4OGG

Crystal Structure of Arabidopsis thaliana DJ-1d with glyoxylate as substrate analog

4OGG の概要

• エントリーDOI: 10.2210/pdb4ogg/pdb
• 関連するPDBエントリー: 4OFW 4OGF
• 分子名称: Protein DJ-1 homolog D (2 entities in total)
• 機能のキーワード: glyoxalase, lyase
• 由来する生物種: Arabidopsis thaliana (mouse-ear cress)
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 125722.62

構造登録者

Choi, D.,Kim, J.,Ryu, K.-S.,Park, C. (登録日: 2014-01-16, 公開日: 2014-10-15, 最終更新日: 2023-09-20)

主引用文献

Choi, D.,Kim, J.,Ha, S.,Kwon, K.,Kim, E.H.,Lee, H.Y.,Ryu, K.S.,Park, C.
Stereospecific mechanism of DJ-1 glyoxalases inferred from their hemithioacetal-containing crystal structures.
Febs J., 281:5447-5462, 2014

PubMed Abstract: DJ-1 family proteins have recently been characterized as novel glyoxalases, although their cofactor-free catalytic mechanisms are not fully understood. Here, we obtained crystals of Arabidopsis thaliana DJ-1d (atDJ-1d) and Homo sapiens DJ-1 (hDJ-1) covalently bound to glyoxylate, an analog of methylglyoxal, forming a hemithioacetal that presumably mimics an intermediate structure in catalysis of methylglyoxal to lactate. The deuteration level of lactate supported the proton transfer mechanism in the enzyme reaction. Differences in the enantiomeric specificity of d/l-lactacte formation observed for the DJ-1 superfamily proteins are explained by the presence of a His residue in the active site with essential Cys and Glu residues. The model for the stereospecificity was further evaluated by a molecular modeling simulation with methylglyoxal hemithioacetal superimposed on the glyoxylate hemithioacetal. The mechanism of DJ-1 glyoxalase provides a basis for understanding the His residue-based stereospecificity.

PubMed: 25283443
DOI: 10.1111/febs.13085

実験手法

X-RAY DIFFRACTION (1.6 Å)