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Protein

ATP-dependent dethiobiotin synthetase BioD

Gene

bioD

Organism
Frankia sp. (strain CcI3)
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 1 (bioB1), Biotin synthase 2 (bioB2)
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 bindingi16Magnesium 2UniRule annotation1
Binding sitei41SubstrateUniRule annotation1
Metal bindingi50Magnesium 2UniRule annotation1
Binding sitei50ATPUniRule annotation1
Metal bindingi109Magnesium 2UniRule annotation1

Regions

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

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:Francci3_3762
OrganismiFrankia sp. (strain CcI3)
Taxonomic identifieri106370 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaFrankialesFrankiaceaeFrankia
Proteomesi
  • UP000001937 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003025111 – 238ATP-dependent dethiobiotin synthetase BioDAdd BLAST238

Interactioni

Protein-protein interaction databases

STRINGi106370.Francci3_3762.

Structurei

3D structure databases

ProteinModelPortaliQ2J6H9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the dethiobiotin synthetase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4107WHG. Bacteria.
COG0132. LUCA.
HOGENOMiHOG000275033.
KOiK01935.
OMAiRCNLADL.
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.

Q2J6H9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTALVVTGTG TGVGKTVVTA AIGALAHDRH HAVAVVKPAQ TGVGPGELGD
60 70 80 90 100
VDLVRDLTGI TDVHELARYP DPLAPATAAR RSGHRAVDLD ELAARIGTLA
110 120 130 140 150
DSRDLVLVEG AGGLLVRYDA GGATLADLAR VLRAPVLVVT AAGLGALNDT
160 170 180 190 200
ALTLEALAHR GLDLAGVVVG SWPAEPDLAC RCNLIDLESL AARPLAGVLP
210 220 230
AGAGLLARLE FLAVARASLQ PALGGTFRAQ EFRARYET
Length:238
Mass (Da):24,273
Last modified:March 7, 2006 - v1
Checksum:iE82AC3C553209B84
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000249 Genomic DNA. Translation: ABD13113.1.
RefSeqiWP_011438137.1. NC_007777.1.

Genome annotation databases

EnsemblBacteriaiABD13113; ABD13113; Francci3_3762.
KEGGifra:Francci3_3762.
PATRICi21930986. VBIFraSp10456_4097.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000249 Genomic DNA. Translation: ABD13113.1.
RefSeqiWP_011438137.1. NC_007777.1.

3D structure databases

ProteinModelPortaliQ2J6H9.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi106370.Francci3_3762.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABD13113; ABD13113; Francci3_3762.
KEGGifra:Francci3_3762.
PATRICi21930986. VBIFraSp10456_4097.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayiUPA00078; UER00161.

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_FRASC
AccessioniPrimary (citable) accession number: Q2J6H9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 11, 2007
Last sequence update: March 7, 2006
Last modified: November 2, 2016
This is version 69 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.