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Protein

ATP-dependent dethiobiotin synthetase BioD

Gene

bioD

Organism
Streptomyces avermitilis (strain ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680)
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 bindingi109 – 1091Magnesium 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi12 – 176ATPUniRule annotation
Nucleotide bindingi109 – 1124ATPUniRule annotation
Nucleotide bindingi200 – 2023ATPUniRule 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

BioCyciSAVE227882:GJU1-7187-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:SAV_7091
OrganismiStreptomyces avermitilis (strain ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680)
Taxonomic identifieri227882 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaStreptomycetalesStreptomycetaceaeStreptomyces
Proteomesi
  • UP000000428 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 – 238238ATP-dependent dethiobiotin synthetase BioDPRO_0000302550Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi227882.SAV_7091.

Structurei

3D structure databases

ProteinModelPortaliQ826T4.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the dethiobiotin synthetase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4107WHG. Bacteria.
COG0132. LUCA.
HOGENOMiHOG000275033.
KOiK01935.
OMAiVLNEYEG.
OrthoDBiEOG6ZWJF4.

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.

Q826T4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSVLVITGTG TEVGKTVTTA AVAAVAVAAG RSVAVLKPAQ TGVRPDERGD
60 70 80 90 100
ADEVARLAGA VTTLELARYP EPLAPATAAR RAGLPPVGPH EVAEAAAKLA
110 120 130 140 150
VEHDLVLVEG AGGLLVRFDD ADGTLADAAR LLDAPVLVVA SAGLGTLNTT
160 170 180 190 200
ELTARELRRR EIGFAGVVIG SWPESPDLAS RCNLADLPAV AGAGLLGAIP
210 220 230
AGAGAHSPVG FRAGAPGWLA PRLGGTWDAD TFASAFVP
Length:238
Mass (Da):23,768
Last modified:June 1, 2003 - v1
Checksum:i4A9CB6361C54E824
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000030 Genomic DNA. Translation: BAC74802.1.
RefSeqiWP_010988486.1. NZ_JZJK01000085.1.

Genome annotation databases

EnsemblBacteriaiBAC74802; BAC74802; SAV_7091.
KEGGisma:SAV_7091.
PATRICi23728342. VBIStrAve112782_7510.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000030 Genomic DNA. Translation: BAC74802.1.
RefSeqiWP_010988486.1. NZ_JZJK01000085.1.

3D structure databases

ProteinModelPortaliQ826T4.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi227882.SAV_7091.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAC74802; BAC74802; SAV_7091.
KEGGisma:SAV_7091.
PATRICi23728342. VBIStrAve112782_7510.

Phylogenomic databases

eggNOGiENOG4107WHG. Bacteria.
COG0132. LUCA.
HOGENOMiHOG000275033.
KOiK01935.
OMAiVLNEYEG.
OrthoDBiEOG6ZWJF4.

Enzyme and pathway databases

UniPathwayiUPA00078; UER00161.
BioCyciSAVE227882:GJU1-7187-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 sequence of an industrial microorganism Streptomyces avermitilis: deducing the ability of producing secondary metabolites."
    Omura S., Ikeda H., Ishikawa J., Hanamoto A., Takahashi C., Shinose M., Takahashi Y., Horikawa H., Nakazawa H., Osonoe T., Kikuchi H., Shiba T., Sakaki Y., Hattori M.
    Proc. Natl. Acad. Sci. U.S.A. 98:12215-12220(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680.
  2. "Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis."
    Ikeda H., Ishikawa J., Hanamoto A., Shinose M., Kikuchi H., Shiba T., Sakaki Y., Hattori M., Omura S.
    Nat. Biotechnol. 21:526-531(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680.

Entry informationi

Entry nameiBIOD_STRAW
AccessioniPrimary (citable) accession number: Q826T4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 11, 2007
Last sequence update: June 1, 2003
Last modified: November 11, 2015
This is version 81 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.