DB code: S00311
| CATH domain | 3.40.50.300 : Rossmann fold | Catalytic domain |
|---|---|---|
| E.C. | 6.3.3.3 | |
| CSA | 1dae | |
| M-CSA | 1dae | |
| MACiE | M0074 | |
| CATH domain | Related DB codes (homologues) |
|---|---|
| 3.40.50.300 : Rossmann fold | S00527 S00547 S00548 S00550 S00554 S00555 S00671 S00672 S00676 S00680 S00682 S00913 S00914 S00301 S00302 S00303 S00304 S00307 S00308 S00305 S00306 S00309 S00310 M00114 M00199 D00129 D00130 D00540 M00186 |
| Uniprot Enzyme Name | UniprotKB | Protein name | Synonyms | RefSeq | Pfam |
|---|---|---|---|---|
| P13000 |
Dethiobiotin synthetase
|
EC
6.3.3.3
Dethiobiotin synthase DTB synthetase DTBS |
NP_415299.1
(Protein)
NC_000913.2 (DNA/RNA sequence) YP_489051.1 (Protein) NC_007779.1 (DNA/RNA sequence) |
PF01656
(CbiA)
[Graphical View] |
| KEGG enzyme name |
|---|
|
dethiobiotin synthase
desthiobiotin synthase |
| UniprotKB: Accession Number | Entry name | Activity | Subunit | Subcellular location | Cofactor |
|---|---|---|---|---|---|
| P13000 | BIOD_ECOLI | ATP + 7,8-diaminononanoate + CO(2) = ADP + phosphate + dethiobiotin. | Homodimer. | Cytoplasm. | Magnesium. |
| KEGG Pathways | Map code | Pathways | E.C. |
|---|---|---|
| MAP00780 | Biotin metabolism |
| Compound table | ||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Cofactors | Substrates | Products | Intermediates | |||||||||||||
| KEGG-id | C00305 | C00002 | C01037 | C00011 | C00063 | C00008 | C00009 | C01909 | C00112 | |||||||
| E.C. |
(8-amino-7-carboxyamino-nonanonate)
|
(carbamic phosphoric acid anhydride)
|
||||||||||||||
| Compound | Magnesium | ATP | 7,8-Diaminononanoate | CO2 | CTP | ADP | Orthophosphate | Dethiobiotin | CDP | Intermediate-1 | Intermediate-2 | |||||
| Type | divalent metal (Ca2+, Mg2+) | amine group,nucleotide | amino acids,amine group,fatty acid | others | amine group,nucleotide | amine group,nucleotide | phosphate group/phosphate ion | amide group,fatty acid | amine group,nucleotide | |||||||
| ChEBI |
18420 18420 |
15422 15422 |
2247 2247 |
16526 16526 |
17677 17677 |
16761 16761 |
26078 26078 |
16691 16691 |
17239 17239 |
|||||||
| PubChem |
888 888 |
5957 5957 |
652 652 |
280 280 |
6176 6176 |
6022 6022 |
1004 22486802 1004 22486802 |
643 643 |
6132 6132 |
|||||||
| 1a82A |
|
|
|
|
|
Bound:_MG | Bound:ATP | Bound:DNN | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
| 1bs1A |
|
|
|
|
|
Bound:2x_MG | Unbound | Unbound | Unbound | Unbound | Bound:ADP | Unbound | Unbound | Unbound | Unbound | Intermediate-analogue:DAA |
| 1byiA |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
| 1dadA |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Bound:ADP | Unbound | Unbound | Unbound | Unbound | Unbound |
| 1daeA |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
| 1dafA |
|
|
|
|
|
Analogue:_CA | Unbound | Unbound | Unbound | Unbound | Bound:ADP | Unbound | Unbound | Unbound | Intermediate-analogue:IKT | Unbound |
| 1dagA |
|
|
|
|
|
Unbound | Analogue:ACP | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Intermediate-bound:DSD | Unbound |
| 1dahA |
|
|
|
|
|
Analogue:_MN | Analogue:ACP | Bound:DNN | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Intermediate-bound:DSD | Unbound |
| 1daiA |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
| 1dakA |
|
|
|
|
|
Bound:2x_MG | Unbound | Unbound | Unbound | Unbound | Bound:ADP | Unbound | Unbound | Unbound | Intermediate-bound:DSD | Intermediate-bound:DPU |
| 1damA |
|
|
|
|
|
Bound:2x_MG | Unbound | Unbound | Unbound | Unbound | Bound:ADP | Bound:PO4 | Bound:DTB | Unbound | Unbound | Unbound |
| 1dbsA |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Analogue:SO4 | Unbound | Unbound | Unbound | Unbound |
| 1dtsA |
|
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|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound |
| Reference for Active-site residues | ||
|---|---|---|
| resource | references | E.C. |
| literature [5] | ||
| Active-site residues | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| PDB | Catalytic residues | Cofactor-binding residues | Modified residues | Main-chain involved in catalysis | Comment | |||||
| 1a82A |
|
|
|
|
|
THR 11;GLU 12;LYS 15;LYS 37 | THR 16;ASP 54;GLU 115(Magnesium binding) | |||
| 1bs1A |
|
|
|
|
|
THR 11;GLU 12;LYS 15;LYS 37 | THR 16;ASP 54;GLU 115(Magnesium binding) | |||
| 1byiA |
|
|
|
|
|
THR 11;GLU 12;LYS 15;LYS 37 | THR 16;ASP 54;GLU 115(Magnesium binding) | |||
| 1dadA |
|
|
|
|
|
THR 11;GLU 12;LYS 15;LYS 37 | THR 16;ASP 54;GLU 115(Magnesium binding) | |||
| 1daeA |
|
|
|
|
|
THR 11;GLU 12;LYS 15;LYS 37 | THR 16;ASP 54;GLU 115(Magnesium binding) | |||
| 1dafA |
|
|
|
|
|
THR 11;GLU 12;LYS 15;LYS 37 | THR 16;ASP 54;GLU 115(Magnesium binding) | |||
| 1dagA |
|
|
|
|
|
THR 11;GLU 12;LYS 15;LYS 37 | THR 16;ASP 54;GLU 115(Magnesium binding) | |||
| 1dahA |
|
|
|
|
|
THR 11;GLU 12;LYS 15;LYS 37 | THR 16;ASP 54;GLU 115(Magnesium binding) | |||
| 1daiA |
|
|
|
|
|
THR 11;GLU 12;LYS 15;LYS 37 | THR 16;ASP 54;GLU 115(Magnesium binding) | |||
| 1dakA |
|
|
|
|
|
THR 11;GLU 12;LYS 15;LYS 37 | THR 16;ASP 54;GLU 115(Magnesium binding) | |||
| 1damA |
|
|
|
|
|
THR 11;GLU 12;LYS 15;LYS 37 | THR 16;ASP 54;GLU 115(Magnesium binding) | |||
| 1dbsA |
|
|
|
|
|
THR 11;GLU 12;LYS 15;LYS 37 | THR 16;ASP 54;GLU 115(Magnesium binding) | |||
| 1dtsA |
|
|
|
|
|
THR 11;GLU 12;LYS 15;LYS 37 | THR 16;ASP 54;GLU 115(Magnesium binding) | |||
| References for Catalytic Mechanism | ||
|---|---|---|
| References | Sections | No. of steps in catalysis |
|
[1]
|
Fig.1, p.1066-1068 | 3 |
|
[2]
|
p.411-412 | |
|
[3]
|
Fig.13, p.10992-10995 | 5 |
|
[4]
|
Fig.1, p.1208-1209, p.1213 | 3 |
|
[5]
|
Scheme 1, p.4758-4760 | 5 |
|
[6]
|
Fig.1, p.384-385 | 3 |
|
[7]
|
Fig.1, Fig.4 p.5498-5499 | 3 |
|
[8]
|
Fig.1, Fig.5, p.2562-2565 | 3 |
|
[11]
|
Fig.2, p.9 | 4 |
| References | |
|---|---|
| [1] | |
| Resource | |
| Comments | X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS). |
| Medline ID | 95187709 |
| PubMed ID | 7881906 |
| Journal | Structure |
| Year | 1994 |
| Volume | 2 |
| Pages | 1061-72 |
| Authors | Alexeev D, Baxter RL, Sawyer L |
| Title | Mechanistic implications and family relationships from the structure of dethiobiotin synthetase. |
| Related PDB | 1dbs |
| Related UniProtKB | P13000 |
| [2] | |
| Resource | |
| Comments | X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS). |
| Medline ID | 94363241 |
| PubMed ID | 8081756 |
| Journal | Structure |
| Year | 1994 |
| Volume | 2 |
| Pages | 407-14 |
| Authors | Huang W, Lindqvist Y, Schneider G, Gibson KJ, Flint D, Lorimer G |
| Title |
Crystal structure of an ATP-dependent carboxylase, |
| Related PDB | 1dts |
| Related UniProtKB | P13000 |
| [3] | |
| Resource | |
| Comments | X-ray crystallography |
| Medline ID | |
| PubMed ID | 7669756 |
| Journal | Biochemistry |
| Year | 1995 |
| Volume | 34 |
| Pages | 10985-95 |
| Authors | Huang W, Jia J, Gibson KJ, Taylor WS, Rendina AR, Schneider G, Lindqvist Y |
| Title |
Mechanism of an ATP-dependent carboxylase, |
| Related PDB | 1dad 1dae 1daf 1dag 1dah 1dai |
| Related UniProtKB | |
| [4] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 8591031 |
| Journal | Structure |
| Year | 1995 |
| Volume | 3 |
| Pages | 1207-15 |
| Authors | Alexeev D, Baxter RL, Smekal O, Sawyer L |
| Title | Substrate binding and carboxylation by dethiobiotin synthetase--a kinetic and X-ray study. |
| Related PDB | |
| Related UniProtKB | |
| [5] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 9125495 |
| Journal | Biochemistry |
| Year | 1997 |
| Volume | 36 |
| Pages | 4751-60 |
| Authors | Yang G, Sandalova T, Lohman K, Lindqvist Y, Rendina AR |
| Title | Active site mutants of Escherichia coli dethiobiotin synthetase: effects of mutations on enzyme catalytic and structural properties. |
| Related PDB | |
| Related UniProtKB | |
| [6] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 9211290 |
| Journal | Methods Enzymol |
| Year | 1997 |
| Volume | 279 |
| Pages | 376-85 |
| Authors | Schneider G, Lindqvist Y |
| Title |
Structure of ATP-dependent carboxylase, |
| Related PDB | |
| Related UniProtKB | |
| [7] | |
| Resource | |
| Comments | X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS). |
| Medline ID | 98245107 |
| PubMed ID | 9576910 |
| Journal | Proc Natl Acad Sci U S A |
| Year | 1998 |
| Volume | 95 |
| Pages | 5495-500 |
| Authors | Kack H, Gibson KJ, Lindqvist Y, Schneider G |
| Title | Snapshot of a phosphorylated substrate intermediate by kinetic crystallography. |
| Related PDB | 1a82 1dak |
| Related UniProtKB | P13000 |
| [8] | |
| Resource | |
| Comments | X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS). |
| Medline ID | 99081548 |
| PubMed ID | 9865950 |
| Journal | Protein Sci |
| Year | 1998 |
| Volume | 7 |
| Pages | 2560-6 |
| Authors | Kack H, Sandmark J, Gibson KJ, Schneider G, Lindqvist Y |
| Title |
Crystal structure of two quaternary complexes of dethiobiotin synthetase, |
| Related PDB | 1bs1 1dam |
| Related UniProtKB | P13000 |
| [9] | |
| Resource | |
| Comments | X-RAY CRYSTALLOGRAPHY (0.97 ANGSTROMS). |
| Medline ID | 99190933 |
| PubMed ID | 10089457 |
| Journal | Acta Crystallogr D Biol Crystallogr |
| Year | 1999 |
| Volume | 55 |
| Pages | 610-24 |
| Authors | Sandalova T, Schneider G, Kack H, Lindqvist Y |
| Title | Structure of dethiobiotin synthetase at 0.97 A resolution. |
| Related PDB | 1byi |
| Related UniProtKB | P13000 |
| [10] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 10966576 |
| Journal | Proteins |
| Year | 2000 |
| Volume | 41 |
| Pages | 238-47 |
| Authors | Galperin MY, Grishin NV |
| Title |
The synthetase domains of cobalamin biosynthesis amidotransferases cobB and cobQ belong to a new family of ATP-dependent amidoligases, |
| Related PDB | |
| Related UniProtKB | |
| [11] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 11322938 |
| Journal | FEBS Lett |
| Year | 2001 |
| Volume | 495 |
| Pages | 7-11 |
| Authors | Schneider G, Lindqvist Y |
| Title | Structural enzymology of biotin biosynthesis. |
| Related PDB | |
| Related UniProtKB | |
| Comments |
|---|
|
This enzyme catalyzes three reactions as follows:
(1) Addition of 7-amine group of 7,8-Diaminononanoate to the double bond of CO2. (2) Transfer of phosphate group from ATP to carboxylate oxygen of the carbamated intermediate. (3) Intramolecular-transfer of acyl group to the 8-amine group of the phosphorylated intermediate. |
| Created | Updated |
|---|---|
| 2004-08-01 | 2009-02-26 |