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Protein

ATP-dependent dethiobiotin synthetase BioD

Gene

bioD

Organism
Vibrio fischeri (strain MJ11)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Catalyzes a mechanistically unusual reaction, the ATP-dependent insertion of CO2 between the N7 and N8 nitrogen atoms of 7,8-diaminopelargonic acid (DAPA) to form an ureido ring.UniRule annotation

Catalytic activityi

ATP + 7,8-diaminononanoate + CO2 = ADP + phosphate + dethiobiotin.UniRule annotation

Cofactori

Mg2+UniRule annotation

Pathwayi: biotin biosynthesis

This protein is involved in step 1 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 bindingi13 – 131Magnesium 1UniRule annotation
Metal bindingi17 – 171Magnesium 2UniRule annotation
Metal bindingi55 – 551Magnesium 2UniRule annotation
Binding sitei55 – 551ATPUniRule annotation
Metal bindingi116 – 1161Magnesium 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi13 – 186ATPUniRule annotation
Nucleotide bindingi116 – 1194ATPUniRule annotation
Nucleotide bindingi176 – 1772ATPUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

Biotin biosynthesis

Keywords - Ligandi

ATP-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

UniPathwayiUPA00078; UER00161.

Names & Taxonomyi

Protein namesi
Recommended name:
ATP-dependent dethiobiotin synthetase BioDUniRule annotation (EC:6.3.3.3UniRule annotation)
Alternative name(s):
DTB synthetaseUniRule annotation
Short name:
DTBSUniRule annotation
Dethiobiotin synthaseUniRule annotation
Gene namesi
Name:bioDUniRule annotation
Ordered Locus Names:VFMJ11_A0867
OrganismiVibrio fischeri (strain MJ11)
Taxonomic identifieri388396 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeAliivibrio
Proteomesi
  • UP000001857 Componenti: Chromosome II

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 226226ATP-dependent dethiobiotin synthetase BioDPRO_1000119886Add
BLAST

Structurei

3D structure databases

ProteinModelPortaliB5EUP7.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the dethiobiotin synthetase family.UniRule annotation

Phylogenomic databases

HOGENOMiHOG000275032.
KOiK01935.
OMAiDATYWKP.
OrthoDBiEOG66B3XT.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
HAMAPiMF_00336. BioD.
InterProiIPR004472. DTB_synth_BioD.
IPR027417. P-loop_NTPase.
[Graphical view]
PIRSFiPIRSF006755. DTB_synth. 1 hit.
SUPFAMiSSF52540. SSF52540. 1 hit.
TIGRFAMsiTIGR00347. bioD. 1 hit.

Sequencei

Sequence statusi: Complete.

B5EUP7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIDAFFIAGT DTDVGKTVAS KAILDALNMK GLRTAAYKPV AAGSEDKGEG
60 70 80 90 100
VQNSDAIHLR AVANVELRYE EVNPYALLMP ASPHIAAEAE NVVIDYSVLS
110 120 130 140 150
EGLASLKEKS DVVLVEGAGG WRVPVSKDDC LSTWVQQEKL PVVLVVGIKL
160 170 180 190 200
GCLSHAMLTA EAIQHDGLEI IGWVANRVNP GTENYAEIIK MLEDKMPAPK
210 220
LGEIPYMPSV KRKNMGKYIH LEALDN
Length:226
Mass (Da):24,409
Last modified:October 14, 2008 - v1
Checksum:i43B797D856C363C1
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001133 Genomic DNA. Translation: ACH64557.1.
RefSeqiWP_005423112.1. NC_011186.1.

Genome annotation databases

EnsemblBacteriaiACH64557; ACH64557; VFMJ11_A0867.
KEGGivfm:VFMJ11_A0867.
PATRICi20125960. VBIVibFis37164_3603.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001133 Genomic DNA. Translation: ACH64557.1.
RefSeqiWP_005423112.1. NC_011186.1.

3D structure databases

ProteinModelPortaliB5EUP7.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACH64557; ACH64557; VFMJ11_A0867.
KEGGivfm:VFMJ11_A0867.
PATRICi20125960. VBIVibFis37164_3603.

Phylogenomic databases

HOGENOMiHOG000275032.
KOiK01935.
OMAiDATYWKP.
OrthoDBiEOG66B3XT.

Enzyme and pathway databases

UniPathwayiUPA00078; UER00161.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
HAMAPiMF_00336. BioD.
InterProiIPR004472. DTB_synth_BioD.
IPR027417. P-loop_NTPase.
[Graphical view]
PIRSFiPIRSF006755. DTB_synth. 1 hit.
SUPFAMiSSF52540. SSF52540. 1 hit.
TIGRFAMsiTIGR00347. bioD. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "Complete sequence of Vibrio fischeri strain MJ11."
    Mandel M.J., Stabb E.V., Ruby E.G., Ferriera S., Johnson J., Kravitz S., Beeson K., Sutton G., Rogers Y.-H., Friedman R., Frazier M., Venter J.C.
    Submitted (AUG-2008) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: MJ11.

Entry informationi

Entry nameiBIOD_VIBFM
AccessioniPrimary (citable) accession number: B5EUP7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 14, 2009
Last sequence update: October 14, 2008
Last modified: November 11, 2015
This is version 55 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

Documents

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

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 one 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.