Skip Header

You are using a version of Internet Explorer that may not display all features of this website. Please upgrade to a modern browser.
Contribute Send feedback
Read comments (?) or add your own

P13000 (BIOD1_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 133. 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 1

EC=6.3.3.3
Alternative name(s):
DTB synthetase 1
Short name=DTBS 1
Dethiobiotin synthase
Gene names
Name:bioD1
Ordered Locus Names:b0778, JW0761
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length225 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
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. Only CTP can partially replace ATP while diaminobiotin is only 37% as effective as 7,8-diaminopelargonic acid. Ref.6 Ref.7

Catalytic activity

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

Cofactor

Magnesium.

Pathway

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

Subunit structure

Homodimer. Ref.7 Ref.9 Ref.10 Ref.13

Subcellular location

Cytoplasm 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
Direct protein sequencing
Reference proteome
Gene Ontology (GO)
   Biological_processbiotin biosynthetic process

Inferred from direct assay Ref.6. Source: UniProtKB

   Cellular_componentcytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionATP binding

Inferred from direct assay Ref.11. Source: UniProtKB

dethiobiotin synthase activity

Inferred from direct assay Ref.7. Source: UniProtKB

magnesium ion binding

Inferred from direct assay Ref.11. Source: UniProtKB

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.2
Chain2 – 225224ATP-dependent dethiobiotin synthetase BioD 1 HAMAP-Rule MF_00336
PRO_0000187961

Regions

Nucleotide binding13 – 186ATP HAMAP-Rule MF_00336
Nucleotide binding116 – 1194ATP HAMAP-Rule MF_00336
Nucleotide binding176 – 1772ATP HAMAP-Rule MF_00336
Nucleotide binding205 – 2073ATP HAMAP-Rule MF_00336

Sites

Metal binding131Magnesium 1
Metal binding171Magnesium 2
Metal binding551Magnesium 2
Metal binding1161Magnesium 2
Binding site421Substrate
Binding site551ATP
Binding site2121ATP

Experimental info

Mutagenesis121T → V: Strong decreased in the affinity for ATP; essential role for this residue in the steady-state affinity for ATP. Ref.8
Mutagenesis131E → A or D: Almost no change in activity. Ref.8
Mutagenesis161K → Q: Complete loss of activity. Ref.8
Mutagenesis381K → L, Q or R: Complete loss of activity. Ref.8
Mutagenesis421S → A or C: Almost no change in activity. Ref.8
Sequence conflict291A → R in AAA23518. Ref.1
Sequence conflict108 – 1092QQ → HK in CAA00967. Ref.3
Sequence conflict198 – 22528APLLG…NLALL → RRCWERSPGLQKIQKMRQPE ST in AAA23518. Ref.1

Secondary structure

.................................................. 225
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P13000 [UniParc].

Last modified January 23, 2007. Version 3.
Checksum: 9AE76F3BE6565780

FASTA22524,140
        10         20         30         40         50         60 
MSKRYFVTGT DTEVGKTVAS CALLQAAKAA GYRTAGYKPV ASGSEKTPEG LRNSDALALQ 

        70         80         90        100        110        120 
RNSSLQLDYA TVNPYTFAEP TSPHIISAQE GRPIESLVMS AGLRALEQQA DWVLVEGAGG 

       130        140        150        160        170        180 
WFTPLSDTFT FADWVTQEQL PVILVVGVKL GCINHAMLTA QVIQHAGLTL AGWVANDVTP 

       190        200        210        220 
PGKRHAEYMT TLTRMIPAPL LGEIPWLAEN PENAATGKYI NLALL 

« Hide

References

« Hide 'large scale' references
[1]"The Escherichia coli biotin biosynthetic enzyme sequences predicted from the nucleotide sequence of the bio operon."
Otsuka A.J., Buoncristiani M.R., Howard P.K., Flamm J., Johnson O., Yamamoto R., Uchida K., Cook C., Ruppert J., Matsuzaki J.
J. Biol. Chem. 263:19577-19585(1988) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"Sequence and crystallization of Escherichia coli dethiobiotin synthetase, the penultimate enzyme of biotin biosynthesis."
Alexeev D., Bury S.M., Boys C.W.G., Turner M.A., Sawyer L., Ramsey A.J., Baxter H.C., Baxter R.L.
J. Mol. Biol. 235:774-776(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-20 AND 224-225.
[3]"Genetic material for expression of biotin synthetase enzymes."
Pearson B.M., McKee R.A.
Patent number GB2216530, 11-OCT-1989
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[4]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[5]"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[6]"Synthesis of desthiobiotin from 7,8-diaminopelargonic acid in biotin auxotrophs of Escherichia coli K-12."
Eisenberg M.A., Krell K.
J. Bacteriol. 98:1227-1231(1969) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN BIOTIN BIOSYNTHESIS.
[7]"The purification and properties of dethiobiotin synthetase."
Krell K., Eisenberg M.A.
J. Biol. Chem. 245:6558-6566(1970) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION AS A DETHIOBIOTIN SYNTHETASE, CATALYTIC ACTIVITY, SUBSTRATES SPECIFICITY, SUBUNIT.
[8]"Active site mutants of Escherichia coli dethiobiotin synthetase: effects of mutations on enzyme catalytic and structural properties."
Yang G., Sandalova T., Lohman K., Lindqvist Y., Rendina A.R.
Biochemistry 36:4751-4760(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF THR-12; GLU-13; LYS-16; LYS-38 AND SER-42.
[9]"Crystal structure of an ATP-dependent carboxylase, dethiobiotin synthetase, at 1.65-A resolution."
Huang W., Lindqvist Y., Schneider G., Gibson K.J., Flint D., Lorimer G.
Structure 2:407-414(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS), SUBUNIT.
[10]"Mechanistic implications and family relationships from the structure of dethiobiotin synthetase."
Sawyer L., Baxter R.L., Alexeev D.
Structure 2:1061-1072(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEX WITH ANALOGS SUBSTRATE, ATP AND MAGNESIUM IONS, SUBUNIT.
[11]"Mechanism of an ATP-dependent carboxylase, dethiobiotin synthetase, based on crystallographic studies of complexes with substrates and a reaction intermediate."
Huang W., Jia J., Gibson K.J., Taylor W.S., Rendina A.R., Schneider G., Lindqvist Y.
Biochemistry 34:10985-10995(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF 2-224 IN COMPLEX WITH ANALOGS SUBSTRATE, ATP AND MAGNESIUM IONS, REACTION MECHANISM.
[12]"Snapshot of a phosphorylated substrate intermediate by kinetic crystallography."
Kaeck H., Gibson K.J., Lindqvist Y., Schneider G.
Proc. Natl. Acad. Sci. U.S.A. 95:5495-5500(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) IN COMPLEX WITH ANALOGS SUBSTRATE, ATP, MAGNESIUM IONS.
[13]"Crystal structure of two quaternary complexes of dethiobiotin synthetase, enzyme-MgADP-AlF3-diaminopelargonic acid and enzyme-MgADP-dethiobiotin-phosphate; implications for catalysis."
Kaeck H., Sandmark J., Gibson K.J., Schneider G., Lindqvist Y.
Protein Sci. 7:2560-2566(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEX WITH ANALOGS SUBSTRATE, ATP AND MAGNESIUM IONS, SUBUNIT.
[14]"Structure of dethiobiotin synthetase at 0.97-A resolution."
Sandalova T., Schneider G., Kack H., Lindqvist Y.
Acta Crystallogr. D 55:610-624(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (0.97 ANGSTROMS).

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
J04423 Genomic DNA. Translation: AAA23518.1.
S68059 Genomic DNA. Translation: AAB29683.2.
A11538 Unassigned DNA. Translation: CAA00967.1.
U00096 Genomic DNA. Translation: AAC73865.1.
AP009048 Genomic DNA. Translation: BAE76365.1.
PIRSYECDB. B64814.
RefSeqNP_415299.1. NC_000913.3.
YP_489051.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1A82X-ray1.80A2-225[»]
1BS1X-ray1.80A2-225[»]
1BYIX-ray0.97A2-225[»]
1DADX-ray1.60A2-224[»]
1DAEX-ray1.70A2-224[»]
1DAFX-ray1.70A2-224[»]
1DAGX-ray1.64A2-224[»]
1DAHX-ray1.64A2-224[»]
1DAIX-ray1.64A2-224[»]
1DAKX-ray1.60A2-225[»]
1DAMX-ray1.80A2-225[»]
1DBSX-ray1.80A2-225[»]
1DTSX-ray1.65A1-225[»]
ProteinModelPortalP13000.
SMRP13000. Positions 2-225.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

IntActP13000. 3 interactions.
STRING511145.b0778.

Proteomic databases

PaxDbP13000.
PRIDEP13000.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC73865; AAC73865; b0778.
BAE76365; BAE76365; BAE76365.
GeneID12930962.
945387.
KEGGecj:Y75_p0751.
eco:b0778.
PATRIC32116757. VBIEscCol129921_0804.

Organism-specific databases

EchoBASEEB0118.
EcoGeneEG10120. bioD1.

Phylogenomic databases

eggNOGCOG0132.
HOGENOMHOG000275032.
KOK01935.
OMAAGWVANV.
OrthoDBEOG66B3XT.
PhylomeDBP13000.
ProtClustDBPRK00090.

Enzyme and pathway databases

BioCycEcoCyc:DETHIOBIOTIN-SYN-MONOMER.
ECOL316407:JW0761-MONOMER.
MetaCyc:DETHIOBIOTIN-SYN-MONOMER.
SABIO-RKP13000.
UniPathwayUPA00078; UER00161.

Gene expression databases

GenevestigatorP13000.

Family and domain databases

Gene3D3.40.50.300. 1 hit.
HAMAPMF_00336. BioD.
InterProIPR002586. CobQ/CobB/MinD/ParA_Nub-bd_dom.
IPR004472. DTB_synth_BioD.
IPR027417. P-loop_NTPase.
[Graphical view]
PfamPF01656. CbiA. 1 hit.
[Graphical view]
PIRSFPIRSF006755. DTB_synth. 1 hit.
SUPFAMSSF52540. SSF52540. 1 hit.
TIGRFAMsTIGR00347. bioD. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP13000.
PROP13000.

Entry information

Entry nameBIOD1_ECOLI
AccessionPrimary (citable) accession number: P13000
Secondary accession number(s): Q2MBJ1
Entry history
Integrated into UniProtKB/Swiss-Prot: January 1, 1990
Last sequence update: January 23, 2007
Last modified: April 16, 2014
This is version 133 of the entry and version 3 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

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene