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Protein

ATP-dependent dethiobiotin synthetase BioD 2

Gene

bioD2

Organism
Escherichia coli (strain K12)
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 1 (bioD1), ATP-dependent dethiobiotin synthetase BioD 2 (bioD2)
  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 bindingi17 – 171Magnesium 2UniRule annotation
Metal bindingi55 – 551Magnesium 2UniRule annotation
Binding sitei55 – 551ATPUniRule annotation
Metal bindingi112 – 1121Magnesium 2UniRule annotation
Binding sitei208 – 2081ATPUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi13 – 186ATPUniRule annotation
Nucleotide bindingi112 – 1154ATPUniRule annotation
Nucleotide bindingi172 – 1732ATPUniRule annotation
Nucleotide bindingi201 – 2033ATPUniRule 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

BioCyciEcoCyc:G6851-MONOMER.
ECOL316407:JW5264-MONOMER.
UniPathwayiUPA00078; UER00161.

Names & Taxonomyi

Protein namesi
Recommended name:
ATP-dependent dethiobiotin synthetase BioD 2UniRule annotation (EC:6.3.3.3UniRule annotation)
Alternative name(s):
DTB synthetase 2UniRule annotation
Short name:
DTBS 2UniRule annotation
Dethiobiotin synthase 2UniRule annotation
Gene namesi
Name:bioD2UniRule annotation
Synonyms:ynfK
Ordered Locus Names:b1593, JW5264
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13849. ynfK.

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 – 231231ATP-dependent dethiobiotin synthetase BioD 2PRO_0000187962Add
BLAST

Proteomic databases

PaxDbiP0A6E9.

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

BioGridi4259412. 13 interactions.
IntActiP0A6E9. 3 interactions.
STRINGi511145.b1593.

Structurei

3D structure databases

ProteinModelPortaliP0A6E9.
SMRiP0A6E9. Positions 3-220.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the dethiobiotin synthetase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105EWW. Bacteria.
COG0132. LUCA.
HOGENOMiHOG000275032.
InParanoidiP0A6E9.
KOiK01935.
OMAiANRINPC.
PhylomeDBiP0A6E9.

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.

P0A6E9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLKRFFITGT DTSVGKTVVS RALLQALASQ GKTVAGYKPV AKGSKETPEG
60 70 80 90 100
LRNKDALVLQ SVSTIELPYE AVNPIALSEE ESSVAHSCPI NYTLISNGLA
110 120 130 140 150
NLTEKVDHVV VEGTGGWRSL MNDLRPLSEW VVQEQLPVLM VVGIQEGCIN
160 170 180 190 200
HALLTAQAIA NDGLPLIGWV ANRINPGLAH YAEIIDVLGK KLPAPLIGEL
210 220 230
PYLPRAEQRE LGQYIRLAML RSVLAVDRVT V
Length:231
Mass (Da):24,981
Last modified:June 7, 2005 - v1
Checksum:i35A04911309A99B0
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC74665.2.
AP009048 Genomic DNA. Translation: BAA15317.2.
PIRiC64915.
RefSeqiNP_416110.4. NC_000913.3.
WP_000919231.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC74665; AAC74665; b1593.
BAA15317; BAA15317; BAA15317.
GeneIDi944927.
KEGGiecj:JW5264.
eco:b1593.
PATRICi32118488. VBIEscCol129921_1664.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC74665.2.
AP009048 Genomic DNA. Translation: BAA15317.2.
PIRiC64915.
RefSeqiNP_416110.4. NC_000913.3.
WP_000919231.1. NZ_LN832404.1.

3D structure databases

ProteinModelPortaliP0A6E9.
SMRiP0A6E9. Positions 3-220.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259412. 13 interactions.
IntActiP0A6E9. 3 interactions.
STRINGi511145.b1593.

Proteomic databases

PaxDbiP0A6E9.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74665; AAC74665; b1593.
BAA15317; BAA15317; BAA15317.
GeneIDi944927.
KEGGiecj:JW5264.
eco:b1593.
PATRICi32118488. VBIEscCol129921_1664.

Organism-specific databases

EchoBASEiEB3610.
EcoGeneiEG13849. ynfK.

Phylogenomic databases

eggNOGiENOG4105EWW. Bacteria.
COG0132. LUCA.
HOGENOMiHOG000275032.
InParanoidiP0A6E9.
KOiK01935.
OMAiANRINPC.
PhylomeDBiP0A6E9.

Enzyme and pathway databases

UniPathwayiUPA00078; UER00161.
BioCyciEcoCyc:G6851-MONOMER.
ECOL316407:JW5264-MONOMER.

Miscellaneous databases

PROiP0A6E9.

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 nameiBIOD2_ECOLI
AccessioniPrimary (citable) accession number: P0A6E9
Secondary accession number(s): P77201, Q8X788
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 7, 2005
Last sequence update: June 7, 2005
Last modified: September 7, 2016
This is version 86 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. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. 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.