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Protein

Biotin synthase

Gene

bioB

Organism
Pelodictyon phaeoclathratiforme (strain DSM 5477 / BU-1)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

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

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.UniRule annotation

Cofactori

Protein has several cofactor binding sites:
  • [4Fe-4S] clusterUniRule annotationNote: Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine.UniRule annotation
  • [2Fe-2S] clusterUniRule annotationNote: Binds 1 [2Fe-2S] cluster. The cluster is coordinated with 3 cysteines and 1 arginine.UniRule annotation

Pathway:ibiotin biosynthesis

This protein is involved in step 2 of the subpathway that synthesizes biotin from 7,8-diaminononanoate.UniRule annotation
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. ATP-dependent dethiobiotin synthetase BioD (bioD)
  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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi76 – 761Iron-sulfur 1 (4Fe-4S-S-AdoMet)UniRule annotation
Metal bindingi80 – 801Iron-sulfur 1 (4Fe-4S-S-AdoMet)UniRule annotation
Metal bindingi83 – 831Iron-sulfur 1 (4Fe-4S-S-AdoMet)UniRule annotation
Metal bindingi155 – 1551Iron-sulfur 2 (2Fe-2S)UniRule annotation
Metal bindingi216 – 2161Iron-sulfur 2 (2Fe-2S)UniRule annotation
Metal bindingi286 – 2861Iron-sulfur 2 (2Fe-2S)UniRule annotation

GO - Molecular functioni

GO - Biological processi

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

BioCyciPPHA324925:GHBF-2892-MONOMER.
UniPathwayiUPA00078; UER00162.

Names & Taxonomyi

Protein namesi
Recommended name:
Biotin synthaseUniRule annotation (EC:2.8.1.6UniRule annotation)
Gene namesi
Name:bioBUniRule annotation
Ordered Locus Names:Ppha_2839
OrganismiPelodictyon phaeoclathratiforme (strain DSM 5477 / BU-1)
Taxonomic identifieri324925 [NCBI]
Taxonomic lineageiBacteriaChlorobiChlorobiaChlorobialesChlorobiaceaeChlorobium/Pelodictyon groupPelodictyon
ProteomesiUP000002724 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 337337Biotin synthasePRO_0000381521Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi324925.Ppha_2839.

Structurei

3D structure databases

ProteinModelPortaliB4SGZ7.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the radical SAM superfamily. Biotin synthase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0502.
HOGENOMiHOG000239958.
KOiK01012.
OMAiHYNINIQ.
OrthoDBiEOG622PMP.

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.

B4SGZ7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDYRTLHPQI AAAYRVLETG SPISQAEALL LAELPGELVL DLASLANKVK
60 70 80 90 100
NRYGTGSAGS ELLHACSIMN AKSGVCGENC RFCAQSRHNR ADIEVYDLVD
110 120 130 140 150
AESVLIEARN CFAEGVSHFG IVTSGYGYKR INPEFQRVLD MIDRLHEELP
160 170 180 190 200
ELSVCASLGM LGEEPAEALA AHGIAHYNIN IQVVPDRYHD LIADTHSVEE
210 220 230 240 250
RIETIKLLRK NNISVCCGGI MGVGETMQER IAMIFALQEL DVSVIPLNVL
260 270 280 290 300
VPIEGTPLAG KEPLSVAEIV KTFAICRLAH PHKIIKFAAG RETIMKDFQG
310 320 330
LLMLSGANGF LTGGYLTTRG RDIADDRRFA SQIASFN
Length:337
Mass (Da):36,779
Last modified:September 23, 2008 - v1
Checksum:i77C6DD5DCA77A329
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001110 Genomic DNA. Translation: ACF44985.1.
RefSeqiWP_012509453.1. NC_011060.1.

Genome annotation databases

EnsemblBacteriaiACF44985; ACF44985; Ppha_2839.
KEGGipph:Ppha_2839.
PATRICi22906539. VBIPelPha134556_3025.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001110 Genomic DNA. Translation: ACF44985.1.
RefSeqiWP_012509453.1. NC_011060.1.

3D structure databases

ProteinModelPortaliB4SGZ7.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi324925.Ppha_2839.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACF44985; ACF44985; Ppha_2839.
KEGGipph:Ppha_2839.
PATRICi22906539. VBIPelPha134556_3025.

Phylogenomic databases

eggNOGiCOG0502.
HOGENOMiHOG000239958.
KOiK01012.
OMAiHYNINIQ.
OrthoDBiEOG622PMP.

Enzyme and pathway databases

UniPathwayiUPA00078; UER00162.
BioCyciPPHA324925:GHBF-2892-MONOMER.

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.
ProtoNetiSearch...

Publicationsi

  1. "Complete sequence of Pelodictyon phaeoclathratiforme BU-1."
    US DOE Joint Genome Institute
    Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N., Liu Z., Li T., Zhao F.
    , Overmann J., Bryant D.A., Richardson P.
    Submitted (JUN-2008) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: DSM 5477 / BU-1.

Entry informationi

Entry nameiBIOB_PELPB
AccessioniPrimary (citable) accession number: B4SGZ7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 28, 2009
Last sequence update: September 23, 2008
Last modified: July 22, 2015
This is version 51 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.