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P12996

- BIOB_ECOLI

UniProt

P12996 - BIOB_ECOLI

Protein

Biotin synthase

Gene

bioB

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 153 (01 Oct 2014)
      Sequence version 2 (01 Nov 1997)
      Previous versions | rss
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    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 = biotin + (sulfur carrier) + 2 L-methionine + 2 5'-deoxyadenosine.

    Cofactori

    Binds 1 4Fe-4S cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine.1 Publication
    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

    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

    1. 2 iron, 2 sulfur cluster binding Source: EcoCyc
    2. 4 iron, 4 sulfur cluster binding Source: EcoCyc
    3. biotin synthase activity Source: EcoCyc
    4. iron ion binding Source: UniProtKB-HAMAP
    5. protein binding Source: IntAct

    GO - Biological processi

    1. biotin biosynthetic process Source: EcoCyc

    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.
    UniPathwayiUPA00078; UER00162.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Biotin synthase (EC:2.8.1.6)
    Gene namesi
    Name:bioB
    Ordered Locus Names:b0775, JW0758
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG10118. bioB.

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi53 – 531C → A: Total loss of activity. 3 Publications
    Mutagenesisi57 – 571C → A: Total loss of activity. 3 Publications
    Mutagenesisi60 – 601C → A: Total loss of activity. 3 Publications
    Mutagenesisi97 – 971C → A: Total loss of activity. 3 Publications
    Mutagenesisi128 – 1281C → A: Total loss of activity. 3 Publications
    Mutagenesisi151 – 1511N → A: Total loss of activity. 2 Publications
    Mutagenesisi152 – 1521H → A: Weak activity. 2 Publications
    Mutagenesisi153 – 1531N → A: Total loss of activity. 2 Publications
    Mutagenesisi155 – 1551D → A: Total loss of activity. 2 Publications
    Mutagenesisi188 – 1881C → A: Total loss of activity. 3 Publications

    PTM / Processingi

    Molecule processing

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

    Proteomic databases

    PaxDbiP12996.
    PRIDEiP12996.

    Expressioni

    Gene expression databases

    GenevestigatoriP12996.

    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 – 123
    Helixi13 – 175
    Helixi20 – 3415
    Beta strandi41 – 499
    Beta strandi53 – 553
    Helixi78 – 9013
    Beta strandi94 – 1007
    Turni107 – 1093
    Helixi110 – 12213
    Beta strandi125 – 1306
    Helixi136 – 14510
    Beta strandi149 – 1513
    Helixi158 – 1647
    Helixi170 – 18415
    Beta strandi186 – 1883
    Beta strandi191 – 1933
    Helixi199 – 21012
    Beta strandi211 – 2144
    Beta strandi217 – 2237
    Helixi240 – 25314
    Beta strandi257 – 2648
    Helixi265 – 2673
    Helixi270 – 27910
    Beta strandi283 – 2853
    Beta strandi287 – 2948
    Helixi298 – 30710

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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.
    KOiK01012.
    OMAiRIMMPAS.
    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

    MAHRPRWTLS QVTELFEKPL LDLLFEAQQV HRQHFDPRQV QVSTLLSIKT    50
    GACPEDCKYC PQSSRYKTGL EAERLMEVEQ VLESARKAKA AGSTRFCMGA 100
    AWKNPHERDM PYLEQMVQGV KAMGLEACMT LGTLSESQAQ RLANAGLDYY 150
    NHNLDTSPEF YGNIITTRTY QERLDTLEKV RDAGIKVCSG GIVGLGETVK 200
    DRAGLLLQLA NLPTPPESVP INMLVKVKGT PLADNDDVDA FDFIRTIAVA 250
    RIMMPTSYVR LSAGREQMNE QTQAMCFMAG ANSIFYGCKL LTTPNPEEDK 300
    DLQLFRKLGL NPQQTAVLAG DNEQQQRLEQ ALMTPDTDEY YNAAAL 346
    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:
    EMBL
    GenBank
    DDBJ
    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.
    YP_489048.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC73862; AAC73862; b0775.
    BAE76362; BAE76362; BAE76362.
    GeneIDi12930955.
    945370.
    KEGGiecj:Y75_p0748.
    eco:b0775.
    PATRICi32116751. VBIEscCol129921_0801.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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 .
    PIRi JC2517. SYECBB.
    RefSeqi NP_415296.1. NC_000913.3.
    YP_489048.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1R30 X-ray 3.40 A/B 2-346 [» ]
    ProteinModelPortali P12996.
    SMRi P12996. Positions 3-315.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-9220N.
    IntActi P12996. 17 interactions.
    MINTi MINT-1292998.
    STRINGi 511145.b0775.

    Proteomic databases

    PaxDbi P12996.
    PRIDEi P12996.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC73862 ; AAC73862 ; b0775 .
    BAE76362 ; BAE76362 ; BAE76362 .
    GeneIDi 12930955.
    945370.
    KEGGi ecj:Y75_p0748.
    eco:b0775.
    PATRICi 32116751. VBIEscCol129921_0801.

    Organism-specific databases

    EchoBASEi EB0116.
    EcoGenei EG10118. bioB.

    Phylogenomic databases

    eggNOGi COG0502.
    HOGENOMi HOG000239957.
    KOi K01012.
    OMAi RIMMPAS.
    OrthoDBi EOG622PMP.
    PhylomeDBi P12996.

    Enzyme and pathway databases

    UniPathwayi UPA00078 ; UER00162 .
    BioCyci EcoCyc:BIOTIN-SYN-MONOMER.
    ECOL316407:JW0758-MONOMER.
    MetaCyc:BIOTIN-SYN-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P12996.
    PROi P12996.

    Gene expression databases

    Genevestigatori P12996.

    Family and domain databases

    Gene3Di 3.20.20.70. 1 hit.
    HAMAPi MF_01694. BioB.
    InterProi IPR013785. Aldolase_TIM.
    IPR010722. BATS_dom.
    IPR002684. Biotin_synth/BioAB.
    IPR024177. Biotin_synthase.
    IPR006638. Elp3/MiaB/NifB.
    IPR007197. rSAM.
    [Graphical view ]
    Pfami PF06968. BATS. 1 hit.
    PF04055. Radical_SAM. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF001619. Biotin_synth. 1 hit.
    SMARTi SM00876. BATS. 1 hit.
    SM00729. Elp3. 1 hit.
    [Graphical view ]
    TIGRFAMsi TIGR00433. bioB. 1 hit.
    ProtoNeti Search...

    Publicationsi

    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, 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, 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.
    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: October 1, 2014
    This is version 153 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