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B2RH08

- BIOB_PORG3

UniProt

B2RH08 - BIOB_PORG3

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Protein

Biotin synthase

Gene

bioB

Organism
Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / JCM 12257)
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 bindingi61 – 611Iron-sulfur 1 (4Fe-4S-S-AdoMet)UniRule annotation
Metal bindingi65 – 651Iron-sulfur 1 (4Fe-4S-S-AdoMet)UniRule annotation
Metal bindingi68 – 681Iron-sulfur 1 (4Fe-4S-S-AdoMet)UniRule annotation
Metal bindingi105 – 1051Iron-sulfur 2 (2Fe-2S)UniRule annotation
Metal bindingi137 – 1371Iron-sulfur 2 (2Fe-2S)UniRule annotation
Metal bindingi197 – 1971Iron-sulfur 2 (2Fe-2S)UniRule annotation
Metal bindingi267 – 2671Iron-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

BioCyciPGIN431947:GC9J-140-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:PGN_0134
OrganismiPorphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / JCM 12257)
Taxonomic identifieri431947 [NCBI]
Taxonomic lineageiBacteriaBacteroidetesBacteroidiaBacteroidalesPorphyromonadaceaePorphyromonas
ProteomesiUP000008842: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 330330Biotin synthasePRO_0000381532Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi431947.PGN_0134.

Structurei

3D structure databases

ProteinModelPortaliB2RH08.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG0502.
HOGENOMiHOG000239958.
KOiK01012.
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.

B2RH08-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MIQTIENRLI NGGEPTFEEA LLLASSADKE ALYETAHRIT RHFMGDKFDT
60 70 80 90 100
CSIINAKSGN CPEDCKWCAQ SRHYATSIEK YGLLSATVCA EQAAYNRRQG
110 120 130 140 150
IGRFSLVASG RTASMNEIRQ MAESFRTIKQ RTDIKCCASL GLLSEEKLQI
160 170 180 190 200
LFDNGVTTYH CNMETAPSFF PSLCSTHTQE EKLATIRAAR RVGMRVCSGG
210 220 230 240 250
IIGMGETMEQ RIEFAFFLHS INVYSIPINI LQPIPGTPLE KTPPLSEEEY
260 270 280 290 300
LTTVALFRLI NPRAFLRFSG GRAQLSPAVQ RKAIYIGINA AITGDLLTTT
310 320 330
GSKAAEDMQL ARECGFQVTN DTDWEVSYDH
Length:330
Mass (Da):36,649
Last modified:July 28, 2009 - v2
Checksum:i843537B62FD8FA5A
GO

Sequence cautioni

The sequence BAG32653.1 differs from that shown. Reason: Erroneous initiation. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP009380 Genomic DNA. Translation: BAG32653.1. Different initiation.
RefSeqiYP_001928250.1. NC_010729.1.

Genome annotation databases

EnsemblBacteriaiBAG32653; BAG32653; PGN_0134.
GeneIDi6330269.
KEGGipgn:PGN_0134.
PATRICi22973179. VBIPorGin26334_0128.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP009380 Genomic DNA. Translation: BAG32653.1 . Different initiation.
RefSeqi YP_001928250.1. NC_010729.1.

3D structure databases

ProteinModelPortali B2RH08.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 431947.PGN_0134.

Protocols and materials databases

DNASUi 6330269.
Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai BAG32653 ; BAG32653 ; PGN_0134 .
GeneIDi 6330269.
KEGGi pgn:PGN_0134.
PATRICi 22973179. VBIPorGin26334_0128.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayi UPA00078 ; UER00162 .
BioCyci PGIN431947:GC9J-140-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. "Determination of the genome sequence of Porphyromonas gingivalis strain ATCC 33277 and genomic comparison with strain W83 revealed extensive genome rearrangements in P. gingivalis."
    Naito M., Hirakawa H., Yamashita A., Ohara N., Shoji M., Yukitake H., Nakayama K., Toh H., Yoshimura F., Kuhara S., Hattori M., Hayashi T., Nakayama K.
    DNA Res. 15:215-225(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 33277 / DSM 20709 / JCM 12257.

Entry informationi

Entry nameiBIOB_PORG3
AccessioniPrimary (citable) accession number: B2RH08
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 28, 2009
Last sequence update: July 28, 2009
Last modified: November 26, 2014
This is version 50 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

Complete proteome

Documents

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

External Data

Dasty 3