Delta).	complete
	GO:0008199	ferric iron binding	PMID:16603772	IDA: Inferred from Direct Assay		F	Strong binding of Fe(+3) and weak binding of Fe(+2).	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	dnaN		PMID:19402753	MALDI(Z-score):24.136689
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Notes

CyaY is proposed to be an iron chaperone that sequesters free, redox active Fe.^[7] In vitro, CyaY can bind iron and prevents the formation of hydroxyl free radicals in the presence of hydrogen peroxide (Fig. 5 of PMID:17244611).

Localization

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

Compartment	Description	Evidence	Reference/Source	Notes
Cytoplasm		Western blot analysis of soluble and membrane fractions (Fig. 5). Visualization of an overproduced CyaY-Gfp fusion protein (Fig. 6).	PMID:17650323
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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 MNDSEFHRLA DQLWLTIEER LDDWDGDSDI DCEINGGVLT ITFENGSKII INRQEPLHQV WLATKQGGYH FDLKGDEWIC DRSGETFWDL LEQAATQQAG ETVSFR
Length	106
Mol. Wt	12.231 kDa
pI	4.1 (calculated)
Extinction coefficient	28,990 - 29,240 (calc based on 1 Y, 5 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	1..106	PF01491 Frataxin-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=cyaY taxon=562,83333 </beststructure>

Models

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Structure figures

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Notes

Gene Product Resources

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Resource type	Source	Notes/Reference
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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:16131659	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947754	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012435	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P27838	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11653	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11653	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947754	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001597	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1606	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	3.15E+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	52.261+/-0.535	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.140625	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	4479	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	963	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	1815	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)
cyaY
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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_000913:3992062..3992102 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:b3807 (EcoliWiki Page)	NCBI GEO profiles for cyaY
microarray	GenExpDB:b3807 (EcoliWiki Page)	Summary of data for cyaY 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 cyaY Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11653	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1606	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3807
EcoGene	EcoGene:EG11653	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001597	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012435	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
Oryza gramene	Q5ZAV6 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPCC11833c (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	CYAY	From SHIGELLACYC
E. coli O157	CYAY	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)	PF01491 Frataxin-like domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:55387
EcoCyc	EcoCyc:EG11653	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11653	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001597	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1606	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012435	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).
↑ Ding, H et al. (2007) Distinct iron binding property of two putative iron donors for the iron-sulfur cluster assembly: IscA and the bacterial frataxin ortholog CyaY under physiological and oxidative stress conditions. J. Biol. Chem. 282 7997-8004 PubMed

cyaY: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 cyaY Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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