1a82

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spinqualitylabelsall models PDB ID 1a82 Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image
, resolution 1.8Å
Ligands:	, and
Activity:	Dethiobiotin synthase, with EC number 6.3.3.3
Coordinates:	save as pdb, mmCIF, xml

DETHIOBIOTIN SYNTHETASE FROM ESCHERICHIA COLI, COMPLEX WITH SUBSTRATES ATP AND DIAMINOPELARGONIC ACID

Overview

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.

About this Structure

1A82 is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.

Reference

Snapshot of a phosphorylated substrate intermediate by kinetic crystallography., Kack H, Gibson KJ, Lindqvist Y, Schneider G, Proc Natl Acad Sci U S A. 1998 May 12;95(10):5495-500. PMID:9576910

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