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Protein

ATP-dependent dethiobiotin synthetase BioD

Gene

bioD

Organism
Magnetospirillum magneticum (strain AMB-1 / ATCC 700264)
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 sitei36 – 361SubstrateUniRule annotation
Metal bindingi97 – 971Magnesium 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi97 – 1004ATPUniRule 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

BioCyciMMAG342108:GJNU-2792-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:amb2762
OrganismiMagnetospirillum magneticum (strain AMB-1 / ATCC 700264)
Taxonomic identifieri342108 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhodospirillalesRhodospirillaceaeMagnetospirillum
Proteomesi
  • UP000007058 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 – 205205ATP-dependent dethiobiotin synthetase BioDPRO_1000079274Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi342108.amb2762.

Structurei

3D structure databases

ProteinModelPortaliQ2W3K9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the dethiobiotin synthetase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105E78. Bacteria.
COG0132. LUCA.
HOGENOMiHOG000275033.
KOiK01935.
OMAiDATYWKP.
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.

Q2W3K9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRGVFVTGTD TDVGKTMVSA WLAQHWRADY WKPIQTGSTE GTDFESVARL
60 70 80 90 100
APAARIHPSA VVLPAPLSPH EAARREKTRI DLSSLVPPVT DRPLVVEGAG
110 120 130 140 150
GIMVPINEVA LMIDLMERLS LPAVVVARSG LGTINHTLMT LEMLRRRRVP
160 170 180 190 200
LLGVVMNGQK NPANRQAIEH FGGVRVLAEI QPLPAVTAAT IAGLPPPTFT

CPGDP
Length:205
Mass (Da):21,998
Last modified:January 10, 2006 - v1
Checksum:i967474C4895FC592
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP007255 Genomic DNA. Translation: BAE51566.1.
RefSeqiWP_011385141.1. NC_007626.1.

Genome annotation databases

EnsemblBacteriaiBAE51566; BAE51566; amb2762.
KEGGimag:amb2762.
PATRICi22439772. VBIMagMag129836_2725.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP007255 Genomic DNA. Translation: BAE51566.1.
RefSeqiWP_011385141.1. NC_007626.1.

3D structure databases

ProteinModelPortaliQ2W3K9.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi342108.amb2762.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAE51566; BAE51566; amb2762.
KEGGimag:amb2762.
PATRICi22439772. VBIMagMag129836_2725.

Phylogenomic databases

eggNOGiENOG4105E78. Bacteria.
COG0132. LUCA.
HOGENOMiHOG000275033.
KOiK01935.
OMAiDATYWKP.
OrthoDBiEOG66B3XT.

Enzyme and pathway databases

UniPathwayiUPA00078; UER00161.
BioCyciMMAG342108:GJNU-2792-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. "Complete genome sequence of the facultative anaerobic magnetotactic bacterium Magnetospirillum sp. strain AMB-1."
    Matsunaga T., Okamura Y., Fukuda Y., Wahyudi A.T., Murase Y., Takeyama H.
    DNA Res. 12:157-166(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: AMB-1 / ATCC 700264.

Entry informationi

Entry nameiBIOD_MAGSA
AccessioniPrimary (citable) accession number: Q2W3K9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 20, 2008
Last sequence update: January 10, 2006
Last modified: December 9, 2015
This is version 73 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.