3D3X

Crystal structure of botulinum neurotoxin serotype E catalytic domain in complex with SNAP-25 substrate peptide

3D3X の概要

• エントリーDOI: 10.2210/pdb3d3x/pdb
• 関連するPDBエントリー: 1T3A 1T3C 1ZKW 1ZKX 1ZL6
• 分子名称: Type E botulinum toxin, SNAP-25 substrate peptide, ZINC ION, ... (5 entities in total)
• 機能のキーワード: bont e, snap-25, enzyme-substrate complex, hydrolase, hydrolase-hydrolase substrate complex, hydrolase/hydrolase substrate
• 由来する生物種: Clostridium butyricum
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 99340.38

構造登録者

Agarwal, R.,Swaminathan, S. (登録日: 2008-05-13, 公開日: 2008-07-08, 最終更新日: 2024-10-30)

主引用文献

Agarwal, R.,Swaminathan, S.
SNAP-25 substrate peptide (residues 180-183) binds to but bypasses cleavage by catalytically active Clostridium botulinum neurotoxin E.
J.Biol.Chem., 283:25944-25951, 2008

PubMed Abstract: Clostridium botulinum neurotoxins are the most potent toxins to humans. The recognition and cleavage of SNAREs are prime evente in exhibiting their toxicity. We report here the crystal structure of the catalytically active full-length botulinum serotype E catalytic domain (BoNT E) in complex with SNAP-25 (a SNARE protein) substrate peptide Arg(180)-Ile(181)-Met(182)-Glu(183) (P1-P3'). It is remarkable that the peptide spanning the scissile bond binds to but bypasses cleavage by the enzyme and inhibits the catalysis fairly with K(i) approximately 69 microm. The inhibitory peptide occupies the active site of BoNT E and shows well defined electron density. The catalytic zinc and the conserved key residue Tyr(350) of the enzyme facilitate the docking of Arg(180) (P1) by interacting with its carbonyl oxygen that displaces the nucleophilic water. The general base Glu(212) side chain interacts with the main chain amino group of P1 and P1'. Conserved Arg(347) of BoNT E stabilizes the proper docking of the Ile(181) (P1') main chain, whereas the hydrophobic pockets stabilize the side chains of Ile(181) (P1') and Met(182) (P2'), and the 250 loop stabilizes Glu(183) (P3'). Structural and functional analysis revealed an important role for the P1' residue and S1' pocket in driving substrate recognition and docking at the active site. This study is the first of its kind and rationalizes the substrate cleavage strategy of BoNT E. Also, our complex structure opens up an excellent opportunity of structure-based drug design for this fast acting and extremely toxic high priority BoNT E.

PubMed: 18658150
DOI: 10.1074/jbc.M803756200

実験手法

X-RAY DIFFRACTION (2.25 Å)