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P12996

- BIOB_ECOLI

UniProt

P12996 - BIOB_ECOLI

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Protein

Biotin synthase

Gene
bioB, b0775, JW0758
Organism
Escherichia coli (strain K12)
Status
Reviewed - 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 = biotin + (sulfur carrier) + 2 L-methionine + 2 5'-deoxyadenosine.UniRule annotation

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
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.
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 synthaseUniRule annotationPRO_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.

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

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti63 – 631S → T in AAA23515. 1 Publication

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

« 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, 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: July 9, 2014
This is version 152 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

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