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B8DPP9

- BIOB_DESVM

UniProt

B8DPP9 - BIOB_DESVM

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Protein

Biotin synthase

Gene

bioB

Organism
Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
Status
Reviewed - 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 = biotin + (sulfur carrier) + 2 L-methionine + 2 5'-deoxyadenosine.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

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi88 – 881Iron-sulfur 1 (4Fe-4S-S-AdoMet)UniRule annotation
Metal bindingi92 – 921Iron-sulfur 1 (4Fe-4S-S-AdoMet)UniRule annotation
Metal bindingi95 – 951Iron-sulfur 1 (4Fe-4S-S-AdoMet)UniRule annotation
Metal bindingi164 – 1641Iron-sulfur 2 (2Fe-2S)UniRule annotation
Metal bindingi233 – 2331Iron-sulfur 2 (2Fe-2S)UniRule annotation

GO - Molecular functioni

  1. 2 iron, 2 sulfur cluster binding Source: UniProtKB-KW
  2. 4 iron, 4 sulfur cluster binding Source: UniProtKB-KW
  3. biotin synthase activity Source: UniProtKB-HAMAP
  4. iron ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. biotin biosynthetic process Source: UniProtKB-HAMAP
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

BioCyciDVUL883:GCJ5-1030-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:DvMF_1001
OrganismiDesulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
Taxonomic identifieri883 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfovibrionaceaeDesulfovibrio
ProteomesiUP000001361: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 364364Biotin synthasePRO_0000381352Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi883.DvMF_1001.

Structurei

3D structure databases

ProteinModelPortaliB8DPP9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG0502.
HOGENOMiHOG000239958.
KOiK01012.
OMAiDETQALC.
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.

B8DPP9-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MNPLLERLCA RLSDTIPPGT ETPYASPSHA RTEEAPWSGI TGEEALAVAR
60 70 80 90 100
LPASDILDIL AVAQAVRSAR KGPLATTCGI VNAKSGRCGE DCAFCAQSSH
110 120 130 140 150
HDTGAPVHAL LGPDALLRHA EELARAGVRR FGIVTSGNAL SEREFDAVCH
160 170 180 190 200
AARLLRDRVD IGLCASLGQL ATGSAESGNR GERARRLKDA GISSYHHNLE
210 220 230 240 250
TARSFFPQVC TTHPYDDDIA TVREAARAGL RTCCGGILGL GETWEHRVEL
260 270 280 290 300
ALTLRELDVD SIPLNFLHPV PGTRLGHRSP LPPMEALRAI AVFRLLHPQR
310 320 330 340 350
DILVCGGRET TLGQWQSWVF AAGANGLMVG NYLTTAGRAL AEDMEMLAAL
360
GVGEIPRNGE EARA
Length:364
Mass (Da):38,891
Last modified:March 3, 2009 - v1
Checksum:i765502FEC70944AD
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001197 Genomic DNA. Translation: ACL07956.1.
RefSeqiWP_012612145.1. NC_011769.1.
YP_002435424.1. NC_011769.1.

Genome annotation databases

EnsemblBacteriaiACL07956; ACL07956; DvMF_1001.
GeneIDi7172896.
KEGGidvm:DvMF_1001.
PATRICi21772033. VBIDesVul86729_1059.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001197 Genomic DNA. Translation: ACL07956.1 .
RefSeqi WP_012612145.1. NC_011769.1.
YP_002435424.1. NC_011769.1.

3D structure databases

ProteinModelPortali B8DPP9.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 883.DvMF_1001.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ACL07956 ; ACL07956 ; DvMF_1001 .
GeneIDi 7172896.
KEGGi dvm:DvMF_1001.
PATRICi 21772033. VBIDesVul86729_1059.

Phylogenomic databases

eggNOGi COG0502.
HOGENOMi HOG000239958.
KOi K01012.
OMAi DETQALC.
OrthoDBi EOG622PMP.

Enzyme and pathway databases

UniPathwayi UPA00078 ; UER00162 .
BioCyci DVUL883:GCJ5-1030-MONOMER.

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. "Complete sequence of Desulfovibrio vulgaris str. 'Miyazaki F'."
    Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S., Sims D., Brettin T., Detter J.C., Han C., Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N., Hazen T.C., Richardson P.
    Submitted (OCT-2008) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Miyazaki F / DSM 19637.

Entry informationi

Entry nameiBIOB_DESVM
AccessioniPrimary (citable) accession number: B8DPP9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 28, 2009
Last sequence update: March 3, 2009
Last modified: November 26, 2014
This is version 42 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