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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

    Pathwayi: 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 2 (bioD2)
    2. 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)DescriptionActionsGraphical viewLength
    Metal bindingi53Iron-sulfur 1 (4Fe-4S-S-AdoMet)1
    Metal bindingi57Iron-sulfur 1 (4Fe-4S-S-AdoMet)1
    Metal bindingi60Iron-sulfur 1 (4Fe-4S-S-AdoMet)1
    Metal bindingi97Iron-sulfur 2 (2Fe-2S)1
    Metal bindingi128Iron-sulfur 2 (2Fe-2S)1
    Metal bindingi188Iron-sulfur 2 (2Fe-2S)1
    Metal bindingi260Iron-sulfur 2 (2Fe-2S)1

    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.
    SABIO-RKP12996.
    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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG10118. bioB.

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi53C → A: Total loss of activity. 2 Publications1
    Mutagenesisi57C → A: Total loss of activity. 2 Publications1
    Mutagenesisi60C → A: Total loss of activity. 2 Publications1
    Mutagenesisi97C → A: Total loss of activity. 2 Publications1
    Mutagenesisi128C → A: Total loss of activity. 2 Publications1
    Mutagenesisi151N → A: Total loss of activity. 1 Publication1
    Mutagenesisi152H → A: Weak activity. 1 Publication1
    Mutagenesisi153N → A: Total loss of activity. 1 Publication1
    Mutagenesisi155D → A: Total loss of activity. 1 Publication1
    Mutagenesisi188C → A: Total loss of activity. 2 Publications1

    Chemistry databases

    DrugBankiDB03754. Tris.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001855521 – 346Biotin synthaseAdd BLAST346

    Proteomic databases

    PaxDbiP12996.
    PRIDEiP12996.

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Binary interactionsi

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

    Protein-protein interaction databases

    BioGridi4259949. 7 interactors.
    DIPiDIP-9220N.
    IntActiP12996. 17 interactors.
    MINTiMINT-1292998.
    STRINGi511145.b0775.

    Structurei

    Secondary structure

    1346
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Turni10 – 12Combined sources3
    Helixi13 – 17Combined sources5
    Helixi20 – 34Combined sources15
    Beta strandi41 – 49Combined sources9
    Beta strandi53 – 55Combined sources3
    Helixi78 – 90Combined sources13
    Beta strandi94 – 100Combined sources7
    Turni107 – 109Combined sources3
    Helixi110 – 122Combined sources13
    Beta strandi125 – 130Combined sources6
    Helixi136 – 145Combined sources10
    Beta strandi149 – 151Combined sources3
    Helixi158 – 164Combined sources7
    Helixi170 – 184Combined sources15
    Beta strandi186 – 188Combined sources3
    Beta strandi191 – 193Combined sources3
    Helixi199 – 210Combined sources12
    Beta strandi211 – 214Combined sources4
    Beta strandi217 – 223Combined sources7
    Helixi240 – 253Combined sources14
    Beta strandi257 – 264Combined sources8
    Helixi265 – 267Combined sources3
    Helixi270 – 279Combined sources10
    Beta strandi283 – 285Combined sources3
    Beta strandi287 – 294Combined sources8
    Helixi298 – 307Combined sources10

    3D structure databases

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

    Miscellaneous databases

    EvolutionaryTraceiP12996.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105CZF. Bacteria.
    COG0502. LUCA.
    HOGENOMiHOG000239957.
    InParanoidiP12996.
    KOiK01012.
    OMAiPFDFIRM.
    PhylomeDBiP12996.

    Family and domain databases

    Gene3Di3.20.20.70. 1 hit.
    HAMAPiMF_01694. BioB. 1 hit.
    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)DescriptionActionsGraphical viewLength
    Sequence conflicti63S → T in AAA23515 (PubMed:3058702).Curated1

    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.
    WP_000951213.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC73862; AAC73862; b0775.
    BAE76362; BAE76362; BAE76362.
    GeneIDi945370.
    KEGGiecj:JW0758.
    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.
    WP_000951213.1. NZ_LN832404.1.

    3D structure databases

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

    Protein-protein interaction databases

    BioGridi4259949. 7 interactors.
    DIPiDIP-9220N.
    IntActiP12996. 17 interactors.
    MINTiMINT-1292998.
    STRINGi511145.b0775.

    Chemistry databases

    DrugBankiDB03754. Tris.

    Proteomic databases

    PaxDbiP12996.
    PRIDEiP12996.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC73862; AAC73862; b0775.
    BAE76362; BAE76362; BAE76362.
    GeneIDi945370.
    KEGGiecj:JW0758.
    eco:b0775.
    PATRICi32116751. VBIEscCol129921_0801.

    Organism-specific databases

    EchoBASEiEB0116.
    EcoGeneiEG10118. bioB.

    Phylogenomic databases

    eggNOGiENOG4105CZF. Bacteria.
    COG0502. LUCA.
    HOGENOMiHOG000239957.
    InParanoidiP12996.
    KOiK01012.
    OMAiPFDFIRM.
    PhylomeDBiP12996.

    Enzyme and pathway databases

    UniPathwayiUPA00078; UER00162.
    BioCyciEcoCyc:BIOTIN-SYN-MONOMER.
    ECOL316407:JW0758-MONOMER.
    MetaCyc:BIOTIN-SYN-MONOMER.
    BRENDAi2.8.1.6. 2026.
    SABIO-RKP12996.

    Miscellaneous databases

    EvolutionaryTraceiP12996.
    PROiP12996.

    Family and domain databases

    Gene3Di3.20.20.70. 1 hit.
    HAMAPiMF_01694. BioB. 1 hit.
    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...

    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: November 2, 2016
    This is version 168 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

    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.