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Protein

Biotin synthase

Gene

bioB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical-based mechanism.1 Publication

Catalytic activityi

Dethiobiotin + sulfur-(sulfur carrier) + 2 S-adenosyl-L-methionine + 2 reduced [2Fe-2S] ferredoxin = biotin + (sulfur carrier) + 2 L-methionine + 2 5'-deoxyadenosine + 2 oxidized [2Fe-2S] ferredoxin.3 Publications

Cofactori

Protein has several cofactor binding sites:
  • [4Fe-4S] cluster1 PublicationNote: Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine.1 Publication
  • [2Fe-2S] cluster1 PublicationNote: Binds 1 [2Fe-2S] cluster. The cluster is coordinated with 3 cysteines and 1 arginine.1 Publication

Kineticsi

  1. KM=2 µM for dethiobiotin1 Publication

    Pathway: biotin biosynthesis

    This protein is involved in step 2 of the subpathway that synthesizes biotin from 7,8-diaminononanoate.
    Proteins known to be involved in the 2 steps of the subpathway in this organism are:
    1. ATP-dependent dethiobiotin synthetase BioD 1 (bioD1), ATP-dependent dethiobiotin synthetase BioD (ynfK), ATP-dependent dethiobiotin synthetase BioD (bioD), ATP-dependent dethiobiotin synthetase BioD 2 (bioD2)
    2. Biotin synthase (bioB), Biotin synthase (bioB)
    This subpathway is part of the pathway biotin biosynthesis, which is itself part of Cofactor biosynthesis.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes biotin from 7,8-diaminononanoate, the pathway biotin biosynthesis and in Cofactor biosynthesis.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi53 – 531Iron-sulfur 1 (4Fe-4S-S-AdoMet)
    Metal bindingi57 – 571Iron-sulfur 1 (4Fe-4S-S-AdoMet)
    Metal bindingi60 – 601Iron-sulfur 1 (4Fe-4S-S-AdoMet)
    Metal bindingi97 – 971Iron-sulfur 2 (2Fe-2S)
    Metal bindingi128 – 1281Iron-sulfur 2 (2Fe-2S)
    Metal bindingi188 – 1881Iron-sulfur 2 (2Fe-2S)
    Metal bindingi260 – 2601Iron-sulfur 2 (2Fe-2S)

    GO - Molecular functioni

    • 2 iron, 2 sulfur cluster binding Source: EcoCyc
    • 4 iron, 4 sulfur cluster binding Source: EcoCyc
    • biotin synthase activity Source: EcoCyc
    • iron ion binding Source: UniProtKB-HAMAP

    GO - Biological processi

    • biotin biosynthetic process Source: EcoCyc
    Complete GO annotation...

    Keywords - Molecular functioni

    Transferase

    Keywords - Biological processi

    Biotin biosynthesis

    Keywords - Ligandi

    2Fe-2S, 4Fe-4S, Iron, Iron-sulfur, Metal-binding, S-adenosyl-L-methionine

    Enzyme and pathway databases

    BioCyciEcoCyc:BIOTIN-SYN-MONOMER.
    ECOL316407:JW0758-MONOMER.
    MetaCyc:BIOTIN-SYN-MONOMER.
    BRENDAi2.8.1.6. 2026.
    UniPathwayiUPA00078; UER00162.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Biotin synthase (EC:2.8.1.63 Publications)
    Gene namesi
    Name:bioB
    Ordered Locus Names:b0775, JW0758
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG10118. bioB.

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi53 – 531C → A: Total loss of activity. 2 Publications
    Mutagenesisi57 – 571C → A: Total loss of activity. 2 Publications
    Mutagenesisi60 – 601C → A: Total loss of activity. 2 Publications
    Mutagenesisi97 – 971C → A: Total loss of activity. 2 Publications
    Mutagenesisi128 – 1281C → A: Total loss of activity. 2 Publications
    Mutagenesisi151 – 1511N → A: Total loss of activity. 1 Publication
    Mutagenesisi152 – 1521H → A: Weak activity. 1 Publication
    Mutagenesisi153 – 1531N → A: Total loss of activity. 1 Publication
    Mutagenesisi155 – 1551D → A: Total loss of activity. 1 Publication
    Mutagenesisi188 – 1881C → A: Total loss of activity. 2 Publications

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 346346Biotin synthasePRO_0000185552Add
    BLAST

    Proteomic databases

    PaxDbiP12996.
    PRIDEiP12996.

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    yafJQ471474EBI-557917,EBI-1114805

    Protein-protein interaction databases

    DIPiDIP-9220N.
    IntActiP12996. 17 interactions.
    MINTiMINT-1292998.
    STRINGi511145.b0775.

    Structurei

    Secondary structure

    1
    346
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Turni10 – 123Combined sources
    Helixi13 – 175Combined sources
    Helixi20 – 3415Combined sources
    Beta strandi41 – 499Combined sources
    Beta strandi53 – 553Combined sources
    Helixi78 – 9013Combined sources
    Beta strandi94 – 1007Combined sources
    Turni107 – 1093Combined sources
    Helixi110 – 12213Combined sources
    Beta strandi125 – 1306Combined sources
    Helixi136 – 14510Combined sources
    Beta strandi149 – 1513Combined sources
    Helixi158 – 1647Combined sources
    Helixi170 – 18415Combined sources
    Beta strandi186 – 1883Combined sources
    Beta strandi191 – 1933Combined sources
    Helixi199 – 21012Combined sources
    Beta strandi211 – 2144Combined sources
    Beta strandi217 – 2237Combined sources
    Helixi240 – 25314Combined sources
    Beta strandi257 – 2648Combined sources
    Helixi265 – 2673Combined sources
    Helixi270 – 27910Combined sources
    Beta strandi283 – 2853Combined sources
    Beta strandi287 – 2948Combined sources
    Helixi298 – 30710Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1R30X-ray3.40A/B2-346[»]
    ProteinModelPortaliP12996.
    SMRiP12996. Positions 3-315.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP12996.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0502.
    HOGENOMiHOG000239957.
    InParanoidiP12996.
    KOiK01012.
    OMAiCGYCPQS.
    OrthoDBiEOG622PMP.
    PhylomeDBiP12996.

    Family and domain databases

    Gene3Di3.20.20.70. 1 hit.
    HAMAPiMF_01694. BioB.
    InterProiIPR013785. Aldolase_TIM.
    IPR010722. BATS_dom.
    IPR002684. Biotin_synth/BioAB.
    IPR024177. Biotin_synthase.
    IPR006638. Elp3/MiaB/NifB.
    IPR007197. rSAM.
    [Graphical view]
    PfamiPF06968. BATS. 1 hit.
    PF04055. Radical_SAM. 1 hit.
    [Graphical view]
    PIRSFiPIRSF001619. Biotin_synth. 1 hit.
    SMARTiSM00876. BATS. 1 hit.
    SM00729. Elp3. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR00433. bioB. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P12996-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MAHRPRWTLS QVTELFEKPL LDLLFEAQQV HRQHFDPRQV QVSTLLSIKT
    60 70 80 90 100
    GACPEDCKYC PQSSRYKTGL EAERLMEVEQ VLESARKAKA AGSTRFCMGA
    110 120 130 140 150
    AWKNPHERDM PYLEQMVQGV KAMGLEACMT LGTLSESQAQ RLANAGLDYY
    160 170 180 190 200
    NHNLDTSPEF YGNIITTRTY QERLDTLEKV RDAGIKVCSG GIVGLGETVK
    210 220 230 240 250
    DRAGLLLQLA NLPTPPESVP INMLVKVKGT PLADNDDVDA FDFIRTIAVA
    260 270 280 290 300
    RIMMPTSYVR LSAGREQMNE QTQAMCFMAG ANSIFYGCKL LTTPNPEEDK
    310 320 330 340
    DLQLFRKLGL NPQQTAVLAG DNEQQQRLEQ ALMTPDTDEY YNAAAL
    Length:346
    Mass (Da):38,648
    Last modified:November 1, 1997 - v2
    Checksum:i550A7899A2DF6082
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti63 – 631S → T in AAA23515 (PubMed:3058702).Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    J04423 Genomic DNA. Translation: AAA23515.1.
    A11530 Unassigned DNA. Translation: CAA00965.1.
    U00096 Genomic DNA. Translation: AAC73862.1.
    AP009048 Genomic DNA. Translation: BAE76362.1.
    PIRiJC2517. SYECBB.
    RefSeqiNP_415296.1. NC_000913.3.

    Genome annotation databases

    EnsemblBacteriaiAAC73862; AAC73862; b0775.
    BAE76362; BAE76362; BAE76362.
    GeneIDi945370.
    KEGGiecj:Y75_p0748.
    eco:b0775.
    PATRICi32116751. VBIEscCol129921_0801.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    J04423 Genomic DNA. Translation: AAA23515.1.
    A11530 Unassigned DNA. Translation: CAA00965.1.
    U00096 Genomic DNA. Translation: AAC73862.1.
    AP009048 Genomic DNA. Translation: BAE76362.1.
    PIRiJC2517. SYECBB.
    RefSeqiNP_415296.1. NC_000913.3.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1R30X-ray3.40A/B2-346[»]
    ProteinModelPortaliP12996.
    SMRiP12996. Positions 3-315.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    DIPiDIP-9220N.
    IntActiP12996. 17 interactions.
    MINTiMINT-1292998.
    STRINGi511145.b0775.

    Proteomic databases

    PaxDbiP12996.
    PRIDEiP12996.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC73862; AAC73862; b0775.
    BAE76362; BAE76362; BAE76362.
    GeneIDi945370.
    KEGGiecj:Y75_p0748.
    eco:b0775.
    PATRICi32116751. VBIEscCol129921_0801.

    Organism-specific databases

    EchoBASEiEB0116.
    EcoGeneiEG10118. bioB.

    Phylogenomic databases

    eggNOGiCOG0502.
    HOGENOMiHOG000239957.
    InParanoidiP12996.
    KOiK01012.
    OMAiCGYCPQS.
    OrthoDBiEOG622PMP.
    PhylomeDBiP12996.

    Enzyme and pathway databases

    UniPathwayiUPA00078; UER00162.
    BioCyciEcoCyc:BIOTIN-SYN-MONOMER.
    ECOL316407:JW0758-MONOMER.
    MetaCyc:BIOTIN-SYN-MONOMER.
    BRENDAi2.8.1.6. 2026.

    Miscellaneous databases

    EvolutionaryTraceiP12996.
    PROiP12996.

    Family and domain databases

    Gene3Di3.20.20.70. 1 hit.
    HAMAPiMF_01694. BioB.
    InterProiIPR013785. Aldolase_TIM.
    IPR010722. BATS_dom.
    IPR002684. Biotin_synth/BioAB.
    IPR024177. Biotin_synthase.
    IPR006638. Elp3/MiaB/NifB.
    IPR007197. rSAM.
    [Graphical view]
    PfamiPF06968. BATS. 1 hit.
    PF04055. Radical_SAM. 1 hit.
    [Graphical view]
    PIRSFiPIRSF001619. Biotin_synth. 1 hit.
    SMARTiSM00876. BATS. 1 hit.
    SM00729. Elp3. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR00433. bioB. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "The Escherichia coli biotin biosynthetic enzyme sequences predicted from the nucleotide sequence of the bio operon."
      Otsuka A.J., Buoncristiani M.R., Howard P.K., Flamm J., Johnson O., Yamamoto R., Uchida K., Cook C., Ruppert J., Matsuzaki J.
      J. Biol. Chem. 263:19577-19585(1988) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "Genetic material for expression of biotin synthetase enzymes."
      Pearson B.M., McKee R.A.
      Patent number GB2216530, 11-OCT-1989
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    4. "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.
    5. "Biotin synthase: purification, characterization as a [2Fe-2S] cluster protein, and in vitro activity of the Escherichia coli bioB gene product."
      Sanyal I., Cohen G., Flint D.H.
      Biochemistry 33:3625-3631(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 1-17, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, SUBUNIT.
    6. "Escherichia coli proteome analysis using the gene-protein database."
      VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
      Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY 2D-GEL.
    7. "Structure-function studies of Escherichia coli biotin synthase via a chemical modification and site-directed mutagenesis approach."
      Farh L., Hwang S.-Y., Steinrauf L., Chiang H.-J., Shiuan D.
      J. Biochem. 130:627-635(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF CYSTEINE RESIDUES.
    8. "The [4Fe-4S]2+ cluster in reconstituted biotin synthase binds S-adenosyl-L-methionine."
      Cosper M.M., Jameson G.N.L., Davydov R., Eidsness M.K., Hoffman B.M., Huynh B.H., Johnson M.K.
      J. Am. Chem. Soc. 124:14006-14007(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: RESONANCE RAMAN SPECTROSCOPY, EPR SPECTROSCOPY, MOSSBAUER SPECTROSCOPY.
    9. "Reductive cleavage of S-adenosylmethionine by biotin synthase from Escherichia coli."
      Ollagnier-de Choudens S., Sanakis Y., Hewitson K.S., Roach P., Muenck E., Fontecave M.
      J. Biol. Chem. 277:13449-13454(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF CYS-53; CYS-57; CYS-60; CYS-97; CYS-128 AND CYS-188, CATALYTIC ACTIVITY, EPR SPECTROSCOPY, MOSSBAUER SPECTROSCOPY.
    10. Cited for: MUTAGENESIS OF CYS-53; CYS-57; CYS-60; CYS-97; CYS-128 AND CYS-188, EPR SPECTROSCOPY, MOSSBAUER SPECTROSCOPY.
    11. "Structural studies of the interaction of S-adenosylmethionine with the [4Fe-4S] clusters in biotin synthase and pyruvate formate-lyase activating enzyme."
      Cosper M.M., Cosper N.J., Hong W., Shokes J.E., Broderick W.E., Broderick J.B., Johnson M.K., Scott R.A.
      Protein Sci. 12:1573-1577(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: ABSORPTION SPECTROSCOPY.
    12. "Iron-sulfur cluster dynamics in biotin synthase: a new [2Fe-2S](1+) cluster."
      Lotierzo M., Bui B.T., Leech H.K., Warren M.J., Marquet A., Rigby S.E.
      Biochem. Biophys. Res. Commun. 381:487-490(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: REACTION MECHANISM.
    13. "Biotin synthase mechanism: mutagenesis of the YNHNLD conserved motif."
      Lotierzo M., Raux E., Tse Sum Bui B., Goasdoue N., Libot F., Florentin D., Warren M.J., Marquet A.
      Biochemistry 45:12274-12281(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF ASN-151; HIS-152; ASN-153 AND ASP-155, CATALYTIC ACTIVITY.
    14. "Crystal structure of biotin synthase, an S-adenosylmethionine-dependent radical enzyme."
      Berkovitch F., Nicolet Y., Wan J.T., Jarrett J.T., Drennan C.L.
      Science 303:76-79(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.4 ANGSTROMS).

    Entry informationi

    Entry nameiBIOB_ECOLI
    AccessioniPrimary (citable) accession number: P12996
    Secondary accession number(s): Q2MBJ4
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 1, 1990
    Last sequence update: November 1, 1997
    Last modified: June 24, 2015
    This is version 160 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

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

    External Data

    Dasty 3

    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 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.