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Protein

ATP-dependent dethiobiotin synthetase BioD

Gene

bioD

Organism
Janthinobacterium sp. (strain Marseille) (Minibacterium massiliensis)
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 bindingi15 – 151Magnesium 1UniRule annotation
Metal bindingi19 – 191Magnesium 2UniRule annotation
Metal bindingi61 – 611Magnesium 2UniRule annotation
Binding sitei61 – 611ATPUniRule annotation
Metal bindingi122 – 1221Magnesium 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi122 – 1254ATPUniRule annotation
Nucleotide bindingi182 – 1832ATPUniRule annotation
Nucleotide bindingi211 – 2133ATPUniRule 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

BioCyciJSP375286:GJ8U-122-MONOMER.
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:mma_0122
OrganismiJanthinobacterium sp. (strain Marseille) (Minibacterium massiliensis)
Taxonomic identifieri375286 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesOxalobacteraceaeJanthinobacterium
Proteomesi
  • UP000006388 Componenti: Chromosome

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 – 236236ATP-dependent dethiobiotin synthetase BioDPRO_1000019561Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi375286.mma_0122.

Structurei

3D structure databases

ProteinModelPortaliA6SU65.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the dethiobiotin synthetase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105E78. Bacteria.
COG0132. LUCA.
HOGENOMiHOG000275032.
KOiK01935.
OMAiCINHAVL.
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.

A6SU65-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTATFNCFVT GTDTEIGKTM ISTALLHALV QQGVKAAAIK SVAAGATAIQ
60 70 80 90 100
TNEGEVWHND DADALAQAAN VVLPRELATP YLLHEACAPH VSAELQGVAI
110 120 130 140 150
DIAHIKNCYV QVREMAEAVV VEGVGGFRVP LSDHADTADL ARELALPVIM
160 170 180 190 200
VVGLRLGCLN HALLTADAIA ARGLKLVGWV ANTVDAGMPF AEDNVAALAA
210 220 230
RLSAPLLGCV PRLAAPLPAA AAAYLDFSCL PNWPKA
Length:236
Mass (Da):24,488
Last modified:August 21, 2007 - v1
Checksum:i149736B6FD05A446
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000269 Genomic DNA. Translation: ABR89188.1.
RefSeqiWP_011979348.1. NC_009659.1.

Genome annotation databases

EnsemblBacteriaiABR89188; ABR89188; mma_0122.
KEGGimms:mma_0122.
PATRICi22152641. VBIJanSp106498_0126.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000269 Genomic DNA. Translation: ABR89188.1.
RefSeqiWP_011979348.1. NC_009659.1.

3D structure databases

ProteinModelPortaliA6SU65.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi375286.mma_0122.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABR89188; ABR89188; mma_0122.
KEGGimms:mma_0122.
PATRICi22152641. VBIJanSp106498_0126.

Phylogenomic databases

eggNOGiENOG4105E78. Bacteria.
COG0132. LUCA.
HOGENOMiHOG000275032.
KOiK01935.
OMAiCINHAVL.
OrthoDBiEOG66B3XT.

Enzyme and pathway databases

UniPathwayiUPA00078; UER00161.
BioCyciJSP375286:GJ8U-122-MONOMER.

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. "Genome analysis of Minibacterium massiliensis highlights the convergent evolution of water-living bacteria."
    Audic S., Robert C., Campagna B., Parinello H., Claverie J.-M., Raoult D., Drancourt M.
    PLoS Genet. 3:1454-1463(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Marseille.

Entry informationi

Entry nameiBIOD_JANMA
AccessioniPrimary (citable) accession number: A6SU65
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: August 21, 2007
Last modified: December 9, 2015
This is version 56 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.