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Protein

ATP-dependent dethiobiotin synthetase BioD

Gene

bioD

Organism
Corynebacterium glutamicum (strain R)
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)DescriptionActionsGraphical viewLength
Metal bindingi16Magnesium 2UniRule annotation1
Binding sitei41SubstrateUniRule annotation1
Metal bindingi107Magnesium 2UniRule annotation1
Binding sitei204ATPUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi107 – 110ATPUniRule annotation4
Nucleotide bindingi197 – 199ATPUniRule 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:cgR_2509
OrganismiCorynebacterium glutamicum (strain R)
Taxonomic identifieri340322 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesCorynebacteriaceaeCorynebacterium
Proteomesi
  • UP000006698 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_00003025031 – 224ATP-dependent dethiobiotin synthetase BioDAdd BLAST224

Structurei

3D structure databases

ProteinModelPortaliA4QH04.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the dethiobiotin synthetase family.UniRule annotation

Phylogenomic databases

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.

A4QH04-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPFLFVSGTG TGVGKTFSTA VLVRYLADQG HDVLPVKLVQ TGELPGEGDI
60 70 80 90 100
FTIERLTGIA GEEFARFKDP LAPNLAARRE GIEPIQFDQI ISWLRGFDDP
110 120 130 140 150
DRIIVVEGAG GLLVRLGEDF TLADVASALN APLVIVTSTG LGSLNAAELS
160 170 180 190 200
VEAANRRGLT VLGVLGGSIP QNPDLATMLN LEEFERVTGV PFWGALPEGL
210 220
SRVEGFVEKQ SFPALDAFKK PPAR
Length:224
Mass (Da):23,856
Last modified:May 15, 2007 - v1
Checksum:i34E32D9E2DECBB1A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP009044 Genomic DNA. Translation: BAF55520.1.
RefSeqiWP_011897849.1. NC_009342.1.

Genome annotation databases

EnsemblBacteriaiBAF55520; BAF55520; cgR_2509.
KEGGicgt:cgR_2509.
PATRICi21509704. VBICorGlu58097_2575.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP009044 Genomic DNA. Translation: BAF55520.1.
RefSeqiWP_011897849.1. NC_009342.1.

3D structure databases

ProteinModelPortaliA4QH04.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAF55520; BAF55520; cgR_2509.
KEGGicgt:cgR_2509.
PATRICi21509704. VBICorGlu58097_2575.

Phylogenomic databases

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_CORGB
AccessioniPrimary (citable) accession number: A4QH04
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 11, 2007
Last sequence update: May 15, 2007
Last modified: November 2, 2016
This is version 61 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

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.