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Protein

Bifunctional ligase/repressor BirA

Gene

birA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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 + apo-[acetyl-CoA:carbon-dioxide ligase (ADP-forming)] = AMP + diphosphate + [acetyl-CoA:carbon-dioxide ligase (ADP-forming)].UniRule annotation2 Publications

Enzyme 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

  • ATP binding Source: UniProtKB-HAMAP
  • biotin-[acetyl-CoA-carboxylase] ligase activity Source: EcoliWiki
  • DNA binding Source: EcoliWiki

GO - Biological processi

  • biotin biosynthetic process Source: EcoliWiki
  • protein biotinylation Source: CACAO
  • regulation of transcription, DNA-templated Source: UniProtKB-HAMAP
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Ligase, Repressor

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

ATP-binding, Biotin, DNA-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciEcoCyc:BIOTINLIG-MONOMER.
ECOL316407:JW3941-MONOMER.
MetaCyc:BIOTINLIG-MONOMER.
BRENDAi6.3.4.15. 2026.

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.

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.

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

Protein-protein interaction databases

BioGridi4263391. 269 interactors.
DIPiDIP-9224N.
IntActiP06709. 7 interactors.
MINTiMINT-1254106.
STRINGi511145.b3973.

Chemistry databases

BindingDBiP06709.

Structurei

Secondary structure

1321
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi5 – 14Combined sources10
Helixi22 – 29Combined sources8
Helixi33 – 45Combined sources13
Beta strandi51 – 53Combined sources3
Turni54 – 56Combined sources3
Beta strandi57 – 59Combined sources3
Helixi69 – 74Combined sources6
Beta strandi76 – 79Combined sources4
Beta strandi81 – 83Combined sources3
Beta strandi85 – 88Combined sources4
Helixi90 – 95Combined sources6
Helixi96 – 100Combined sources5
Beta strandi106 – 110Combined sources5
Beta strandi129 – 139Combined sources11
Helixi143 – 145Combined sources3
Helixi147 – 163Combined sources17
Beta strandi170 – 172Combined sources3
Turni173 – 175Combined sources3
Beta strandi176 – 179Combined sources4
Beta strandi182 – 192Combined sources11
Beta strandi195 – 197Combined sources3
Beta strandi199 – 208Combined sources10
Turni216 – 218Combined sources3
Turni226 – 230Combined sources5
Helixi235 – 256Combined sources22
Helixi259 – 261Combined sources3
Helixi262 – 268Combined sources7
Turni270 – 273Combined sources4
Beta strandi274 – 280Combined sources7
Beta strandi283 – 292Combined sources10
Turni294 – 296Combined sources3
Beta strandi298 – 302Combined sources5
Beta strandi305 – 311Combined sources7
Beta strandi313 – 316Combined sources4

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...

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
Contains 1 BPL/LPL catalytic domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiENOG4105HJX. Bacteria.
COG0340. LUCA.
COG1654. LUCA.
HOGENOMiHOG000041812.
InParanoidiP06709.
KOiK03524.
OMAiDVCHVVL.
PhylomeDBiP06709.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
HAMAPiMF_00978. Bifunct_BirA. 1 hit.
InterProiIPR030855. 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.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PANTHERiPTHR12835. PTHR12835. 1 hit.
PfamiPF02237. BPL_C. 1 hit.
PF03099. BPL_LplA_LipB. 1 hit.
PF08279. HTH_11. 1 hit.
[Graphical view]
SUPFAMiSSF46785. SSF46785. 1 hit.
SSF50037. SSF50037. 1 hit.
TIGRFAMsiTIGR00121. birA_ligase. 1 hit.
TIGR00122. birA_repr_reg. 1 hit.
PROSITEiPS51733. BPL_LPL_CATALYTIC. 1 hit.
[Graphical view]

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.
PATRICi32123467. VBIEscCol129921_4090.

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.
MINTiMINT-1254106.
STRINGi511145.b3973.

Chemistry databases

BindingDBiP06709.
ChEMBLiCHEMBL3559644.

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.
PATRICi32123467. VBIEscCol129921_4090.

Organism-specific databases

EchoBASEiEB0121.
EcoGeneiEG10123. birA.

Phylogenomic databases

eggNOGiENOG4105HJX. Bacteria.
COG0340. LUCA.
COG1654. LUCA.
HOGENOMiHOG000041812.
InParanoidiP06709.
KOiK03524.
OMAiDVCHVVL.
PhylomeDBiP06709.

Enzyme and pathway databases

BioCyciEcoCyc:BIOTINLIG-MONOMER.
ECOL316407:JW3941-MONOMER.
MetaCyc:BIOTINLIG-MONOMER.
BRENDAi6.3.4.15. 2026.

Miscellaneous databases

EvolutionaryTraceiP06709.
PROiP06709.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
HAMAPiMF_00978. Bifunct_BirA. 1 hit.
InterProiIPR030855. 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.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PANTHERiPTHR12835. PTHR12835. 1 hit.
PfamiPF02237. BPL_C. 1 hit.
PF03099. BPL_LplA_LipB. 1 hit.
PF08279. HTH_11. 1 hit.
[Graphical view]
SUPFAMiSSF46785. SSF46785. 1 hit.
SSF50037. SSF50037. 1 hit.
TIGRFAMsiTIGR00121. birA_ligase. 1 hit.
TIGR00122. birA_repr_reg. 1 hit.
PROSITEiPS51733. BPL_LPL_CATALYTIC. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiBIRA_ECOLI
AccessioniPrimary (citable) accession number: P06709
Secondary accession number(s): Q2M8R4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 1, 1988
Last sequence update: January 1, 1988
Last modified: November 2, 2016
This is version 161 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.