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Gene |

Product(s) |

Expression|

Evolution |

References |

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Standard Name	birA
Gene Synonym(s)	ECK3965, b3973, JW3941, bioR, dhbB^[1], dhbB
Product Desc.	Bifunctional biotin protein ligase, biotin operon repressor; biotin-[acetyl-CoA carboxylase] holoenzyme synthase; monomeric^[2]
Product Synonyms(s)	bifunctional biotin-[acetylCoA carboxylase] holoenzyme synthetase and DNA-binding transcriptional repressor, bio-5'-AMP-binding^[1], B3973^[3]^[1], BirA^[3]^[1], BioR^[3]^[1], DhbB^[3]^[1], biotin-[acetylCoA carboxylase] holoenzyme synthetase and biotin operon repressor^[3]^[1], biotin ligase^[3]^[1], BirA transcriptional repressor^[3]^[1] , bioR, dhbB, ECK3965, JW3941, b3973
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): murB^[3]
Regulation/Activity
Quick Links
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Notes

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Biotinyl-5'-AMP is the co-repressor and is also synthesized by BirA (Cronan, 1988). BirA biotinylates AccB on K122. The biotin operon is regulated by the rate of protein biotination (Cronan, 1989).^[2]

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	birA
Mnemonic	Biotin retention
Synonyms	ECK3965, b3973, JW3941, bioR, dhbB^[1], dhbB
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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	89.9 minutes	MG1655: 4171105..4172070 <gbrowseImage> name=NC_000913:4171105..4172070 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 4152693..4153658 <gbrowseImage> name=NC_012967:4152693..4153658 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 4060785..4061750 <gbrowseImage> name=NC_012759:4060785..4061750 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3463599..3462634 <gbrowseImage> name=NC_007779:3462634..3463599 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4270802..4271767 <gbrowseImage> name=NC_010473:4270802..4271767 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	AA change(s)	Phenotype: Description	Reference	Availability	Comments
birAK70E	K70E	(in strain: RDD012)			Strain variation; seeded from UniProt:P06709
birAP61A	P61A	(in strain: RDD012)			Strain variation; seeded from UniProt:P06709
birA136				CGSC:26552
			PMID:17765263
birA91				CGSC:27579
birA207				CGSC:27582
birA85				CGSC:27584
birA1				CGSC:27593
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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
JW3941	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAGGATAACACCGTGCCACT Primer 2:CCTTTTTCTGCACTACGCAGGGA
E11C11	Kohara Phage	Genobase	PMID:3038334
argE86::Tn10	Linked marker	CAG12185 = CGSC7471^[4]	est. P1 cotransduction: 51% ^[5]
thiC39::Tn10	Linked marker	CAG18500 = CGSC7472^[4]	est. P1 cotransduction: 42% ^[5] Synonyms:thi-39::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:EG10123	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10123	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000119	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948469	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0121	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013001	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	BirA
Synonyms	bifunctional biotin-[acetylCoA carboxylase] holoenzyme synthetase and DNA-binding transcriptional repressor, bio-5'-AMP-binding^[1], B3973^[3]^[1], BirA^[3]^[1], BioR^[3]^[1], DhbB^[3]^[1], biotin-[acetylCoA carboxylase] holoenzyme synthetase and biotin operon repressor^[3]^[1], biotin ligase^[3]^[1], BirA transcriptional repressor^[3]^[1] , bioR, dhbB, ECK3965, JW3941, b3973
Product description	Bifunctional biotin protein ligase, biotin operon repressor; biotin-[acetyl-CoA carboxylase] holoenzyme synthase; monomeric^[2]
EC number (for enzymes)	6.3.4.15^[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:0000166	nucleotide binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0547	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003677	DNA binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0238	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004143	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004077	biotin-(acetyl-CoA-carboxylase) ligase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004408	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004077	biotin-(acetyl-CoA-carboxylase) ligase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:6.3.4.15	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0067	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006350	transcription	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0804	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009102	biotin biosynthetic process	PMID:6456358	IMP: Inferred from Mutant Phenotype		P		complete
	GO:0006355	regulation of transcription, DNA-dependent	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004409	P	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	PMID:6456358	IC: Inferred by Curator		C		Missing: with/from
	GO:0006464	protein modification process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003142	P	Seeded from EcoCyc (v14.0)	complete
	GO:0003677	DNA binding	PMID:6456358	IDA: Inferred from Direct Assay		F		complete
	GO:0006464	protein modification process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004143	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016564	transcription repressor activity	PMID:6456358	IEP: Inferred from Expression Pattern		F		complete
	GO:0006464	protein modification process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004408	P	Seeded from EcoCyc (v14.0)	complete
	GO:0004077	biotin-(acetyl-CoA-carboxylase) ligase activity	PMID:7024555	IDA: Inferred from Direct Assay		F		complete
	GO:0016564	transcription repressor activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004409	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	nanE	PMID:15690043	Experiment(s):EBI-879022
Protein	glpB	PMID:15690043	Experiment(s):EBI-882266
Protein	nfrB	PMID:15690043	Experiment(s):EBI-882266
Protein	rplU	PMID:15690043	Experiment(s):EBI-882266
Protein	rplV	PMID:15690043	Experiment(s):EBI-882266
Protein	rpsC	PMID:15690043	Experiment(s):EBI-882266
Protein	rpsN	PMID:15690043	Experiment(s):EBI-882266
Protein	rplU	PMID:19402753	LCMS(ID Probability):99.6
Protein	rpsN	PMID:19402753	LCMS(ID Probability):99.6
Protein	nanE	PMID:19402753	MALDI(Z-score):38.087873
Protein	glpB	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
cytoplasm			From EcoCyc^[6]
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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 MKDNTVPLKL IALLANGEFH SGEQLGETLG MSRAAINKHI QTLRDWGVDV FTVPGKGYSL PEPIQLLNAK QILGQLDGGS VAVLPVIDST NQYLLDRIGE LKSGDACIAE YQQAGRGRRG RKWFSPFGAN LYLSMFWRLE QGPAAAIGLS LVIGIVMAEV LRKLGADKVR VKWPNDLYLQ DRKLAGILVE LTGKTGDAAQ IVIGAGINMA MRRVEESVVN QGWITLQEAG INLDRNTLAA MLIRELRAAL ELFEQEGLAP YLSRWEKLDN FINRPVKLII GDKEIFGISR GIDKQGALLL EQDGIIKPWM GGEISLRSAE K
Length	321
Mol. Wt	35.313 kDa
pI	8.1 (calculated)
Extinction coefficient	47,440 - 47,565 (calc based on 6 Y, 7 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	References
Domain	271..317	PF02237 Biotin protein ligase C terminal domain	PMID:19920124
Domain	83..208	PF03099 Biotin/lipoate A/B protein ligase family	PMID:19920124
Domain	8..59	PF08279 HTH 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=birA 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:16131807	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948469	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013001	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P06709	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10123	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10123	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948469	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000119	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0121	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	9.329+/-0.059	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.049222798	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	515	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	131	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	224	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)
murB
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Figure courtesy of RegulonDB

</protect>

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_000913:4171085..4171125 source=MG1655 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

</protect>

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:b3973 (EcoliWiki Page)	NCBI GEO profiles for birA
microarray	GenExpDB:b3973 (EcoliWiki Page)	Summary of data for birA 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 birA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10123	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0121	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3973
EcoGene	EcoGene:EG10123	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000119	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013001	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
Caenorhabditis briggsae	WBGene00025634 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000016275 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-030131-5333 (score: 1.000; bootstrap: 100%) ZDB-EST-050302-139 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0188109 (score: 1.000; bootstrap: 100%) DDB0188108 (score: 0.823) DDB0188228 (score: 0.498)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000029718 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000020423 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000002291 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPBC30D107c (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000028542 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	BIRA	From SHIGELLACYC
E. coli O157	BIRA	From ECOO157CYC
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Notes

Families

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<protect> See Help:Evolution_families for help entering or editing information in this section of EcoliWiki.

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF02237 Biotin protein ligase C terminal domain
Pfam (EcoliWiki Page)	PF03099 Biotin/lipoate A/B protein ligase family
Pfam (EcoliWiki Page)	PF08279 HTH domain
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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 ^1.11 ^1.12 ^1.13 ^1.14 ^1.15 ^1.16 ^1.17 ^1.18 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^3.00 ^3.01 ^3.02 ^3.03 ^3.04 ^3.05 ^3.06 ^3.07 ^3.08 ^3.09 ^3.10 ^3.11 ^3.12 ^3.13 ^3.14 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 CGSC: The Coli Genetics Stock Center
↑ ^5.0 ^5.1 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).
↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7

birA: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 birA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Notes

Families

Notes

Links

References

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