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Protein

Bifunctional ligase/repressor BirA

Gene

birA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Acts both as a biotin--[acetyl-CoA-carboxylase] ligase and a biotin-operon repressor. In the presence of ATP, BirA activates biotin to form the BirA-biotinyl-5'-adenylate (BirA-bio-5'-AMP or holoBirA) complex. HoloBirA can either transfer the biotinyl moiety to the biotin carboxyl carrier protein (BCCP) subunit of acetyl-CoA carboxylase, or bind to the biotin operator site and inhibit transcription of the operon.UniRule annotation4 Publications

Catalytic activityi

ATP + biotin + [biotin carboxyl-carrier protein]-L-lysine = AMP + diphosphate + [biotin carboxyl-carrier protein]-N6-biotinyl-L-lysine.UniRule annotation2 Publications

Activity regulationi

The switch between the enzymatic activity and the repressor activity is regulated by cellular demand for biotin. The switch occurs by swapping of protein interaction partners by holoBirA. In conditions of high biotin demand, holoBirA associates with apoBCCP to transfer biotin. In conditions of low biotin demand, holoBirA dimerizes, binds DNA and represses transcription of the biotin operon.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei112BiotinUniRule annotation2 Publications1
Binding sitei183BiotinUniRule annotation2 Publications1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi22 – 41H-T-H motifUniRule annotationAdd BLAST20

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionDNA-binding, Ligase, Repressor
Biological processTranscription, Transcription regulation
LigandATP-binding, Biotin, Nucleotide-binding

Enzyme and pathway databases

BioCyciEcoCyc:BIOTINLIG-MONOMER
MetaCyc:BIOTINLIG-MONOMER
BRENDAi6.3.4.15 2026

Protein family/group databases

MoonProtiP06709

Names & Taxonomyi

Protein namesi
Recommended name:
Bifunctional ligase/repressor BirAUniRule annotation
Alternative name(s):
Biotin operon repressorUniRule annotation
Biotin--[acetyl-CoA-carboxylase] ligaseUniRule annotation (EC:6.3.4.15UniRule annotation)
Biotin--protein ligaseUniRule annotation
Biotin-[acetyl-CoA carboxylase] synthetaseUniRule annotation
Gene namesi
Name:birAUniRule annotation
Synonyms:bioR, dhbB
Ordered Locus Names:b3973, JW3941
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10123 birA

Subcellular locationi

GO - Cellular componenti

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi52T → I: Does not affect repressor activity. 1 Publication1
Mutagenesisi52T → S: 5-fold increase of repressor activity. Increases binding to DNA. 1 Publication1
Mutagenesisi57G → S: Lack of repressor activity. Does not bind DNA. 1 Publication1
Mutagenesisi58Y → F: Lack of repressor activity. 1 Publication1
Mutagenesisi58Y → T: Does not affect repressor activity. 1 Publication1

Chemistry databases

ChEMBLiCHEMBL3559644
DrugBankiDB04651 BIOTINOL-5-AMP

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000649321 – 321Bifunctional ligase/repressor BirAAdd BLAST321

Proteomic databases

PaxDbiP06709
PRIDEiP06709

Interactioni

Subunit structurei

Monomer in solution. Interacts with BCCP. Homodimerizes to bind DNA. Interaction with the corepressor bio-5'-AMP increases dimerization.6 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
nanEP0A7612EBI-545740,EBI-561432

GO - Molecular functioni

Protein-protein interaction databases

BioGridi4263391, 269 interactors
DIPiDIP-9224N
IntActiP06709, 7 interactors
STRINGi316385.ECDH10B_4162

Chemistry databases

BindingDBiP06709

Structurei

Secondary structure

1321
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

DisProtiDP00349
ProteinModelPortaliP06709
SMRiP06709
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP06709

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini67 – 254BPL/LPL catalyticPROSITE-ProRule annotationAdd BLAST188

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni89 – 91Biotin binding3
Regioni116 – 118Biotin binding3

Domaini

Contains an N-terminal helix-turn-helix DNA-binding domain, connected via a linker to the central catalytic domain and the C-terminal domain, which plays roles in dimerization, catalytic function and DNA binding. The N-terminal domain is required for both ligase and repressor activities. It may orient the active site and thereby play an important role in enzymatic activity.4 Publications

Sequence similaritiesi

Belongs to the biotin--protein ligase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105HJX Bacteria
COG0340 LUCA
COG1654 LUCA
HOGENOMiHOG000041812
InParanoidiP06709
KOiK03524
PhylomeDBiP06709

Family and domain databases

CDDicd16442 BPL, 1 hit
Gene3Di1.10.10.10, 1 hit
HAMAPiMF_00978 Bifunct_BirA, 1 hit
InterProiView protein in InterPro
IPR030855 Bifunct_BirA
IPR004408 Biotin_CoA_COase_ligase
IPR004409 Biotin_operon_repress_HTH
IPR003142 BPL_C
IPR004143 BPL_LPL_catalytic
IPR013196 HTH_11
IPR008988 Transcriptional_repressor_C
IPR036388 WH-like_DNA-bd_sf
IPR036390 WH_DNA-bd_sf
PANTHERiPTHR12835:SF5 PTHR12835:SF5, 1 hit
PfamiView protein in Pfam
PF02237 BPL_C, 1 hit
PF03099 BPL_LplA_LipB, 1 hit
PF08279 HTH_11, 1 hit
SUPFAMiSSF46785 SSF46785, 1 hit
SSF50037 SSF50037, 1 hit
TIGRFAMsiTIGR00121 birA_ligase, 1 hit
TIGR00122 birA_repr_reg, 1 hit
PROSITEiView protein in PROSITE
PS51733 BPL_LPL_CATALYTIC, 1 hit

Sequencei

Sequence statusi: Complete.

P06709-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MKDNTVPLKL IALLANGEFH SGEQLGETLG MSRAAINKHI QTLRDWGVDV
60 70 80 90 100
FTVPGKGYSL PEPIQLLNAK QILGQLDGGS VAVLPVIDST NQYLLDRIGE
110 120 130 140 150
LKSGDACIAE YQQAGRGRRG RKWFSPFGAN LYLSMFWRLE QGPAAAIGLS
160 170 180 190 200
LVIGIVMAEV LRKLGADKVR VKWPNDLYLQ DRKLAGILVE LTGKTGDAAQ
210 220 230 240 250
IVIGAGINMA MRRVEESVVN QGWITLQEAG INLDRNTLAA MLIRELRAAL
260 270 280 290 300
ELFEQEGLAP YLSRWEKLDN FINRPVKLII GDKEIFGISR GIDKQGALLL
310 320
EQDGIIKPWM GGEISLRSAE K
Length:321
Mass (Da):35,312
Last modified:January 1, 1988 - v1
Checksum:iB80AEBCEEE1BD2D4
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural varianti61P → A in strain: RDD012. 1
Natural varianti70K → E in strain: RDD012. 1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M10123 Genomic DNA Translation: AAA23520.1
M15820 Genomic DNA Translation: AAA23521.1
L14557 Genomic DNA Translation: AAA24186.1
U00006 Genomic DNA Translation: AAC43075.1
U00096 Genomic DNA Translation: AAC76951.1
AP009048 Genomic DNA Translation: BAE77342.1
PIRiB24029 BVECBF
RefSeqiNP_418404.1, NC_000913.3
WP_000654630.1, NZ_LN832404.1

Genome annotation databases

EnsemblBacteriaiAAC76951; AAC76951; b3973
BAE77342; BAE77342; BAE77342
GeneIDi948469
KEGGiecj:JW3941
eco:b3973
PATRICifig|1411691.4.peg.2735

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M10123 Genomic DNA Translation: AAA23520.1
M15820 Genomic DNA Translation: AAA23521.1
L14557 Genomic DNA Translation: AAA24186.1
U00006 Genomic DNA Translation: AAC43075.1
U00096 Genomic DNA Translation: AAC76951.1
AP009048 Genomic DNA Translation: BAE77342.1
PIRiB24029 BVECBF
RefSeqiNP_418404.1, NC_000913.3
WP_000654630.1, NZ_LN832404.1

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1BIAX-ray2.30A1-321[»]
1BIBX-ray2.80A1-321[»]
1HXDX-ray2.40A/B1-321[»]
1K67model-A65-317[»]
2EWNX-ray2.80A/B1-321[»]
4WF2X-ray2.31A1-321[»]
DisProtiDP00349
ProteinModelPortaliP06709
SMRiP06709
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4263391, 269 interactors
DIPiDIP-9224N
IntActiP06709, 7 interactors
STRINGi316385.ECDH10B_4162

Chemistry databases

BindingDBiP06709
ChEMBLiCHEMBL3559644
DrugBankiDB04651 BIOTINOL-5-AMP

Protein family/group databases

MoonProtiP06709

Proteomic databases

PaxDbiP06709
PRIDEiP06709

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76951; AAC76951; b3973
BAE77342; BAE77342; BAE77342
GeneIDi948469
KEGGiecj:JW3941
eco:b3973
PATRICifig|1411691.4.peg.2735

Organism-specific databases

EchoBASEiEB0121
EcoGeneiEG10123 birA

Phylogenomic databases

eggNOGiENOG4105HJX Bacteria
COG0340 LUCA
COG1654 LUCA
HOGENOMiHOG000041812
InParanoidiP06709
KOiK03524
PhylomeDBiP06709

Enzyme and pathway databases

BioCyciEcoCyc:BIOTINLIG-MONOMER
MetaCyc:BIOTINLIG-MONOMER
BRENDAi6.3.4.15 2026

Miscellaneous databases

EvolutionaryTraceiP06709
PROiPR:P06709

Family and domain databases

CDDicd16442 BPL, 1 hit
Gene3Di1.10.10.10, 1 hit
HAMAPiMF_00978 Bifunct_BirA, 1 hit
InterProiView protein in InterPro
IPR030855 Bifunct_BirA
IPR004408 Biotin_CoA_COase_ligase
IPR004409 Biotin_operon_repress_HTH
IPR003142 BPL_C
IPR004143 BPL_LPL_catalytic
IPR013196 HTH_11
IPR008988 Transcriptional_repressor_C
IPR036388 WH-like_DNA-bd_sf
IPR036390 WH_DNA-bd_sf
PANTHERiPTHR12835:SF5 PTHR12835:SF5, 1 hit
PfamiView protein in Pfam
PF02237 BPL_C, 1 hit
PF03099 BPL_LplA_LipB, 1 hit
PF08279 HTH_11, 1 hit
SUPFAMiSSF46785 SSF46785, 1 hit
SSF50037 SSF50037, 1 hit
TIGRFAMsiTIGR00121 birA_ligase, 1 hit
TIGR00122 birA_repr_reg, 1 hit
PROSITEiView protein in PROSITE
PS51733 BPL_LPL_CATALYTIC, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiBIRA_ECOLI
AccessioniPrimary (citable) accession number: P06709
Secondary accession number(s): Q2M8R4
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 1, 1988
Last sequence update: January 1, 1988
Last modified: November 7, 2018
This is version 174 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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