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Standard Name	cyoD
Gene Synonym(s)	ECK0423, b0429, JW0419^[1], JW0419
Product Desc.	cytochrome bo terminal oxidase subunit IV^[2]^[3]; Component of [[:Category:Complex:cytochrome bo terminal oxidase\|cytochrome bo terminal oxidase]]^[2]^[3] Cytochrome o oxidase subunit IV; cytochrome bo(3) ubiquinol oxidase subunit IV^[4]
Product Synonyms(s)	cytochrome o ubiquinol oxidase subunit IV^[1], B0429^[2]^[1], CyoD^[2]^[1] , ECK0423, JW0419, b0429
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): cyoABCDE^[2], OP00141
Regulation/Activity
Quick Links
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Notes

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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	cyoD
Mnemonic	Cytochrome o oxidase
Synonyms	ECK0423, b0429, JW0419^[1], JW0419
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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	9.63 minutes	MG1655: 447270..446941 <gbrowseImage> name=NC_000913:446941..447270 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 418749..418420 <gbrowseImage> name=NC_012967:418420..418749 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 349700..350029 <gbrowseImage> name=NC_012759:349700..350029 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 447270..446941 <gbrowseImage> name=NC_007779:446941..447270 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 386601..386272 <gbrowseImage> name=NC_010473:386272..386601 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
cyoD(del) (Keio:JW0419)	deletion	deletion			PMID:16738554	Shigen CGSC8583^[5]
cyoD::Tn5KAN-2 (FB20170)	Insertion at nt 171 in Plus orientation				PMID:15262929	E. coli Genome Project:FB20170	does not contain pKD46
cyoD(del)::kan	deletion		Biolog:respiration	unable to respire L-Alanine	PMID:16095938
cyoD(del)::kan	deletion		Biolog:respiration	unable to respire L-Asparagine	PMID:16095938
cyoD(del)::kan	deletion		Biolog:respiration	unable to respire L-Aspartate	PMID:16095938
cyoD786(del)::kan					PMID:16738554	CGSC:100478
cyoD786(del)::FRT	deletion		Mutagenesis Rate	Decrease in Stress Induced Mutagenesis (SIM).	PMID:23224554	Parent Strain: SMR4562 Experimental Strain: SMR12574	The SIM was reduced significantly with a decrease in SIM by 68 to 89 percent. See table S3 for full experimental results.
cyoD786(del)::FRT	deletion		Sensitivity to	UV sensitivity	PMID:23224554	Parent Strain: SMR4562 Experimental Strain: SMR12574	The mutation conferred and increase in UV sensitivity. See table S7 and S1 for a summary of experimental data.
SMR4562 cyoD786(del)::FRTKanFRT yiaG-yfp FRTcatFRT	Deletion & Insertion		Sigma ^S activity	Decrease in Sigma^S activity	PMID:23224554	Parent Strain: SMR10582 Experimental Strain: SMR13035	See table S8 for full experimental results.
CAG45114 cyoD786(del)::FRTKanFRT	deletion		Sigma^E activity	Decrease in Sigma^E activity	PMID:23224554	Parental Strain: CAG45114 Experimental Strain: SMR15293	See Table S11 for experimental calculations
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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
JW0419	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAGTCATTCTACCGATCACAG Primer 2:CCGTGCATCATCATGTTGTAGTT
2H5	Kohara Phage	Genobase	PMID:3038334
tsx-247::Tn10	Linked marker	CAG12148 = CGSC7337^[5]	est. P1 cotransduction: 58% ^[6]
zaj-3054::Tn10	Linked marker	CAG12017 = CGSC7339^[5]	est. P1 cotransduction: 65% ^[6] Synonyms:zba-3054::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:EG10181	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10181	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000176	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:944918	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0178	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001487	Escherichia coli str. K-12 substr. MG1655
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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	CyoD
Synonyms	cytochrome o ubiquinol oxidase subunit IV^[1], B0429^[2]^[1], CyoD^[2]^[1] , ECK0423, JW0419, b0429
Product description	cytochrome bo terminal oxidase subunit IV^[2]^[3]; Component of [[:Category:Complex:cytochrome bo terminal oxidase\|cytochrome bo terminal oxidase]]^[2]^[3] Cytochrome o oxidase subunit IV; cytochrome bo(3) ubiquinol oxidase subunit IV^[4]
EC number (for enzymes)	1.10.3.-^[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:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0997	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-1003	C	Seeded from EcoCyc (v14.0)	complete
	GO:0006810	transport	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0813	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009055	electron carrier activity	PMID:3301837	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0009060	aerobic respiration	PMID:2981797	IMP: Inferred from Mutant Phenotype		P	Seeded from EcoCyc (v14.0)	complete
	GO:0009486	cytochrome bo3 ubiquinol oxidase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012141	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009486	cytochrome bo3 ubiquinol oxidase activity	PMID:1322173	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0016020	membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0472	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005171	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0812	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-9909	C	Seeded from EcoCyc (v14.0)	complete
	GO:0022900	electron transport chain	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0249	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0560	P	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 [[:Category:Complex:cytochrome bo terminal oxidase\|cytochrome bo terminal oxidase]]	could be indirect
Protein	dmsA		PMID:19402753	MALDI(Z-score):24.292561
Protein	ynfF		PMID:19402753	MALDI(Z-score):29.448488
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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
plasma membrane	C-terminus localized to the periplasm with 3 predicted transmembrane domains	Daley et al. (2005) ^[7]
plasma membrane			From EcoCyc^[3]
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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 MSHSTDHSGA SHGSVKTYMT GFILSIILTV IPFWMVMTGA ASPAVILGTI LAMAVVQVLV HLVCFLHMNT KSDEGWNMTA FVFTVLIIAI LVVGSIWIMW NLNYNMMMH
Length	109
Mol. Wt	12.028 kDa
pI	7.2 (calculated)
Extinction coefficient	24,980 - 25,105 (calc based on 2 Y, 4 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	18..100	PF03626 Prokaryotic Cytochrome C oxidase subunit IV		PMID:19920124
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<motif_map/>

Click the image to view raw output from TMHMM.

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=cyoD 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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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:16128414	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:944918	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001487	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0ABJ6	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10181	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10181	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:944918	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000176	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0178	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	114.088+/-1.211	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.25973+/-0.0257	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by FISH	PMID:20671182
mRNA	Ecoli K-12	0.907294833	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	16777	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	4458	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	9627	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)
cyoABCDE
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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_000913:447250..447290 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

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:b0429 (EcoliWiki Page)	NCBI GEO profiles for cyoD
microarray	GenExpDB:b0429 (EcoliWiki Page)	Summary of data for cyoD 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 cyoD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10181	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0178	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0429
EcoGene	EcoGene:EG10181	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000176	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001487	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	CYOD	From SHIGELLACYC
E. coli O157	CYOD	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)	PF03626 Prokaryotic Cytochrome C oxidase subunit IV
EcoCyc	EcoCyc:EG10181	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10181	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000176	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0178	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001487	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 ^1.8 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 ^3.4 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 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).
↑ Daley, DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 1321-3 PubMed

cyoD: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 cyoD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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