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Overview for MACiE Entry M0074

Version history

General Information

EC Number: 6.3.3.3 (A member of the Ligases, Forming carbon-nitrogen bonds, Cyclo-ligases)

Enzyme Name: dethiobiotin synthase

Biological Species: Escherichia coli (Bacteria)

Catalytic Chain UniprotKB Accession Codes:

  • P13000 - ATP-dependent dethiobiotin synthetase BioD 1

Representative PDB Code: 1bs1 - DETHIOBIOTIN SYNTHETASE COMPLEXED WITH DETHIOBIOTIN, ADP , INORGANICPHOSPHATE AND MAGNESIUM (Resolution = 1.80 Å).

Catalytic CATH Codes:

  • 3.40.50.300 - P-loop containing nucleotide triphosphate hydrolases

Display structure information

Overall Reaction:

Image of ATP

Image of carbon dioxide

Image of 7,8-diaminononanoate

right arrow

Image of proton

Image of dethiobiotin

Image of ADP

Image of phosphate

ATP
C00002
CHEBI:30616
carbon dioxide
C00011
CHEBI:16526
7,8-diaminononanoate
C01037
CHEBI:17830
proton
C00080
CHEBI:24636
dethiobiotin
C01909
CHEBI:57861
ADP
C00008
CHEBI:456216
phosphate
C00009
CHEBI:39745

Overall Comment: Mg(II) can be replaced by any divalent metal ion.


View similar reactions


Stepwise Description of the Reaction

Step 1Water deprotonates the 7,8-diaminononanoate substrate, activating it for a nucleophilic attack upon the carbon dioxide in an addition reaction. Lys37 stabilises the formation of the negatively charged intermediate.
Step 2The carboxylated intermediate acts as a nucleophile and attacks the gamma phosphate of ATP in a substitution reaction. Lys37, Lys15 and two Mg(II) ions stabilise the intermediates.
Step 3The newly attached phosphate group deprotonates the terminal primary amine, which in turn acts as a nucleophile to attack the phosphorylated carbonyl carbon in an internal addition reaction. Lys37, Lys15 and the main chain amide of Ser41 all stabilise the intermediates.
Step 4The oxyanion formed re-forms the carbonyl group, cleaving the P-O bond in a conjugate base elimination reaction. The leaving phosphate group deprotonates the newly formed secondary amine. Lys15, Lys37 and the main chain amide of Ser41 all stabilise the intermediates.

View similar reactions (composite manual annotation)


Catalytic Residues Involved

Type Number Chain Location of Function
Lys 15 A Side Chain
Lys 37 A Side Chain
Ser 41 A Main Chain Amide

Metal Cofactors for M0074

Type Het group Number Chain
magnesium MG 901 x Overview
magnesium MG 902 x Overview

References

  1. G. Yang et al. (1997), Biochemistry, 36, 4751-4760. Active site mutants of Escherichia coli dethiobiotin synthetase: effects of mutations on enzyme catalytic and structural properties.
    Medline: 9125495
  2. H. Kack et al. (1998), Proc. Natl Acad. Sci. USA, 95, 5495-5500. Snapshot of a phosphorylated substrate intermediate by kinetic crystallography.
    Medline: 9576910
  3. H. Kack et al. (1998), Protein Sci., 7, 2560-2566. Crystal structure of two quaternary complexes of dethiobiotin synthetase, enzyme-MgADP-AlF3-diaminopelargonic acid and enzyme-MgADP-dethiobiotin-phosphate.
    Medline: 9865950

Homologue information for M0074 (1bs1)

CSA Homologues

MACiE Homologues (within the PDB)

MACiE Homologues (within UniprotKB/SwissProt)



Entries with at least one Catalytic CATH code in common (different mechanisms):

MACiE Entry Enzyme Name
EC Number
PDB code CATH code Composite
Reaction Similarity
Catalytic Machinery
Similarity
M0212 nitrogenase
1.18.6.1
1n2c 3.40.50.300
0.06230.3176Compare
M0290 adenylate kinase
2.7.4.3
1zio 3.40.50.300
0.05260.0208Compare
M0154 estrone sulfotransferase
2.8.2.4
1hy3 3.40.50.300
0.04760.54Compare
M0178 H+-transporting two-sector ATPase
3.6.3.14
1e79 3.40.50.300
0.14280.2161Compare

View a comparison of the other reactions in MACiE with the CATH domain 3.40.50.300


Links to this entry in other databases

Link to EC-PDB-SUM Link to PDB-SUM Link to RCSB PDB Link to PDBe Link to CSA
Link to MetaCyc Link to KEGG Link to BRENDA Link to ExplorENZ
Link to EzCatDB

GOA logo
magnesium ion binding (molecular function)
dethiobiotin synthase activity (molecular function)
ATP binding (molecular function)
biotin biosynthetic process (biological process)
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