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P69954 (BIOD_YERPS) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 49. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | 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
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
Synonyms:bioD2
Ordered Locus Names:YPTB2191
OrganismYersinia pseudotuberculosis [Complete proteome] [HAMAP]
Taxonomic identifier633 [NCBI]
Taxonomic lineageBacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Yersinia

Protein attributes

Sequence length222 AA.
Sequence statusComplete.
Protein existenceInferred from homology

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 MF_00336

Catalytic activity

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

Cofactor

Magnesium By similarity. HAMAP MF_00336

Pathway

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

Subunit structure

Homodimer By similarity. HAMAP MF_00336

Subcellular location

Cytoplasm By similarity HAMAP 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
Gene Ontology (GO)
   Biological processbiotin biosynthetic process

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular componentcytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular functionATP binding

Inferred from electronic annotation. Source: UniProtKB-KW

dethiobiotin synthase activity

Inferred from sequence or structural similarity. Source: UniProtKB

magnesium ion binding

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 222222ATP-dependent dethiobiotin synthetase BioD HAMAP MF_00336
PRO_0000188004

Regions

Nucleotide binding112 – 1154ATP By similarity
Nucleotide binding172 – 1732ATP By similarity
Nucleotide binding201 – 2033ATP By similarity

Sites

Metal binding171Magnesium 2 By similarity
Metal binding551Magnesium 2 By similarity
Metal binding1121Magnesium 2 By similarity
Binding site421Substrate By similarity
Binding site551ATP By similarity
Binding site2081ATP By similarity

Secondary structure

1 .................................... 222
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P69954 [UniParc].

Last modified January 4, 2005. Version 1.
Checksum: 4E17C7A0BC32EF85

FASTA22224,192
        10         20         30         40         50         60 
MLTRLFVTGT DTAVGKTVVS RALLQALSQN GRTAVGYKPV ATESKETSEG LRNQDALILQ 

        70         80         90        100        110        120 
ASSSIELNYQ EVNPYPLQGD VIHACTDTLI NYEKMTEGLQ CLSAKADTVI VEGCGGWKVM 

       130        140        150        160        170        180 
MNDQRFYSDW VVQEQLPVIL VVGIKLGCIN HALLTAQAII NDGLPLLGWV ANRINPGLAH 

       190        200        210        220 
YAETIAMLRD RLAAPQLGQL PYLPRPEEKP LAKYLDLTAI SG

« Hide

References

« Hide 'large scale' references
[1]"Genetic environment of the ypmA superantigen gene of Yersinia pseudotuberculosis."
Carnoy C.A., Floquet S., Herwegh S., Devalckenaere A., Simonet M.
Submitted (AUG-2001) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: AH.
[2]"Genetic environment of the superantigen genes of Yersinia pseudotuberculosis."
Carnoy C., Floquet S., Simonet M.
Submitted (AUG-2001) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: YPT1 / Serotype 3.
[3]"Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis."
Chain P.S.G., Carniel E., Larimer F.W., Lamerdin J., Stoutland P.O., Regala W.M., Georgescu A.M., Vergez L.M., Land M.L., Motin V.L., Brubaker R.R., Fowler J., Hinnebusch J., Marceau M., Medigue C., Simonet M., Chenal-Francisque V., Souza B. expand/collapse author list , Dacheux D., Elliott J.M., Derbise A., Hauser L.J., Garcia E.
Proc. Natl. Acad. Sci. U.S.A. 101:13826-13831(2004) [PubMed: 15358858] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: IP32953 / Serotype I.
[4]"Theoretical model of putative dethiobiotin synthetase."
Narasimham N.R., Mallena S.C.
Submitted (JUN-2002) to the PDB data bank
Cited for: 3D-STRUCTURE MODELING.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		AF335466 Genomic DNA. Translation: AAK28549.1.
AF414083 Genomic DNA. Translation: AAL02239.1.
BX936398 Genomic DNA. Translation: CAH21429.1.
RefSeqYP_070708.1. NC_006155.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1M0Amodel-A1-222[»]
ProteinModelPortalP69954.
ModBaseSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID2955289.
GenomeReviewsGene locus YPTB2191 in contig BX936398_GR.
KEGGyps:YPTB2191.
PATRIC18643248. VBIYerPse22266_2682.

Organism-specific databases

CMRSearch...

Phylogenomic databases

HOGENOMHBG650065.
OMAINPGLSH.
ProtClustDBPRK12374.

Enzyme and pathway databases

BioCycYPSE273123:YPTB2191-MONOMER.

Family and domain databases

HAMAPMF_00336. BioD.
[Tree]
InterProIPR002586. CbiA_P_synth.
IPR004472. DTB_synth_BioD.
[Graphical view]
KOK01935.
PfamPF01656. CbiA. 1 hit.
[Graphical view]
PIRSFPIRSF006755. DTB_synth. 1 hit.
TIGRFAMsTIGR00347. BioD. 1 hit.
ProtoNetSearch...

Entry information

Entry nameBIOD_YERPS
AccessionPrimary (citable) accession number: P69954
Secondary accession number(s): Q66AD9, Q9AGD4
Entry history
Integrated into UniProtKB/Swiss-Prot: January 4, 2005
Last sequence update: January 4, 2005
Last modified: January 25, 2012
This is version 49 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

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