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Protein

ATP-dependent dethiobiotin synthetase BioD

Gene

bioD

Organism
Ilyobacter polytropus (strain DSM 2926 / CuHBu1)
Status
Unreviewed-Annotation score: Annotation score: 4 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 annotationSAAS annotation

Catalytic activityi

ATP + 7,8-diaminononanoate + CO2 = ADP + phosphate + dethiobiotin.UniRule annotationSAAS annotation
ATP + thymidine = ADP + thymidine 5'-phosphate.UniRule annotation

Cofactori

Mg2+UniRule annotationSAAS annotation

Pathwayi: biotin biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes biotin from 7,8-diaminononanoate.UniRule annotationSAAS 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), 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
Active sitei94Proton acceptorUniRule annotation1
Metal bindingi150ZincUniRule annotation1
Metal bindingi153ZincUniRule annotation1
Metal bindingi188ZincUniRule annotation1
Metal bindingi191ZincUniRule annotation1
Metal bindingi213Magnesium 1UniRule annotation1
Metal bindingi217Magnesium 2UniRule annotation1
Binding sitei242SubstrateUniRule annotation1
Metal bindingi255Magnesium 2UniRule annotation1
Binding sitei255ATPUniRule annotation1
Metal bindingi314Magnesium 2UniRule annotation1
Binding sitei405ATPUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi17 – 24ATPUniRule annotation8
Nucleotide bindingi93 – 96ATPUniRule annotation4
Nucleotide bindingi376 – 377ATPUniRule annotation2

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywordsi

Molecular functionKinaseUniRule annotation, LigaseUniRule annotationSAAS annotationImported, Transferase
Biological processBiotin biosynthesisUniRule annotationSAAS annotation, DNA synthesisUniRule annotation
LigandATP-bindingUniRule annotationSAAS annotation, MagnesiumUniRule annotationSAAS annotation, Metal-bindingUniRule annotationSAAS annotation, Nucleotide-binding, ZincUniRule annotation

Enzyme and pathway databases

BioCyciIPOL572544:GJ9I-1573-MONOMER.
UniPathwayiUPA00078; UER00161.

Names & Taxonomyi

Protein namesi
Recommended name:
ATP-dependent dethiobiotin synthetase BioDUniRule annotation (EC:2.7.1.21UniRule annotation, EC:6.3.3.3UniRule annotation)
Alternative name(s):
DTB synthetaseUniRule annotation
Dethiobiotin synthaseUniRule annotation
Short name:
DTBSUniRule annotation
Thymidine kinaseUniRule annotation
Gene namesi
Name:bioDUniRule annotation
Synonyms:tdkUniRule annotation
Ordered Locus Names:Ilyop_1552Imported
OrganismiIlyobacter polytropus (strain DSM 2926 / CuHBu1)Imported
Taxonomic identifieri572544 [NCBI]
Taxonomic lineageiBacteriaFusobacteriaFusobacterialesFusobacteriaceaeIlyobacter
Proteomesi
  • UP000006875 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotationSAAS annotation

GO - Cellular componenti

Keywords - Cellular componenti

CytoplasmUniRule annotationSAAS annotation

Interactioni

Subunit structurei

Homotetramer.UniRule annotation

Protein-protein interaction databases

STRINGi572544.Ilyop_1552.

Family & Domainsi

Sequence similaritiesi

Belongs to the dethiobiotin synthetase family.UniRule annotationSAAS annotation
Belongs to the thymidine kinase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4107UGU. Bacteria.
COG0132. LUCA.
COG1435. LUCA.
HOGENOMiHOG000109206.
KOiK00857.
OMAiNGEPAYY.
OrthoDBiPOG091H0659.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
HAMAPiMF_00336. BioD. 1 hit.
MF_00124. Thymidine_kinase. 1 hit.
InterProiIPR004472. DTB_synth_BioD.
IPR027417. P-loop_NTPase.
IPR001267. Thymidine_kinase.
IPR020633. Thymidine_kinase_CS.
[Graphical view]
PANTHERiPTHR11441. PTHR11441. 1 hit.
PfamiPF00265. TK. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 2 hits.
TIGRFAMsiTIGR00347. bioD. 1 hit.
PROSITEiPS00603. TK_CELLULAR_TYPE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

E3H8R7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MHFLLTEGMG WIEVITGGMF SGKSEELIRR LIRSKYASQK VVAFKHSIDK
60 70 80 90 100
RYDESNVVSH SSIFIEGVPA ASVKEMEKIF YEKYSDAEVI GIDEVQFFGE
110 120 130 140 150
PVVEFCEKLS DMGKRVIVAG LDQDFRGEPF EPIDSLLAKA EYVDKLSAIC
160 170 180 190 200
AVCGNPASRT QRLVNGEPAY YNDPVVLVGA SESYEARCRK CHVVKREDNK
210 220 230 240 250
EGKLYFIVGT DTDIGKTYAG LKLVKQEMDK GLKVTAIKPV ETGSETFPEN
260 270 280 290 300
LEGSDSYAYA RLLGKNVEDV NIFFYKKPMS PDAAAEADET SVDIKTIKEK
310 320 330 340 350
IDKELLENDV VFVEGAGGLL VPFVENYMYL DLLVDYRKKS EVILISGNVL
360 370 380 390 400
GTINHTLLTI DVLKRNDIKI KGVVFNNKEN IEDKKFLKNN VETVKRIGKV
410
EILAENEYGE
Length:410
Mass (Da):45,957
Last modified:January 11, 2011 - v1
Checksum:iC26462E2FC69FFDF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP002281 Genomic DNA. Translation: ADO83331.1.

Genome annotation databases

EnsemblBacteriaiADO83331; ADO83331; Ilyop_1552.
KEGGiipo:Ilyop_1552.
PATRICi42646847. VBIIlyPol34265_1600.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP002281 Genomic DNA. Translation: ADO83331.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi572544.Ilyop_1552.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiADO83331; ADO83331; Ilyop_1552.
KEGGiipo:Ilyop_1552.
PATRICi42646847. VBIIlyPol34265_1600.

Phylogenomic databases

eggNOGiENOG4107UGU. Bacteria.
COG0132. LUCA.
COG1435. LUCA.
HOGENOMiHOG000109206.
KOiK00857.
OMAiNGEPAYY.
OrthoDBiPOG091H0659.

Enzyme and pathway databases

UniPathwayiUPA00078; UER00161.
BioCyciIPOL572544:GJ9I-1573-MONOMER.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
HAMAPiMF_00336. BioD. 1 hit.
MF_00124. Thymidine_kinase. 1 hit.
InterProiIPR004472. DTB_synth_BioD.
IPR027417. P-loop_NTPase.
IPR001267. Thymidine_kinase.
IPR020633. Thymidine_kinase_CS.
[Graphical view]
PANTHERiPTHR11441. PTHR11441. 1 hit.
PfamiPF00265. TK. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 2 hits.
TIGRFAMsiTIGR00347. bioD. 1 hit.
PROSITEiPS00603. TK_CELLULAR_TYPE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiE3H8R7_ILYPC
AccessioniPrimary (citable) accession number: E3H8R7
Entry historyiIntegrated into UniProtKB/TrEMBL: January 11, 2011
Last sequence update: January 11, 2011
Last modified: January 18, 2017
This is version 49 of the entry and version 1 of the sequence. See complete history.
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Caution

Lacks conserved residue(s) required for the propagation of feature annotation.UniRule annotation

Keywords - Technical termi

Complete proteome, Reference proteomeImported

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.