3R6Q

A triclinic-lattice structure of aspartase from Bacillus sp. YM55-1

3R6Q の概要

• エントリーDOI: 10.2210/pdb3r6q/pdb
• 関連するPDBエントリー: 3R6V 3R6Y
• 分子名称: Aspartase, CALCIUM ION (3 entities in total)
• 機能のキーワード: aspartase, aspartate ammonia lyase, lyase
• 由来する生物種: Bacillus sp.
• タンパク質・核酸の鎖数: 8
• 化学式量合計: 413720.13

構造登録者

Fibriansah, G.,Puthan Veetil, V.,Poelarends, G.J.,Thunnissen, A.-M.W.H. (登録日: 2011-03-22, 公開日: 2011-07-13, 最終更新日: 2023-09-13)

主引用文献

Fibriansah, G.,Veetil, V.P.,Poelarends, G.J.,Thunnissen, A.M.
Structural basis for the catalytic mechanism of aspartate ammonia lyase.
Biochemistry, 50:6053-6062, 2011

PubMed Abstract: Aspartate ammonia lyases (or aspartases) catalyze the reversible deamination of L-aspartate into fumarate and ammonia. The lack of crystal structures of complexes with substrate, product, or substrate analogues so far precluded determination of their precise mechanism of catalysis. Here, we report crystal structures of AspB, the aspartase from Bacillus sp. YM55-1, in an unliganded state and in complex with L-aspartate at 2.4 and 2.6 Å resolution, respectively. AspB forces the bound substrate to adopt a high-energy, enediolate-like conformation that is stabilized, in part, by an extensive network of hydrogen bonds between residues Thr101, Ser140, Thr141, and Ser319 and the substrate's β-carboxylate group. Furthermore, substrate binding induces a large conformational change in the SS loop (residues G(317)SSIMPGKVN(326)) from an open conformation to one that closes over the active site. In the closed conformation, the strictly conserved SS loop residue Ser318 is at a suitable position to act as a catalytic base, abstracting the Cβ proton of the substrate in the first step of the reaction mechanism. The catalytic importance of Ser318 was confirmed by site-directed mutagenesis. Site-directed mutagenesis of SS loop residues, combined with structural and kinetic analysis of a stable proteolytic AspB fragment, further suggests an important role for the small C-terminal domain of AspB in controlling the conformation of the SS loop and, hence, in regulating catalytic activity. Our results provide evidence supporting the notion that members of the aspartase/fumarase superfamily use a common catalytic mechanism involving general base-catalyzed formation of a stabilized enediolate intermediate.

PubMed: 21661762
DOI: 10.1021/bi200497y

実験手法

X-RAY DIFFRACTION (2.4 Å)