EzCatDB: S00311

DB codeS00311
CATH domainDomain 13.40.50.300Catalytic domain
E.C.6.3.3.3
CSA1dae
MACiEM0074

CATH domainRelated DB codes (homologues)
3.40.50.300S00527,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

Enzyme Name
Swiss-protKEGG

P13000
Protein nameDethiobiotin synthetasedethiobiotin synthase
desthiobiotin synthase
SynonymsEC 6.3.3.3
Dethiobiotin synthase
DTB synthetase
DTBS

KEGG pathways
MAP codePathways
MAP00780Biotin metabolism

Swiss-prot:Accession NumberP13000
Entry nameBIOD_ECOLI
ActivityATP + 7,8-diaminononanoate + CO(2) = ADP + phosphate + dethiobiotin.
SubunitHomodimer.
Subcellular locationCytoplasm.
CofactorMagnesium.


CofactorsSubstratesProductsintermediates
KEGG-idC00305C00002C01037C00011C00063C00008C00009C01909C00112

CompoundMagnesiumATP7,8-DiaminononanoateCO2CTPADPOrthophosphateDethiobiotinCDPIntermediate-1 Intermediate-2
Typedivalent metal (Ca2+, Mg2+)amine group,nucleotideamino acids,amine group,fatty acidothersamine group,nucleotideamine group,nucleotidephosphate group/phosphate ionamide group,fatty acidamine group,nucleotide

1a82ABound:_MGBound:ATPBound:DNNUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1bs1ABound:2x_MGUnboundUnboundUnboundUnboundBound:ADPUnboundUnboundUnboundUnboundIntermediate-analogue:DAA
1byiAUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1dadAUnboundUnboundUnboundUnboundUnboundBound:ADPUnboundUnboundUnboundUnboundUnbound
1daeAUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundIntermediate-analogue:IKTUnbound
1dafAAnalogue:_CAUnboundUnboundUnboundUnboundBound:ADPUnboundUnboundUnboundIntermediate-bound:DSDUnbound
1dagAUnboundAnalogue:ACPUnboundUnboundUnboundUnboundUnboundUnboundUnboundIntermediate-bound:DSDUnbound
1dahAAnalogue:_MNAnalogue:ACPBound:DNNUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1daiAUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundIntermediate-bound:DSDUnbound
1dakABound:2x_MGUnboundUnboundUnboundUnboundBound:ADPUnboundUnboundUnboundUnboundIntermediate-bound:DPU
1damABound:2x_MGUnboundUnboundUnboundUnboundBound:ADPBound:PO4Bound:DTBUnboundUnboundUnbound
1dbsAUnboundUnboundUnboundUnboundUnboundUnboundAnalogue:SO4UnboundUnboundUnboundUnbound
1dtsAUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
literature [5]
pdbCatalytic residuesCofactor-binding residues
1a82ATHR 11;GLU 12;LYS 15;LYS 37
THR 16;ASP 54;GLU 115(Magnesium binding)
1bs1ATHR 11;GLU 12;LYS 15;LYS 37
THR 16;ASP 54;GLU 115(Magnesium binding)
1byiATHR 11;GLU 12;LYS 15;LYS 37
THR 16;ASP 54;GLU 115(Magnesium binding)
1dadATHR 11;GLU 12;LYS 15;LYS 37
THR 16;ASP 54;GLU 115(Magnesium binding)
1daeATHR 11;GLU 12;LYS 15;LYS 37
THR 16;ASP 54;GLU 115(Magnesium binding)
1dafATHR 11;GLU 12;LYS 15;LYS 37
THR 16;ASP 54;GLU 115(Magnesium binding)
1dagATHR 11;GLU 12;LYS 15;LYS 37
THR 16;ASP 54;GLU 115(Magnesium binding)
1dahATHR 11;GLU 12;LYS 15;LYS 37
THR 16;ASP 54;GLU 115(Magnesium binding)
1daiATHR 11;GLU 12;LYS 15;LYS 37
THR 16;ASP 54;GLU 115(Magnesium binding)
1dakATHR 11;GLU 12;LYS 15;LYS 37
THR 16;ASP 54;GLU 115(Magnesium binding)
1damATHR 11;GLU 12;LYS 15;LYS 37
THR 16;ASP 54;GLU 115(Magnesium binding)
1dbsATHR 11;GLU 12;LYS 15;LYS 37
THR 16;ASP 54;GLU 115(Magnesium binding)
1dtsATHR 11;GLU 12;LYS 15;LYS 37
THR 16;ASP 54;GLU 115(Magnesium binding)

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[1]Fig.1, p.1066-10683
[2]p.411-412
[3]Fig.13, p.10992-109955
[4]Fig.1, p.1208-1209, p.12133
[5]Scheme 1, p.4758-47605
[6]Fig.1, p.384-3853
[7]Fig.1, Fig.4 p.5498-54993
[8]Fig.1, Fig.5, p.2562-25653
[11]Fig.2, p.94

references
[1]
CommentsX-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
Medline ID95187709
PubMed ID7881906
JournalStructure
Year1994
Volume2
Pages1061-72
AuthorsAlexeev D, Baxter RL, Sawyer L
TitleMechanistic implications and family relationships from the structure of dethiobiotin synthetase.
Related PDB1dbs
Related Swiss-protP13000
[2]
CommentsX-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS).
Medline ID94363241
PubMed ID8081756
JournalStructure
Year1994
Volume2
Pages407-14
AuthorsHuang W, Lindqvist Y, Schneider G, Gibson KJ, Flint D, Lorimer G
TitleCrystal structure of an ATP-dependent carboxylase, dethiobiotin synthetase, at 1.65 A resolution.
Related PDB1dts
Related Swiss-protP13000
[3]
CommentsX-ray crystallography
PubMed ID7669756
JournalBiochemistry
Year1995
Volume34
Pages10985-95
AuthorsHuang W, Jia J, Gibson KJ, Taylor WS, Rendina AR, Schneider G, Lindqvist Y
TitleMechanism of an ATP-dependent carboxylase, dethiobiotin synthetase, based on crystallographic studies of complexes with substrates and a reaction intermediate.
Related PDB1dad,1dae,1daf,1dag,1dah,1dai
[4]
PubMed ID8591031
JournalStructure
Year1995
Volume3
Pages1207-15
AuthorsAlexeev D, Baxter RL, Smekal O, Sawyer L
TitleSubstrate binding and carboxylation by dethiobiotin synthetase--a kinetic and X-ray study.
[5]
PubMed ID9125495
JournalBiochemistry
Year1997
Volume36
Pages4751-60
AuthorsYang G, Sandalova T, Lohman K, Lindqvist Y, Rendina AR
TitleActive site mutants of Escherichia coli dethiobiotin synthetase: effects of mutations on enzyme catalytic and structural properties.
[6]
PubMed ID9211290
JournalMethods Enzymol
Year1997
Volume279
Pages376-85
AuthorsSchneider G, Lindqvist Y
TitleStructure of ATP-dependent carboxylase, dethiobiotin synthase.
[7]
CommentsX-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
Medline ID98245107
PubMed ID9576910
JournalProc Natl Acad Sci U S A
Year1998
Volume95
Pages5495-500
AuthorsKack H, Gibson KJ, Lindqvist Y, Schneider G
TitleSnapshot of a phosphorylated substrate intermediate by kinetic crystallography.
Related PDB1a82,1dak
Related Swiss-protP13000
[8]
CommentsX-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
Medline ID99081548
PubMed ID9865950
JournalProtein Sci
Year1998
Volume7
Pages2560-6
AuthorsKack H, Sandmark J, Gibson KJ, Schneider G, Lindqvist Y
TitleCrystal structure of two quaternary complexes of dethiobiotin synthetase, enzyme-MgADP-AlF3-diaminopelargonic acid and enzyme-MgADP-dethiobiotin-phosphate; implications for catalysis.
Related PDB1bs1,1dam
Related Swiss-protP13000
[9]
CommentsX-RAY CRYSTALLOGRAPHY (0.97 ANGSTROMS).
Medline ID99190933
PubMed ID10089457
JournalActa Crystallogr D Biol Crystallogr
Year1999
Volume55
Pages610-24
AuthorsSandalova T, Schneider G, Kack H, Lindqvist Y
TitleStructure of dethiobiotin synthetase at 0.97 A resolution.
Related PDB1byi
Related Swiss-protP13000
[10]
PubMed ID10966576
JournalProteins
Year2000
Volume41
Pages238-47
AuthorsGalperin MY, Grishin NV
TitleThe synthetase domains of cobalamin biosynthesis amidotransferases cobB and cobQ belong to a new family of ATP-dependent amidoligases, related to dethiobiotin synthetase.
[11]
PubMed ID11322938
JournalFEBS Lett
Year2001
Volume495
Pages7-11
AuthorsSchneider G, Lindqvist Y
TitleStructural enzymology of biotin biosynthesis.

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.

createdupdated
2004-08-012009-02-26
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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