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
15422
2247
16526
17677
16761
26078
16691
17239
PubChem 888
5957
652
280
6176
6022
1004
22486802
643
6132
1a82A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Bound:ATP Bound:DNN Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1bs1A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_MG Unbound Unbound Unbound Unbound Bound:ADP Unbound Unbound Unbound Unbound Intermediate-analogue:DAA
1byiA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1dadA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Bound:ADP Unbound Unbound Unbound Unbound Unbound
1daeA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Intermediate-analogue:IKT Unbound
1dafA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:_CA Unbound Unbound Unbound Unbound Bound:ADP Unbound Unbound Unbound Intermediate-bound:DSD Unbound
1dagA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:ACP Unbound Unbound Unbound Unbound Unbound Unbound Unbound Intermediate-bound:DSD Unbound
1dahA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:_MN Analogue:ACP Bound:DNN Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1daiA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Intermediate-bound:DSD Unbound
1dakA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_MG Unbound Unbound Unbound Unbound Bound:ADP Unbound Unbound Unbound Unbound Intermediate-bound:DPU
1damA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_MG Unbound Unbound Unbound Unbound Bound:ADP Bound:PO4 Bound:DTB Unbound Unbound Unbound
1dbsA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Analogue:SO4 Unbound Unbound Unbound Unbound
1dtsA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain 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 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 11;GLU 12;LYS 15;LYS 37 THR 16;ASP 54;GLU 115(Magnesium binding)
1bs1A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 11;GLU 12;LYS 15;LYS 37 THR 16;ASP 54;GLU 115(Magnesium binding)
1byiA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 11;GLU 12;LYS 15;LYS 37 THR 16;ASP 54;GLU 115(Magnesium binding)
1dadA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 11;GLU 12;LYS 15;LYS 37 THR 16;ASP 54;GLU 115(Magnesium binding)
1daeA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 11;GLU 12;LYS 15;LYS 37 THR 16;ASP 54;GLU 115(Magnesium binding)
1dafA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 11;GLU 12;LYS 15;LYS 37 THR 16;ASP 54;GLU 115(Magnesium binding)
1dagA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 11;GLU 12;LYS 15;LYS 37 THR 16;ASP 54;GLU 115(Magnesium binding)
1dahA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 11;GLU 12;LYS 15;LYS 37 THR 16;ASP 54;GLU 115(Magnesium binding)
1daiA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 11;GLU 12;LYS 15;LYS 37 THR 16;ASP 54;GLU 115(Magnesium binding)
1dakA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 11;GLU 12;LYS 15;LYS 37 THR 16;ASP 54;GLU 115(Magnesium binding)
1damA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 11;GLU 12;LYS 15;LYS 37 THR 16;ASP 54;GLU 115(Magnesium binding)
1dbsA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 11;GLU 12;LYS 15;LYS 37 THR 16;ASP 54;GLU 115(Magnesium binding)
1dtsA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain 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, dethiobiotin synthetase, at 1.65 A resolution.
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, dethiobiotin synthetase, based on crystallographic studies of complexes with substrates and a reaction intermediate.
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, dethiobiotin synthase.
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, enzyme-MgADP-AlF3-diaminopelargonic acid and enzyme-MgADP-dethiobiotin-phosphate; implications for catalysis.
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 to dethiobiotin synthetase.
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