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P12996

- BIOB_ECOLI

UniProt

P12996 - BIOB_ECOLI

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Protein

Biotin synthase

Gene

bioB

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.

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

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

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. 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.

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 – 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.
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

        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.
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:
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 .
PIRi JC2517. SYECBB.
RefSeqi NP_415296.1. NC_000913.3.
YP_489048.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
InParanoidi P12996.
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: November 26, 2014
This is version 155 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