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Protein

ATP-dependent dethiobiotin synthetase BioD

Gene

bioD

Organism
Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

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), ATP-dependent dethiobiotin synthetase BioD (bioD)
  2. Biotin synthase (bioB), 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 bindingi12Magnesium 1UniRule annotation1
Metal bindingi16Magnesium 2UniRule annotation1
Binding sitei41SubstrateUniRule annotation1
Metal bindingi52Magnesium 2UniRule annotation1
Binding sitei52ATPUniRule annotation1
Metal bindingi114Magnesium 2UniRule annotation1
Binding sitei225ATPUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi114 – 117ATPUniRule annotation4
Nucleotide bindingi174 – 175ATPUniRule annotation2

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:FTT_0934c
OrganismiFrancisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4)
Taxonomic identifieri177416 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaThiotrichalesFrancisellaceaeFrancisella
Proteomesi
  • UP000001174 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_00003025081 – 225ATP-dependent dethiobiotin synthetase BioDAdd BLAST225

Interactioni

Subunit structurei

Homodimer.UniRule annotation1 Publication

Protein-protein interaction databases

STRINGi177416.FTT_0934c.

Structurei

Secondary structure

1225
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 13Combined sources12
Helixi15 – 28Combined sources14
Beta strandi33 – 36Combined sources4
Beta strandi38 – 43Combined sources6
Beta strandi45 – 50Combined sources6
Helixi51 – 59Combined sources9
Turni60 – 62Combined sources3
Helixi66 – 69Combined sources4
Beta strandi71 – 78Combined sources8
Helixi80 – 86Combined sources7
Helixi93 – 101Combined sources9
Helixi102 – 105Combined sources4
Beta strandi109 – 118Combined sources10
Beta strandi122 – 126Combined sources5
Helixi129 – 136Combined sources8
Beta strandi140 – 145Combined sources6
Helixi150 – 163Combined sources14
Beta strandi168 – 175Combined sources8
Helixi183 – 194Combined sources12
Beta strandi199 – 205Combined sources7
Helixi208 – 218Combined sources11

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3OF5X-ray1.52A/B1-225[»]
ProteinModelPortaliQ5NGB5.
SMRiQ5NGB5.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ5NGB5.

Family & Domainsi

Sequence similaritiesi

Belongs to the dethiobiotin synthetase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105E78. Bacteria.
COG0132. LUCA.
HOGENOMiHOG000275032.
KOiK01935.
OMAiCINHAVL.

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.

Q5NGB5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKKFFIIGTD TEVGKTYIST KLIEVCEHQN IKSLCLKPVA SGQSQFSELC
60 70 80 90 100
EDVESILNAY KHKFTAAEIN LISFNQAVAP HIIAAKTKVD ISIENLKQFI
110 120 130 140 150
EDKYNQDLDI LFIEGAGGLL TPYSDHTTQL DLIKALQIPV LLVSAIKVGC
160 170 180 190 200
INHTLLTINE LNRHNIKLAG WIANCNDSNI KYIDEQINTI EELSGYKCSA
210 220
KISRNADYLD FIDLSKILIS PEENE
Length:225
Mass (Da):25,189
Last modified:February 1, 2005 - v1
Checksum:i30D1D017AAAC89AC
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ749949 Genomic DNA. Translation: CAG45567.1.
RefSeqiWP_003020969.1. NZ_CP010290.1.
YP_169927.1. NC_006570.2.

Genome annotation databases

EnsemblBacteriaiCAG45567; CAG45567; FTT_0934c.
GeneIDi3190963.
KEGGiftu:FTT_0934c.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ749949 Genomic DNA. Translation: CAG45567.1.
RefSeqiWP_003020969.1. NZ_CP010290.1.
YP_169927.1. NC_006570.2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3OF5X-ray1.52A/B1-225[»]
ProteinModelPortaliQ5NGB5.
SMRiQ5NGB5.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi177416.FTT_0934c.

Protocols and materials databases

DNASUi3190963.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAG45567; CAG45567; FTT_0934c.
GeneIDi3190963.
KEGGiftu:FTT_0934c.

Phylogenomic databases

eggNOGiENOG4105E78. Bacteria.
COG0132. LUCA.
HOGENOMiHOG000275032.
KOiK01935.
OMAiCINHAVL.

Enzyme and pathway databases

UniPathwayiUPA00078; UER00161.

Miscellaneous databases

EvolutionaryTraceiQ5NGB5.

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_FRATT
AccessioniPrimary (citable) accession number: Q5NGB5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 11, 2007
Last sequence update: February 1, 2005
Last modified: November 2, 2016
This is version 74 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  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.