PDBsum entry: 1a82

Biotin biosynthesis

PDB id: 1a82

Contents

Protein chain

224 a.a. *

Ligands

DNN

ATP

Metals

_MG

Waters ×219

* Residue conservation analysis

PDB id:

1a82

Name:

Biotin biosynthesis

Title:

Dethiobiotin synthetase from escherichia coli, complex with atp and diaminopelargonic acid

Structure:

Dethiobiotin synthetase. Chain: a. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Cellular_location: cytoplasm. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Homo-Dimer (from PDB file)

Resolution:

1.80Å R-factor: 0.190 R-free: 0.246

Authors:

H.Kaeck,K.J.Gibson,Y.Lindqvist,G.Schneider

Key ref:

H.Käck et al. (1998). Snapshot of a phosphorylated substrate intermediate by kinetic crystallography. Proc Natl Acad Sci U S A, 95, 5495-5500. PubMed id: 9576910 DOI: 10.1073/pnas.95.10.5495

Date:

31-Mar-98 Release date: 11-May-99

Protein chain

P13000  (BIOD1_ECOLI) -  ATP-dependent dethiobiotin synthetase BioD 1

Seq: 225 a.a.

Struc: 224 a.a.

Enzyme reactions

• Enzyme class: E.C.6.3.3.3 - Dethiobiotin synthase.
• Reaction: ATP + 7,8-diaminononanoate + CO₂ = ADP + phosphate + dethiobiotin

ATP (Bound ligand (Het Group name = ATP) corresponds exactly) + 7,8-diaminononanoate (Bound ligand (Het Group name = DNN) corresponds exactly) + CO(2) = ADP + phosphate + dethiobiotin

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: biotin biosynthetic process (1 term)
• Biochemical function: nucleotide binding (6 terms)

reference

DOI no: 10.1073/pnas.95.10.5495

Proc Natl Acad Sci U S A 95:5495-5500 (1998)

PubMed id: 9576910

Snapshot of a phosphorylated substrate intermediate by kinetic crystallography.

H.Käck, K.J.Gibson, Y.Lindqvist, G.Schneider.

ABSTRACT

The ATP-dependent enzyme dethiobiotin synthetase from Escherichia coli catalyses the formation of dethiobiotin from CO2 and 7, 8-diaminopelargonic acid. The reaction is initiated by the formation of a carbamate and proceeds through a phosphorylated intermediate, a mixed carbamic phosphoric anhydride. Here, we report the crystal structures at 1.9- and 1.6-A resolution, respectively, of the enzyme-MgATP-diaminopelargonic acid and enzyme-MgADP-carbamic-phosphoric acid anhydride complexes, observed by using kinetic crystallography. Reaction initiation by addition of either NaHCO3 or diaminopelargonic acid to crystals already containing cosubstrates resulted in the accumulation of the phosphorylated intermediate at the active site. The phosphoryl transfer step shows inversion of the configuration at the phosphorus atom, consistent with an in-line attack by the carbamate oxygen onto the phosphorus atom of ATP. A key feature in the structure of the complex of the enzyme with the reaction intermediate is two magnesium ions, bridging the phosphates at the cleavage site. These magnesium ions compensate the negative charges at both phosphate groups after phosphoryl transfer and contribute to the stabilization of the reaction intermediate.

Selected figure(s)

Figure 4.
Fig. 4. Polar interactions of the substrate (a) and the reaction intermediate (b) with protein atoms at the active site of DTBS. Hydrogen bonds (cutoff distance 3.2 Å) are shown with dotted lines. Coordination bonds from atoms of the protein and the substrate/reaction intermediate to the Mg2+ ions are included.

Figure 6.
Fig. 6. Refined structure of the metal sites of the complex of DTBS with ADP and a reaction intermediate, the mixed carbamic-phosphoric acid anhydride. Golden spheres indicate magnesium ions, and red spheres indicate solvent molecules. Coordination bonds are shown by dotted lines.

Figures were selected by an automated process.