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P06709

- BIRA_ECOLI

UniProt

P06709 - BIRA_ECOLI

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Protein
Bifunctional ligase/repressor BirA
Gene
birA, bioR, dhbB, b3973, JW3941
Organism
Escherichia coli (strain K12)
Status
Reviewed - 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.4 Publications

Catalytic activityi

ATP + biotin + apo-[acetyl-CoA:carbon-dioxide ligase (ADP-forming)] = AMP + diphosphate + [acetyl-CoA:carbon-dioxide ligase (ADP-forming)].2 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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei112 – 1121Biotin
Binding sitei183 – 1831Biotin

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi22 – 4120H-T-H motif1 Publication
Add
BLAST

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. DNA binding Source: EcoliWiki
  3. biotin-[acetyl-CoA-carboxylase] ligase activity Source: EcoliWiki

GO - Biological processi

  1. biotin biosynthetic process Source: EcoliWiki
  2. protein biotinylation Source: CACAO
  3. regulation of transcription, DNA-templated Source: UniProtKB-KW
  4. 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.

Names & Taxonomyi

Protein namesi
Recommended name:
Bifunctional ligase/repressor BirA
Alternative name(s):
Biotin operon repressor
Biotin--[acetyl-CoA-carboxylase] ligase (EC:6.3.4.15)
Biotin--protein ligase
Biotin-[acetyl-CoA carboxylase] synthetase
Gene namesi
Name:birA
Synonyms:bioR, dhbB
Ordered Locus Names:b3973, JW3941
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG10123. birA.

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi52 – 521T → I: Does not affect repressor activity. 1 Publication
Mutagenesisi52 – 521T → S: 5-fold increase of repressor activity. Increases binding to DNA. 1 Publication
Mutagenesisi57 – 571G → S: Lack of repressor activity. Does not bind DNA. 1 Publication
Mutagenesisi58 – 581Y → F: Lack of repressor activity. 1 Publication
Mutagenesisi58 – 581Y → T: Does not affect repressor activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 321321Bifunctional ligase/repressor BirAUniRule annotation
PRO_0000064932Add
BLAST

Proteomic databases

PaxDbiP06709.

Expressioni

Gene expression databases

GenevestigatoriP06709.

Interactioni

Subunit structurei

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

Protein-protein interaction databases

DIPiDIP-9224N.
IntActiP06709. 7 interactions.
MINTiMINT-1254106.
STRINGi511145.b3973.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi5 – 1410
Helixi22 – 298
Helixi33 – 4513
Beta strandi51 – 533
Turni54 – 563
Beta strandi57 – 593
Helixi69 – 746
Beta strandi76 – 794
Beta strandi81 – 833
Beta strandi85 – 884
Helixi90 – 956
Helixi96 – 1005
Beta strandi106 – 1105
Beta strandi129 – 13911
Helixi143 – 1453
Helixi147 – 16317
Beta strandi170 – 1723
Turni173 – 1753
Beta strandi176 – 1794
Beta strandi182 – 19211
Beta strandi195 – 1973
Beta strandi199 – 20810
Turni216 – 2183
Turni226 – 2305
Helixi235 – 25622
Helixi259 – 2613
Helixi262 – 2687
Turni270 – 2734
Beta strandi274 – 2807
Beta strandi283 – 29210
Turni294 – 2963
Beta strandi298 – 3025
Beta strandi305 – 3117
Beta strandi313 – 3164

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1BIAX-ray2.30A1-321[»]
1BIBX-ray2.80A1-321[»]
1HXDX-ray2.40A/B1-321[»]
1K67model-A65-317[»]
2EWNX-ray2.80A/B1-321[»]
DisProtiDP00349.
ProteinModelPortaliP06709.
SMRiP06709. Positions 3-320.

Miscellaneous databases

EvolutionaryTraceiP06709.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni89 – 913Biotin bindingUniRule annotation
Regioni116 – 1183Biotin bindingUniRule annotation

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

Phylogenomic databases

eggNOGiCOG0340.
HOGENOMiHOG000041812.
KOiK03524.
OMAiADVCHVV.
OrthoDBiEOG6DNTBX.
PhylomeDBiP06709.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
HAMAPiMF_00978. Bifunct_BirA.
InterProiIPR004408. Biotin_CoA_COase_ligase.
IPR004409. Biotin_operon_repress_HTH.
IPR003142. BPL_C.
IPR004143. BPL_LipA_LipB.
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]
SUPFAMiSSF50037. SSF50037. 1 hit.
TIGRFAMsiTIGR00121. birA_ligase. 1 hit.
TIGR00122. birA_repr_reg. 1 hit.

Sequencei

Sequence statusi: Complete.

P06709-1 [UniParc]FASTAAdd to Basket

« Hide

MKDNTVPLKL IALLANGEFH SGEQLGETLG MSRAAINKHI QTLRDWGVDV    50
FTVPGKGYSL PEPIQLLNAK QILGQLDGGS VAVLPVIDST NQYLLDRIGE 100
LKSGDACIAE YQQAGRGRRG RKWFSPFGAN LYLSMFWRLE QGPAAAIGLS 150
LVIGIVMAEV LRKLGADKVR VKWPNDLYLQ DRKLAGILVE LTGKTGDAAQ 200
IVIGAGINMA MRRVEESVVN QGWITLQEAG INLDRNTLAA MLIRELRAAL 250
ELFEQEGLAP YLSRWEKLDN FINRPVKLII GDKEIFGISR GIDKQGALLL 300
EQDGIIKPWM GGEISLRSAE K 321
Length:321
Mass (Da):35,312
Last modified:January 1, 1988 - v1
Checksum:iB80AEBCEEE1BD2D4
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti61 – 611P → A in strain: RDD012.
Natural varianti70 – 701K → E in strain: RDD012.

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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.
YP_491483.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC76951; AAC76951; b3973.
BAE77342; BAE77342; BAE77342.
GeneIDi12934397.
948469.
KEGGiecj:Y75_p3219.
eco:b3973.
PATRICi32123467. VBIEscCol129921_4090.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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 .
PIRi B24029. BVECBF.
RefSeqi NP_418404.1. NC_000913.3.
YP_491483.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1BIA X-ray 2.30 A 1-321 [» ]
1BIB X-ray 2.80 A 1-321 [» ]
1HXD X-ray 2.40 A/B 1-321 [» ]
1K67 model - A 65-317 [» ]
2EWN X-ray 2.80 A/B 1-321 [» ]
DisProti DP00349.
ProteinModelPortali P06709.
SMRi P06709. Positions 3-320.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-9224N.
IntActi P06709. 7 interactions.
MINTi MINT-1254106.
STRINGi 511145.b3973.

Proteomic databases

PaxDbi P06709.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC76951 ; AAC76951 ; b3973 .
BAE77342 ; BAE77342 ; BAE77342 .
GeneIDi 12934397.
948469.
KEGGi ecj:Y75_p3219.
eco:b3973.
PATRICi 32123467. VBIEscCol129921_4090.

Organism-specific databases

EchoBASEi EB0121.
EcoGenei EG10123. birA.

Phylogenomic databases

eggNOGi COG0340.
HOGENOMi HOG000041812.
KOi K03524.
OMAi ADVCHVV.
OrthoDBi EOG6DNTBX.
PhylomeDBi P06709.

Enzyme and pathway databases

BioCyci EcoCyc:BIOTINLIG-MONOMER.
ECOL316407:JW3941-MONOMER.
MetaCyc:BIOTINLIG-MONOMER.

Miscellaneous databases

EvolutionaryTracei P06709.
PROi P06709.

Gene expression databases

Genevestigatori P06709.

Family and domain databases

Gene3Di 1.10.10.10. 1 hit.
HAMAPi MF_00978. Bifunct_BirA.
InterProi IPR004408. Biotin_CoA_COase_ligase.
IPR004409. Biotin_operon_repress_HTH.
IPR003142. BPL_C.
IPR004143. BPL_LipA_LipB.
IPR013196. HTH_11.
IPR008988. Transcriptional_repressor_C.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view ]
PANTHERi PTHR12835. PTHR12835. 1 hit.
Pfami PF02237. BPL_C. 1 hit.
PF03099. BPL_LplA_LipB. 1 hit.
PF08279. HTH_11. 1 hit.
[Graphical view ]
SUPFAMi SSF50037. SSF50037. 1 hit.
TIGRFAMsi TIGR00121. birA_ligase. 1 hit.
TIGR00122. birA_repr_reg. 1 hit.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Nucleotide sequence of the birA gene encoding the biotin operon repressor and biotin holoenzyme synthetase functions of Escherichia coli."
    Howard P.K., Shaw J., Otsuka A.J.
    Gene 35:321-331(1985) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "DNA-binding and enzymatic domains of the bifunctional biotin operon repressor (BirA) of Escherichia coli."
    Buoncristiani M.R., Howard P.K., Otsuka A.J.
    Gene 44:255-261(1986) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. "Analysis of the Escherichia coli genome. IV. DNA sequence of the region from 89.2 to 92.8 minutes."
    Blattner F.R., Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L.
    Nucleic Acids Res. 21:5408-5417(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  5. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  6. "Cloning and identification of the Escherichia coli murB DNA sequence, which encodes UDP-N-acetylenolpyruvoylglucosamine reductase."
    Pucci M.J., Discotto L.F., Dougherty T.J.
    J. Bacteriol. 174:1690-1693(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-76.
    Strain: RDD012.
  7. "Cloning, sequencing, and expression of the pantothenate kinase (coaA) gene of Escherichia coli."
    Song W.-J., Jackowski S.
    J. Bacteriol. 174:6411-6417(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 226-321.
  8. "Purification and properties of the biotin repressor. A bifunctional protein."
    Eisenberg M.A., Prakash O., Hsiung S.C.
    J. Biol. Chem. 257:15167-15173(1982) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBUNIT.
  9. "The E. coli bio operon: transcriptional repression by an essential protein modification enzyme."
    Cronan J.E. Jr.
    Cell 58:427-429(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  10. "Kinetics of biotinyl-5'-adenylate synthesis catalyzed by the Escherichia coli repressor of biotin biosynthesis and the stability of the enzyme-product complex."
    Xu Y., Beckett D.
    Biochemistry 33:7354-7360(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY.
  11. "Coupling of protein assembly and DNA binding: biotin repressor dimerization precedes biotin operator binding."
    Streaker E.D., Beckett D.
    J. Mol. Biol. 325:937-948(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DNA-BINDING, SUBUNIT.
  12. "The wing of a winged helix-turn-helix transcription factor organizes the active site of BirA, a bifunctional repressor/ligase."
    Chakravartty V., Cronan J.E.
    J. Biol. Chem. 288:36029-36039(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: DOMAIN, MUTAGENESIS OF THR-52; GLY-57 AND TYR-58.
    Strain: K12.
  13. "Protein:protein interactions in control of a transcriptional switch."
    Adikaram P.R., Beckett D.
    J. Mol. Biol. 425:4584-4594(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: ENZYME REGULATION, SUBUNIT, INTERACTION WITH BCCP.
  14. "Escherichia coli biotin holoenzyme synthetase/bio repressor crystal structure delineates the biotin- and DNA-binding domains."
    Wilson K.P., Shewchuk L.M., Brennan R.G., Otsuka A.J., Matthews B.W.
    Proc. Natl. Acad. Sci. U.S.A. 89:9257-9261(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) IN COMPLEX WITH BIOTIN, DOMAIN.
  15. "Corepressor-induced organization and assembly of the biotin repressor: a model for allosteric activation of a transcriptional regulator."
    Weaver L.H., Kwon K., Beckett D., Matthews B.W.
    Proc. Natl. Acad. Sci. U.S.A. 98:6045-6050(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS) IN COMPLEX WITH BIOTIN, SUBUNIT, DOMAIN.
  16. "Co-repressor induced order and biotin repressor dimerization: a case for divergent followed by convergent evolution."
    Wood Z.A., Weaver L.H., Brown P.H., Beckett D., Matthews B.W.
    J. Mol. Biol. 357:509-523(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.80 ANGSTROMS) IN COMPLEX WITH BIOTINOL-5'-AMP, SUBUNIT, DOMAIN.

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: May 14, 2014
This is version 143 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

External Data

Dasty 3

Similar proteinsi