1DAK

DETHIOBIOTIN SYNTHETASE FROM ESCHERICHIA COLI, COMPLEX REACTION INTERMEDIATE ADP AND MIXED ANHYDRIDE

1DAK の概要

• エントリーDOI: 10.2210/pdb1dak/pdb
• 分子名称: DETHIOBIOTIN SYNTHETASE, PHOSPHATE ION, MAGNESIUM ION, ... (6 entities in total)
• 機能のキーワード: phoshporyl transfer, biotin biosynthesis, ligase, kinetic crystallography
• 由来する生物種: Escherichia coli
• 細胞内の位置: Cytoplasm: P13000
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 24911.33

構造登録者

Kaeck, H.,Gibson, K.J.,Lindqvist, Y.,Schneider, G. (登録日: 1998-03-31, 公開日: 1999-04-06, 最終更新日: 2024-05-22)

主引用文献

Kack, H.,Gibson, K.J.,Lindqvist, Y.,Schneider, G.
Snapshot of a phosphorylated substrate intermediate by kinetic crystallography.
Proc.Natl.Acad.Sci.USA, 95:5495-5500, 1998

PubMed 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.

PubMed: 9576910
DOI: 10.1073/pnas.95.10.5495

実験手法

X-RAY DIFFRACTION (1.6 Å)