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Protein

ATP-dependent dethiobiotin synthetase BioD

Gene

bioD

Organism
Rhodococcus jostii (strain RHA1)
Status
Reviewed-Annotation score: -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)DescriptionActionsGraphical viewLength
Metal bindingi12Magnesium 1UniRule annotation1
Metal bindingi16Magnesium 2UniRule annotation1
Binding sitei41SubstrateUniRule annotation1
Metal bindingi50Magnesium 2UniRule annotation1
Binding sitei50ATPUniRule annotation1
Metal bindingi109Magnesium 2UniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi12 – 17ATPUniRule annotation6
Nucleotide bindingi109 – 112ATPUniRule annotation4
Nucleotide bindingi200 – 202ATPUniRule annotation3

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionLigase
Biological processBiotin biosynthesis
LigandATP-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciRJOS101510:G1G71-1050-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:RHA1_ro01053
OrganismiRhodococcus jostii (strain RHA1)
Taxonomic identifieri101510 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesNocardiaceaeRhodococcus
Proteomesi
  • UP000008710 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003025421 – 231ATP-dependent dethiobiotin synthetase BioDAdd BLAST231

Interactioni

Protein-protein interaction databases

STRINGi101510.RHA1_ro01053

Structurei

3D structure databases

ProteinModelPortaliQ0SHV6
SMRiQ0SHV6
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the dethiobiotin synthetase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4107WHG Bacteria
COG0132 LUCA
HOGENOMiHOG000275033
KOiK01935
OMAiDYWKPIQ
OrthoDBiPOG091H004W

Family and domain databases

HAMAPiMF_00336 BioD, 1 hit
InterProiView protein in InterPro
IPR004472 DTB_synth_BioD
IPR027417 P-loop_NTPase
PANTHERiPTHR43210 PTHR43210, 1 hit
PIRSFiPIRSF006755 DTB_synth, 1 hit
SUPFAMiSSF52540 SSF52540, 1 hit
TIGRFAMsiTIGR00347 bioD, 1 hit

Sequencei

Sequence statusi: Complete.

Q0SHV6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSILVVTGTS TDVGKTVVTA ALAAAAREAG LSVAVCKPAQ TGVAPGGPGD
60 70 80 90 100
LAEVTRLSGV TAVVELARYP EPLAPDTAAR RSGLPMLRCA DVVETVRALD
110 120 130 140 150
DGHDLVLVEG AGGLLVRLGA EGFTLVDLAR ALDAPAVVVA AAGLGTLNHT
160 170 180 190 200
ELTIRALSAA GLACAGTVIG SWPDEPGLAE RCNLDDLPAV TGVDVVGSVP
210 220 230
AGSGRLASAS FGAAASTWFD STWLKSTLTR L
Length:231
Mass (Da):23,047
Last modified:September 5, 2006 - v1
Checksum:i3287C064D24AF150
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000431 Genomic DNA Translation: ABG92880.1
RefSeqiWP_011594202.1, NC_008268.1

Genome annotation databases

EnsemblBacteriaiABG92880; ABG92880; RHA1_ro01053
GeneIDi4219563
KEGGirha:RHA1_ro01053
PATRICifig|101510.16.peg.1076

Similar proteinsi

Entry informationi

Entry nameiBIOD_RHOJR
AccessioniPrimary (citable) accession number: Q0SHV6
Entry historyiIntegrated into UniProtKB/Swiss-Prot: September 11, 2007
Last sequence update: September 5, 2006
Last modified: May 23, 2018
This is version 79 of the entry and version 1 of the sequence. See 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

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