5XD7

Crystal structure analysis of 3,6-anhydro-L-galactonate cycloisomerase

5XD7 の概要

• エントリーDOI: 10.2210/pdb5xd7/pdb
• 関連するPDBエントリー: 5XD8 5XD9
• 分子名称: 3,6-anhydro-alpha-L-galactonate cycloisomerase, MAGNESIUM ION, ACETIC ACID, ... (4 entities in total)
• 機能のキーワード: enolase superfamily, 3, 6-anhydro-l-galactonate cycloisomerase, lyase, barrel domain, capping domain, isomerase
• 由来する生物種: Vibrio sp. (strain EJY3)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 41429.40

構造登録者

Lee, S.,Choi, I.-G.,Kim, H.-Y. (登録日: 2017-03-27, 公開日: 2017-09-27, 最終更新日: 2023-11-22)

主引用文献

Lee, S.,Kim, K.H.,Kim, H.-Y.,Choi, I.-G.
Crystal structure analysis of 3,6-anhydro-l-galactonate cycloisomerase suggests emergence of novel substrate specificity in the enolase superfamily.
Biochem. Biophys. Res. Commun., 491:217-222, 2017

PubMed Abstract: 3,6-Anydro-l-galatonate cycloisomerase (ACI) catalyzes the cycloisomerization of a 3,6-anhydro-l-galactonic acid known as a novel metabolite in agarolytic bacteria. Here, we present 3-D structures of ACI from Vibrio sp. strain EJY3 (VejACI) in native and mutant forms at 2.2 Å and 2.6 Å resolutions, respectively. The enzyme belongs to the mandelate racemase subgroup of the enolase superfamily catalyzing common β-elimination reactions by α-carbon deprotonation of substrates. The structure of VejACI revealed a notable 20s loop region in the capping domain, which can be a highly conserved structural motif in ACI homologs of agar metabolism. By comparing mutant (mVejAC/H300 N) and native VejACI structures, we identified a conformational change of Ile142 in VejACI that causes spatial expansion in the binding pocket. These observations imply that Ile142 and the 20s loop play important roles in enzymatic reactivity and substrate specificity. The structural phylogenetic analysis of the enolase superfamily including ACIs revealed sequential, structural, and functional relationships related to the emergence of novel substrate specificity.

PubMed: 28716734
DOI: 10.1016/j.bbrc.2017.07.080

実験手法

X-RAY DIFFRACTION (2.198 Å)