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O24872 (BIOD_HELPY) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 88. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
ATP-dependent dethiobiotin synthetase BioD

EC=6.3.3.3
Alternative name(s):
DTB synthetase
Short name=DTBS
Dethiobiotin synthase
Gene names
Name:bioD
Ordered Locus Names:HP_0029
OrganismHelicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori) [Reference proteome] [HAMAP]
Taxonomic identifier85962 [NCBI]
Taxonomic lineageBacteriaProteobacteriaEpsilonproteobacteriaCampylobacteralesHelicobacteraceaeHelicobacter

Protein attributes

Sequence length218 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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 By similarity. HAMAP-Rule MF_00336

Catalytic activity

ATP + 7,8-diaminononanoate + CO2 = ADP + phosphate + dethiobiotin. HAMAP-Rule MF_00336

Cofactor

Magnesium By similarity. HAMAP-Rule MF_00336

Pathway

Cofactor biosynthesis; biotin biosynthesis; biotin from 7,8-diaminononanoate: step 1/2. HAMAP-Rule MF_00336

Subunit structure

Homodimer. Ref.3

Subcellular location

Cytoplasm By similarity HAMAP-Rule MF_00336.

Sequence similarities

Belongs to the dethiobiotin synthetase family.

Ontologies

Keywords
   Biological processBiotin biosynthesis
   Cellular componentCytoplasm
   LigandATP-binding
Magnesium
Metal-binding
Nucleotide-binding
   Molecular functionLigase
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processbiotin biosynthetic process

Inferred from electronic annotation. Source: UniProtKB-HAMAP

   Cellular_componentcytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionATP binding

Inferred from electronic annotation. Source: UniProtKB-HAMAP

dethiobiotin synthase activity

Inferred from sequence or structural similarity. Source: UniProtKB

magnesium ion binding

Inferred from electronic annotation. Source: UniProtKB-HAMAP

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 218218ATP-dependent dethiobiotin synthetase BioD HAMAP-Rule MF_00336
PRO_0000187971

Regions

Nucleotide binding9 – 157ATP HAMAP-Rule MF_00336
Nucleotide binding116 – 1194ATP HAMAP-Rule MF_00336
Nucleotide binding151 – 1544Substrate HAMAP-Rule MF_00336

Sites

Metal binding101Magnesium 1 By similarity
Metal binding141Magnesium 2
Metal binding501Magnesium 2
Metal binding1161Magnesium 2
Binding site351ATP
Binding site391Substrate
Binding site501ATP
Binding site631ATP
Binding site1751ATP

Secondary structure

............................................. 218
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
O24872 [UniParc].

Last modified January 1, 1998. Version 1.
Checksum: C818F3D3A88C6015

FASTA21824,407
        10         20         30         40         50         60 
MLFISATNTN AGKTTCARLL AQYCNACGVK TILLKPIETG VNDAINHSSD AHLFLQDNRL 

        70         80         90        100        110        120 
LDRSLTLKDI SFYRYHKVSA PLIAQQEEDP NAPIDTDNLT QRLHNFTKTY DLVIVEGAGG 

       130        140        150        160        170        180 
LCVPITLEEN MLDFALKLKA KMLLISHDNL GLINDCLLND FLLKSHQLDY KIAINLKGNN 

       190        200        210 
TAFHSISLPY IELFNTRSNN PIVIFQQSLK VLMSFALK 

« Hide

References

« Hide 'large scale' references
[1]"The complete genome sequence of the gastric pathogen Helicobacter pylori."
Tomb J.-F., White O., Kerlavage A.R., Clayton R.A., Sutton G.G., Fleischmann R.D., Ketchum K.A., Klenk H.-P., Gill S.R., Dougherty B.A., Nelson K.E., Quackenbush J., Zhou L., Kirkness E.F., Peterson S.N., Loftus B.J., Richardson D.L., Dodson R.J. expand/collapse author list , Khalak H.G., Glodek A., McKenney K., FitzGerald L.M., Lee N., Adams M.D., Hickey E.K., Berg D.E., Gocayne J.D., Utterback T.R., Peterson J.D., Kelley J.M., Cotton M.D., Weidman J.F., Fujii C., Bowman C., Watthey L., Wallin E., Hayes W.S., Borodovsky M., Karp P.D., Smith H.O., Fraser C.M., Venter J.C.
Nature 388:539-547(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 700392 / 26695.
[2]"Crystal structure of dethiobiotin synthetase (biod) from Helicobacter pylori."
Midwest center for structural genomics (MCSG)
Submitted (MAR-2009) to the PDB data bank
Cited for: X-RAY CRYSTALLOGRAPHY (1.47 ANGSTROMS).
[3]"Crystal structure of dethiobiotin synthetase (biod) from Helicobacter pylori cocrystallized with ATP."
Midwest center for structural genomics (MCSG)
Submitted (MAY-2010) to the PDB data bank
Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) IN COMPLEX WITH ANALOGS SUBSTRATE, ATP AND MAGNESIUM IONS, SUBUNIT.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AE000511 Genomic DNA. Translation: AAD07100.1.
PIRE64523.
RefSeqNP_206831.1. NC_000915.1.
YP_006933951.1. NC_018939.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2QMOX-ray1.47A1-218[»]
3MLEX-ray2.80A/B/C/D/E/F1-218[»]
3QXCX-ray1.34A1-218[»]
3QXHX-ray1.36A1-218[»]
3QXJX-ray1.38A1-218[»]
3QXSX-ray1.35A1-218[»]
3QXXX-ray1.36A1-218[»]
3QY0X-ray1.60A1-218[»]
ProteinModelPortalO24872.
SMRO24872. Positions 1-218.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

MINTMINT-8303355.
STRING85962.HP0029.

Proteomic databases

PRIDEO24872.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAD07100; AAD07100; HP_0029.
GeneID899125.
KEGGheo:C694_00135.
hpy:HP0029.
PATRIC20591257. VBIHelPyl33062_0030.

Phylogenomic databases

eggNOGCOG0132.
KOK01935.
OMAEENMLDF.
OrthoDBEOG66B3XT.

Enzyme and pathway databases

BioCycHPY:HP0029-MONOMER.
UniPathwayUPA00078; UER00161.

Family and domain databases

Gene3D3.40.50.300. 1 hit.
HAMAPMF_00336. BioD.
InterProIPR004472. DTB_synth_BioD.
IPR027417. P-loop_NTPase.
[Graphical view]
PIRSFPIRSF006755. DTB_synth. 1 hit.
SUPFAMSSF52540. SSF52540. 1 hit.
TIGRFAMsTIGR00347. bioD. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceO24872.

Entry information

Entry nameBIOD_HELPY
AccessionPrimary (citable) accession number: O24872
Entry history
Integrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: January 1, 1998
Last modified: July 9, 2014
This is version 88 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

Helicobacter pylori

Helicobacter pylori (strain 26695): entries and gene names