Dethiobiotin synthetase (P13000)

Identification
Name:Dethiobiotin synthetase
Synonyms:
  • DTB synthetase
  • DTBS
  • Dethiobiotin synthase
Gene Name:bioD
Enzyme Class:
Biological Properties
General Function:Involved in magnesium ion binding
Specific Function:ATP + 7,8-diaminononanoate + CO(2) = ADP + phosphate + dethiobiotin
Cellular Location:Cytoplasm
SMPDB Pathways:
KEGG Pathways:
KEGG Reactions:
1.0Thumb+1.0Thumb+1.0Thumb ↔ 1.0Thumb+1.0Thumb+3.0Thumb+1.0Thumb
1.0Adenosine triphosphate + 1.0Carbon dioxide + 1.07,8-Diaminononanoate ↔ 1.0ADP + 1.0Dethiobiotin + 3.0Hydrogen ion + 1.0Phosphate
ReactionCard
1.0Thumb+1.0Thumb+1.0Thumb ↔ 1.0Thumb+1.0Thumb+1.0Thumb
1.0Adenosine triphosphate + 1.07,8-Diaminononanoate + 1.0Carbon dioxide ↔ 1.0ADP + 1.0Phosphate + 1.0Dethiobiotin
ReactionCard
SMPDB Reactions:
1.07,8-Diaminononanoate+1.0Thumb+1.0Thumb+1.0Thumb → 1.0Thumb+1.0Adenosine diphosphate+1.0Thumb+1.0Thumb
1.07,8-Diaminononanoate + 1.0Adenosine triphosphate + 1.0Carbon dioxide + 1.07,8-Diaminononanoate → 1.0Dethiobiotin + 1.0Adenosine diphosphate + 1.0Phosphate + 1.0ADP
ReactionCard
EcoCyc Reactions:
1.0Thumb+1.0Thumb+1.0Thumb ↔ 1.0Thumb+1.0Thumb+3.0Thumb+1.0Thumb
1.0Adenosine triphosphate + 1.0Carbon dioxide + 1.07,8-Diaminononanoate ↔ 1.0ADP + 1.0Dethiobiotin + 3.0Hydrogen ion + 1.0Phosphate
ReactionCard
Complex Reactions:
1.0Thumb+1.0Thumb+1.0Thumb → 1.0Thumb+1.0Thumb+1.0Thumb
1.0Adenosine triphosphate + 1.07,8-Diaminononanoate + 1.0Carbon dioxide → 1.0ADP + 1.0Inorganic phosphate + 1.0Dethiobiotin
ReactionCard
Metabolites:
ECMDB IDNameView
ECMDB201097,8-DiaminononanoateMetaboCard
ECMDB00538Adenosine triphosphateMetaboCard
ECMDB01341ADPMetaboCard
ECMDB04030Carbon dioxideMetaboCard
ECMDB03581DethiobiotinMetaboCard
ECMDB21225Hydrogen ionMetaboCard
ECMDB21380Inorganic phosphateMetaboCard
ECMDB01429PhosphateMetaboCard
GO Classification:
Function
adenyl nucleotide binding
adenyl ribonucleotide binding
ATP binding
binding
catalytic activity
cation binding
cyclo-ligase activity
dethiobiotin synthase activity
ion binding
ligase activity
ligase activity, forming carbon-nitrogen bonds
magnesium ion binding
metal ion binding
nucleoside binding
purine nucleoside binding
Process
biotin biosynthetic process
biotin metabolic process
metabolic process
small molecule metabolic process
vitamin metabolic process
water-soluble vitamin metabolic process
Gene Properties
Blattner:b0778
Gene OrientationClockwise
Centisome Percentage:17.49
Left Sequence End811493
Right Sequence End812170
Gene Sequence:
>678 bp
ATGAGTGCGTCGTTGGCGATCCTGACCATCGGCATTGTACCTATGCAGGAAGTTTTGCCG
CTCCTGACGGAATACATTGACGAAGATAATATTTCCCATCATAGCCTGCTGGGGAAGTTA
AGTCGTGAAGAAGTGATGGCGGAGTACGCGCCAGAAGCAGGCGAAGACACCATTCTCACA
TTATTAAATGACAACCAGCTGGCCCATGTTTCGCGTCGCAAAGTGGAGCGTGACCTGCAA
GGTGTGGTTGAAGTGCTCGATAATCAGGGTTATGACGTCATTTTATTAATGAGTACAGCA
AACATTAGTAGTATGACTGCGCGTAATACGATCTTTCTTGAGCCGTCGCGAATATTGCCT
CCACTGGTTTCCTCTATTGTTGAAGATCATCAGGTGGGGGTTATCGTTCCGGTTGAGGAG
ATGCTGCCCGTTCAGGCGCAAAAATGGCAAATTTTGCAGAAATCGCCGGTATTTTCATTG
GGTAACCCCATTCATGATTCAGAACAAAAAATCATTGATGCCGGGAAAGAATTACTGGCA
AAAGGGGCTGATGTCATCATGCTGGATTGTTTAGGATTTCACCAACGTCATCGCGATTTA
CTGCAAAAACAGCTCGATGTTCCTGTCTTGCTGTCTAACGTATTGATTGCACGGCTGGCT
GCGGAATTACTGGTGTAA
Protein Properties
Pfam Domain Function:
Protein Residues:225
Protein Molecular Weight:24139
Protein Theoretical pI:6
PDB File:1DAM
Signaling Regions:
  • None
Transmembrane Regions:
  • None
Protein Sequence:
>Dethiobiotin synthetase
MSKRYFVTGTDTEVGKTVASCALLQAAKAAGYRTAGYKPVASGSEKTPEGLRNSDALALQ
RNSSLQLDYATVNPYTFAEPTSPHIISAQEGRPIESLVMSAGLRALEQQADWVLVEGAGG
WFTPLSDTFTFADWVTQEQLPVILVVGVKLGCINHAMLTAQVIQHAGLTLAGWVANDVTP
PGKRHAEYMTTLTRMIPAPLLGEIPWLAENPENAATGKYINLALL
References
External Links:
ResourceLink
Uniprot ID:P13000
Uniprot Name:BIOD_ECOLI
GenBank Gene ID:AP009048
Genebank Protein ID:85674531
PDB ID:1DAM
Ecogene ID:EG10120
Ecocyc:EG10120
ColiBase:b0778
Kegg Gene:b0778
EchoBASE ID:EB0118
CCDB:BIOD_ECOLI
BacMap:16128746
General Reference:
  • Alexeev, D., Baxter, R. L., Sawyer, L. (1994). "Mechanistic implications and family relationships from the structure of dethiobiotin synthetase." Structure 2:1061-1072. Pubmed: 7881906
  • Alexeev, D., Bury, S. M., Boys, C. W., Turner, M. A., Sawyer, L., Ramsey, A. J., Baxter, H. C., Baxter, R. L. (1994). "Sequence and crystallization of Escherichia coli dethiobiotin synthetase, the penultimate enzyme of biotin biosynthesis." J Mol Biol 235:774-776. Pubmed: 8289297
  • Blattner, F. R., Plunkett, G. 3rd, 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. (1997). "The complete genome sequence of Escherichia coli K-12." Science 277:1453-1462. Pubmed: 9278503
  • Hayashi, K., Morooka, N., Yamamoto, Y., Fujita, K., Isono, K., Choi, S., Ohtsubo, E., Baba, T., Wanner, B. L., Mori, H., Horiuchi, T. (2006). "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Mol Syst Biol 2:2006.0007. Pubmed: 16738553
  • Huang, W., Lindqvist, Y., Schneider, G., Gibson, K. J., Flint, D., Lorimer, G. (1994). "Crystal structure of an ATP-dependent carboxylase, dethiobiotin synthetase, at 1.65 A resolution." Structure 2:407-414. Pubmed: 8081756
  • Kack, H., Gibson, K. J., Lindqvist, Y., Schneider, G. (1998). "Snapshot of a phosphorylated substrate intermediate by kinetic crystallography." Proc Natl Acad Sci U S A 95:5495-5500. Pubmed: 9576910
  • Kack, H., Sandmark, J., Gibson, K. J., Schneider, G., Lindqvist, Y. (1998). "Crystal structure of two quaternary complexes of dethiobiotin synthetase, enzyme-MgADP-AlF3-diaminopelargonic acid and enzyme-MgADP-dethiobiotin-phosphate; implications for catalysis." Protein Sci 7:2560-2566. Pubmed: 9865950
  • Otsuka, A. J., Buoncristiani, M. R., Howard, P. K., Flamm, J., Johnson, C., Yamamoto, R., Uchida, K., Cook, C., Ruppert, J., Matsuzaki, J. (1988). "The Escherichia coli biotin biosynthetic enzyme sequences predicted from the nucleotide sequence of the bio operon." J Biol Chem 263:19577-19585. Pubmed: 3058702
  • Sandalova, T., Schneider, G., Kack, H., Lindqvist, Y. (1999). "Structure of dethiobiotin synthetase at 0.97 A resolution." Acta Crystallogr D Biol Crystallogr 55:610-624. Pubmed: 10089457
  • Yang, G., Sandalova, T., Lohman, K., Lindqvist, Y., Rendina, A. R. (1997). "Active site mutants of Escherichia coli dethiobiotin synthetase: effects of mutations on enzyme catalytic and structural properties." Biochemistry 36:4751-4760. Pubmed: 9125495