3WYB

Structure of a meso-diaminopimelate dehydrogenase

3WYB の概要

• エントリーDOI: 10.2210/pdb3wyb/pdb
• 関連するPDBエントリー: 3WYC
• 分子名称: Meso-diaminopimelate D-dehydrogenase (2 entities in total)
• 機能のキーワード: rossmann fold, oxidoreductase
• 由来する生物種: Ureibacillus thermosphaericus
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 74279.23

構造登録者

Sakuraba, H.,Akita, H.,Ohshima, T. (登録日: 2014-08-25, 公開日: 2015-05-06, 最終更新日: 2024-03-20)

主引用文献

Akita, H.,Seto, T.,Ohshima, T.,Sakuraba, H.
Structural insight into the thermostable NADP(+)-dependent meso-diaminopimelate dehydrogenase from Ureibacillus thermosphaericus
Acta Crystallogr.,Sect.D, 71:1136-1146, 2015

PubMed Abstract: Crystal structures of the thermostable meso-diaminopimelate dehydrogenase (DAPDH) from Ureibacillus thermosphaericus were determined for the enzyme in the apo form and in complex with NADP(+) and N-tris(hydroxymethyl)methyl-2-aminoethanesulfonic acid. The main-chain coordinates of the enzyme showed notable similarity to those of Symbiobacterium thermophilum DAPDH. However, the subunit arrangement of U. thermosphaericus DAPDH (a dimer) was totally different from that of the S. thermophilum enzyme (a hexamer). Structural comparison with the dimeric enzyme from the mesophile Corynebacterium glutamicum revealed that the presence of large numbers of intrasubunit and intersubunit hydrophobic interactions, as well as the extensive formation of intersubunit ion-pair networks, were likely to be the main factors contributing to the higher thermostability of U. thermosphaericus DAPDH. This differs from S. thermophilum DAPDH, within which the unique hexameric assembly is likely to be responsible for its high thermostability. Analysis of the active site of U. thermosphaericus DAPDH revealed the key factors responsible for the marked difference in substrate specificity between DAPDH and the D-amino acid dehydrogenase recently created from DAPDH by introducing five point mutations [Akita et al. (2012). Biotechnol. Lett. 34, 1693-1699; 1701-1702].

PubMed: 25945579
DOI: 10.1107/S1399004715003673

実験手法

X-RAY DIFFRACTION (2.4 Å)