2ZTL

Closed conformation of D-3-hydroxybutyrate dehydrogenase complexed with NAD+ and L-3-hydroxybutyrate

2ZTL の概要

• エントリーDOI: 10.2210/pdb2ztl/pdb
• 関連するPDBエントリー: 1WMB 1X1T 2ZTM
• 分子名称: D(-)-3-hydroxybutyrate dehydrogenase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, (3S)-3-HYDROXYBUTANOIC ACID, ... (6 entities in total)
• 機能のキーワード: short chain dehydrogenase/reductase, sdr family, nad, nadh, hbdh, oxidoreductase
• 由来する生物種: Pseudomonas fragi
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 110060.48

構造登録者

Nakashima, K.,Nakajima, Y.,Ito, K.,Yoshimoto, T. (登録日: 2008-10-07, 公開日: 2009-08-25, 最終更新日: 2023-11-01)

主引用文献

Nakashima, K.,Ito, K.,Nakajima, Y.,Yamazawa, R.,Miyakawa, S.,Yoshimoto, T.
Closed complex of the D-3-hydroxybutyrate dehydrogenase induced by an enantiomeric competitive inhibitor.
J.Biochem., 145:467-479, 2009

PubMed Abstract: D-3-Hydroxybutyrate dehydrogenase (HBDH) from Pseudomonas fragi showed a strict stereospecificity to the d-enantiomer of 3-hydroxybutyrate (d-3-HB) as a substrate. The l-enantiomer acts as a competitive inhibitor, with a K(i) value comparable to the K(m) value for d-3-HB. We have determined the crystal structures of the ternary complex of HBDH-NAD(+)-l-3-HB and the binary complex of HBDH-NAD(+). The former structure showed a so-called closed-form conformation, which is considered an active form for catalysis, while the latter stayed mostly in a open-form conformation. The determined structures along with the site-directed mutagenesis confirmed the substrate recognition mechanism that we proposed previously. The hydrogen bonding interaction between Gln196, located in the moving helix, and the carboxyl group of the substrate/inhibitor is important for the stable ternary complex formation. Finally, the crystal structures of the Thr190 mutants, T190S and T190A, indicate that the Thr190 is a key residue for the open-closed conformational change. T190S retained 37% of the activity. In T190A, however, the activity decreased to 0.1% that of the wild-type enzyme. Fixing the position of the hydroxyl group of Thr190 to form hydrogen bonds to the pyrophosphate moiety and the carboxamide of NAD(+) seems to be a significant factor for the open-closed conformational change.

PubMed: 19122202
DOI: 10.1093/jb/mvn186

実験手法

X-RAY DIFFRACTION (1.8 Å)