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P12996 (BIOB_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 149. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Biotin synthase

EC=2.8.1.6
Gene names
Name:bioB
Ordered Locus Names:b0775, JW0758
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length346 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical-based mechanism. Ref.5

Catalytic activity

Dethiobiotin + sulfur-(sulfur carrier) + 2 S-adenosyl-L-methionine = biotin + (sulfur carrier) + 2 L-methionine + 2 5'-deoxyadenosine. HAMAP-Rule MF_01694

Cofactor

Binds 1 4Fe-4S cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Ref.5

Binds 1 2Fe-2S cluster. The cluster is coordinated with 3 cysteines and 1 arginine. Ref.5

Pathway

Cofactor biosynthesis; biotin biosynthesis; biotin from 7,8-diaminononanoate: step 2/2. HAMAP-Rule MF_01694

Subunit structure

Homodimer. Ref.5

Sequence similarities

Belongs to the radical SAM superfamily. Biotin synthase family.

Biophysicochemical properties

Kinetic parameters:

KM=2 µM for dethiobiotin Ref.5

Binary interactions

With

Entry

#Exp.

IntAct

Notes

yafJQ471474EBI-557917,EBI-1114805

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 346346Biotin synthase HAMAP-Rule MF_01694
PRO_0000185552

Sites

Metal binding531Iron-sulfur 1 (4Fe-4S-S-AdoMet)
Metal binding571Iron-sulfur 1 (4Fe-4S-S-AdoMet)
Metal binding601Iron-sulfur 1 (4Fe-4S-S-AdoMet)
Metal binding971Iron-sulfur 2 (2Fe-2S)
Metal binding1281Iron-sulfur 2 (2Fe-2S)
Metal binding1881Iron-sulfur 2 (2Fe-2S)
Metal binding2601Iron-sulfur 2 (2Fe-2S)

Experimental info

Mutagenesis531C → A: Total loss of activity. Ref.7 Ref.9 Ref.10
Mutagenesis571C → A: Total loss of activity. Ref.7 Ref.9 Ref.10
Mutagenesis601C → A: Total loss of activity. Ref.7 Ref.9 Ref.10
Mutagenesis971C → A: Total loss of activity. Ref.7 Ref.9 Ref.10
Mutagenesis1281C → A: Total loss of activity. Ref.7 Ref.9 Ref.10
Mutagenesis1511N → A: Total loss of activity. Ref.7 Ref.13
Mutagenesis1521H → A: Weak activity. Ref.7 Ref.13
Mutagenesis1531N → A: Total loss of activity. Ref.7 Ref.13
Mutagenesis1551D → A: Total loss of activity. Ref.7 Ref.13
Mutagenesis1881C → A: Total loss of activity. Ref.7 Ref.9 Ref.10
Sequence conflict631S → T in AAA23515. Ref.1

Secondary structure

................................................. 346
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P12996 [UniParc].

Last modified November 1, 1997. Version 2.
Checksum: 550A7899A2DF6082

FASTA34638,648
        10         20         30         40         50         60 
MAHRPRWTLS QVTELFEKPL LDLLFEAQQV HRQHFDPRQV QVSTLLSIKT GACPEDCKYC 

        70         80         90        100        110        120 
PQSSRYKTGL EAERLMEVEQ VLESARKAKA AGSTRFCMGA AWKNPHERDM PYLEQMVQGV 

       130        140        150        160        170        180 
KAMGLEACMT LGTLSESQAQ RLANAGLDYY NHNLDTSPEF YGNIITTRTY QERLDTLEKV 

       190        200        210        220        230        240 
RDAGIKVCSG GIVGLGETVK DRAGLLLQLA NLPTPPESVP INMLVKVKGT PLADNDDVDA 

       250        260        270        280        290        300 
FDFIRTIAVA RIMMPTSYVR LSAGREQMNE QTQAMCFMAG ANSIFYGCKL LTTPNPEEDK 

       310        320        330        340 
DLQLFRKLGL NPQQTAVLAG DNEQQQRLEQ ALMTPDTDEY YNAAAL 

« Hide

References

« Hide 'large scale' references
[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]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
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]"The iron-sulfur center of biotin synthase: site-directed mutants."
Hewitson K.S., Ollagnier-de Choudens S., Sanakis Y., Shaw N.M., Baldwin J.E., Muenck E., Roach P.L., Fontecave M.
J. Biol. Inorg. Chem. 7:83-93(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.
[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).
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
J04423 Genomic DNA. Translation: AAA23515.1.
A11530 Unassigned DNA. Translation: CAA00965.1.
U00096 Genomic DNA. Translation: AAC73862.1.
AP009048 Genomic DNA. Translation: BAE76362.1.
PIRSYECBB. JC2517.
RefSeqNP_415296.1. NC_000913.3.
YP_489048.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1R30X-ray3.40A/B2-346[»]
ProteinModelPortalP12996.
SMRP12996. Positions 3-315.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-9220N.
IntActP12996. 16 interactions.
MINTMINT-1292998.
STRING511145.b0775.

Proteomic databases

PaxDbP12996.
PRIDEP12996.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC73862; AAC73862; b0775.
BAE76362; BAE76362; BAE76362.
GeneID12930955.
945370.
KEGGecj:Y75_p0748.
eco:b0775.
PATRIC32116751. VBIEscCol129921_0801.

Organism-specific databases

EchoBASEEB0116.
EcoGeneEG10118. bioB.

Phylogenomic databases

eggNOGCOG0502.
HOGENOMHOG000239957.
KOK01012.
OMAADRFCMG.
OrthoDBEOG622PMP.
PhylomeDBP12996.
ProtClustDBPRK15108.

Enzyme and pathway databases

BioCycEcoCyc:BIOTIN-SYN-MONOMER.
ECOL316407:JW0758-MONOMER.
MetaCyc:BIOTIN-SYN-MONOMER.
UniPathwayUPA00078; UER00162.

Gene expression databases

GenevestigatorP12996.

Family and domain databases

Gene3D3.20.20.70. 1 hit.
HAMAPMF_01694. BioB.
InterProIPR013785. Aldolase_TIM.
IPR010722. BATS_dom.
IPR002684. Biotin_synth/BioAB.
IPR024177. Biotin_synthase.
IPR006638. Elp3/MiaB/NifB.
IPR007197. rSAM.
[Graphical view]
PfamPF06968. BATS. 1 hit.
PF04055. Radical_SAM. 1 hit.
[Graphical view]
PIRSFPIRSF001619. Biotin_synth. 1 hit.
SMARTSM00876. BATS. 1 hit.
SM00729. Elp3. 1 hit.
[Graphical view]
TIGRFAMsTIGR00433. bioB. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP12996.
PROP12996.

Entry information

Entry nameBIOB_ECOLI
AccessionPrimary (citable) accession number: P12996
Secondary accession number(s): Q2MBJ4
Entry history
Integrated into UniProtKB/Swiss-Prot: January 1, 1990
Last sequence update: November 1, 1997
Last modified: April 16, 2014
This is version 149 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene