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P06709

- BIRA_ECOLI

UniProt

P06709 - BIRA_ECOLI

Protein

Bifunctional ligase/repressor BirA

Gene

birA

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 144 (01 Oct 2014)
      Sequence version 1 (01 Jan 1988)
      Previous versions | rss
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    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 PublicationsUniRule annotation

    Catalytic activityi

    ATP + biotin + apo-[acetyl-CoA:carbon-dioxide ligase (ADP-forming)] = AMP + diphosphate + [acetyl-CoA:carbon-dioxide ligase (ADP-forming)].2 PublicationsUniRule annotation

    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 – 1121Biotin2 PublicationsUniRule annotation
    Binding sitei183 – 1831Biotin2 PublicationsUniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    DNA bindingi22 – 4120H-T-H motifUniRule annotationAdd
    BLAST

    GO - Molecular functioni

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

    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 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 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 BirAPRO_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.6 Publications

    Protein-protein interaction databases

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

    Structurei

    Secondary structure

    1
    321
    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.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP06709.

    Family & Domainsi

    Region

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

    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

    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

    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: October 1, 2014
    This is version 144 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