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Protein

ATP-dependent dethiobiotin synthetase BioD

Gene

bioD

Organism
Sphingopyxis alaskensis (strain DSM 13593 / LMG 18877 / RB2256) (Sphingomonas alaskensis)
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 sitei36SubstrateUniRule annotation1
Metal bindingi43Magnesium 2UniRule annotation1
Binding sitei43ATPUniRule annotation1
Metal bindingi94Magnesium 2UniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi94 – 97ATPUniRule annotation4
Nucleotide bindingi178 – 180ATPUniRule 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:Sala_1474
OrganismiSphingopyxis alaskensis (strain DSM 13593 / LMG 18877 / RB2256) (Sphingomonas alaskensis)
Taxonomic identifieri317655 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaSphingomonadalesSphingomonadaceaeSphingopyxis
Proteomesi
  • UP000006578 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_10000597111 – 202ATP-dependent dethiobiotin synthetase BioDAdd BLAST202

Interactioni

Protein-protein interaction databases

STRINGi317655.Sala_1474.

Structurei

3D structure databases

ProteinModelPortaliQ1GT35.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the dethiobiotin synthetase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105E78. Bacteria.
COG0132. LUCA.
HOGENOMiHOG000275033.
KOiK01935.
OMAiLILCART.
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.

Q1GT35-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTRFVVTGTD TGIGKTIFSA SLARATGTPY WKPVQSGLEE ETDSEIVARL
60 70 80 90 100
AGVPVRPEAY RLVTPASPHI AAEIDGVAID IERLTPPPGE LIVEGAGGAL
110 120 130 140 150
VPVTRRTLYA ELFARWQVPV IVCARTSLGT INHSLLTIEA LKRRDVPIHG
160 170 180 190 200
VVFIGDAVED SEAIIADVSG VRRLGRLPVV APLTSENLAA AFGANFDIAD

FR
Length:202
Mass (Da):21,507
Last modified:June 27, 2006 - v1
Checksum:i6747C389422C5B50
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000356 Genomic DNA. Translation: ABF53187.1.
RefSeqiWP_011541767.1. NC_008048.1.

Genome annotation databases

EnsemblBacteriaiABF53187; ABF53187; Sala_1474.
KEGGisal:Sala_1474.
PATRICi23692186. VBISphAla23391_1525.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000356 Genomic DNA. Translation: ABF53187.1.
RefSeqiWP_011541767.1. NC_008048.1.

3D structure databases

ProteinModelPortaliQ1GT35.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi317655.Sala_1474.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABF53187; ABF53187; Sala_1474.
KEGGisal:Sala_1474.
PATRICi23692186. VBISphAla23391_1525.

Phylogenomic databases

eggNOGiENOG4105E78. Bacteria.
COG0132. LUCA.
HOGENOMiHOG000275033.
KOiK01935.
OMAiLILCART.
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_SPHAL
AccessioniPrimary (citable) accession number: Q1GT35
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 5, 2008
Last sequence update: June 27, 2006
Last modified: November 2, 2016
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.