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Protein

ATP-dependent dethiobiotin synthetase BioD

Gene

bioD

Organism
Rhodococcus erythropolis (strain PR4 / NBRC 100887)
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 bindingi12 – 121Magnesium 1UniRule annotation
Metal bindingi16 – 161Magnesium 2UniRule annotation
Binding sitei41 – 411SubstrateUniRule annotation
Metal bindingi50 – 501Magnesium 2UniRule annotation
Binding sitei50 – 501ATPUniRule annotation
Metal bindingi110 – 1101Magnesium 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi12 – 176ATPUniRule annotation
Nucleotide bindingi110 – 1134ATPUniRule annotation
Nucleotide bindingi201 – 2033ATPUniRule 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

BioCyciRERY234621:GHDE-3544-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:RER_35030
OrganismiRhodococcus erythropolis (strain PR4 / NBRC 100887)
Taxonomic identifieri234621 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesNocardiaceaeRhodococcus
Proteomesi
  • UP000002204 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 – 227227ATP-dependent dethiobiotin synthetase BioDPRO_1000205213Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi234621.RER_35030.

Family & Domainsi

Sequence similaritiesi

Belongs to the dethiobiotin synthetase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4107WHG. Bacteria.
COG0132. LUCA.
HOGENOMiHOG000275033.
KOiK01935.
OMAiCINHAVL.
OrthoDBiPOG091H004W.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
HAMAPiMF_00336. BioD. 1 hit.
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.

C1A0S6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSIFLVTGTS TDVGKTVVTA ALASVALQSG KSVAVLKPAQ TGVDVDGAGD
60 70 80 90 100
LAEIERLTGG GVTLVELARY PEPLAPDTAA RRSGLPLLAL DDVVRVARDL
110 120 130 140 150
DTTHDLTLIE GAGGLLVRLG VDGFTARDLA AALAAPVVLV VASGLGTLNH
160 170 180 190 200
TALTVEALGA SGVECAGLVI GSWPQEPDLA ERCNREDLVS VSGVPLLGLM
210 220
PAGSGSESVQ EFAQTAWGAL GKSPLAI
Length:227
Mass (Da):22,840
Last modified:May 26, 2009 - v1
Checksum:iFC1BA3EE550859A2
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP008957 Genomic DNA. Translation: BAH34211.1.
RefSeqiWP_020908046.1. NC_012490.1.

Genome annotation databases

EnsemblBacteriaiBAH34211; BAH34211; RER_35030.
GeneIDi7712582.
KEGGirer:RER_35030.
PATRICi23193482. VBIRhoEry66701_4019.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP008957 Genomic DNA. Translation: BAH34211.1.
RefSeqiWP_020908046.1. NC_012490.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi234621.RER_35030.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAH34211; BAH34211; RER_35030.
GeneIDi7712582.
KEGGirer:RER_35030.
PATRICi23193482. VBIRhoEry66701_4019.

Phylogenomic databases

eggNOGiENOG4107WHG. Bacteria.
COG0132. LUCA.
HOGENOMiHOG000275033.
KOiK01935.
OMAiCINHAVL.
OrthoDBiPOG091H004W.

Enzyme and pathway databases

UniPathwayiUPA00078; UER00161.
BioCyciRERY234621:GHDE-3544-MONOMER.

Family and domain databases

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

Entry informationi

Entry nameiBIOD_RHOE4
AccessioniPrimary (citable) accession number: C1A0S6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 22, 2009
Last sequence update: May 26, 2009
Last modified: September 7, 2016
This is version 54 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

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.