3WBF

Crystal Structure of meso-diaminopimelate dehydrogenase from Symbiobacterium thermophilum co-crystallized with NADP+ and DAP

3WBF の概要

• エントリーDOI: 10.2210/pdb3wbf/pdb
• 関連するPDBエントリー: 3WB9 3WBB
• 分子名称: Diaminopimelate dehydrogenase, 2,6-DIAMINOPIMELIC ACID, GLYCEROL, ... (5 entities in total)
• 機能のキーワード: domain motion, thermo-stable, d-amino acid dehydrogenase, oxidoreductase
• 由来する生物種: Symbiobacterium thermophilum
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 104211.54

構造登録者

Liu, W.D.,Li, Z.,Huang, C.H.,Guo, R.T.,Wu, Q.Q.,Zhu, D.M. (登録日: 2013-05-15, 公開日: 2014-03-26, 最終更新日: 2023-11-15)

主引用文献

Liu, W.,Li, Z.,Huang, C.H.,Guo, R.T.,Zhao, L.,Zhang, D.,Chen, X.,Wu, Q.,Zhu, D.
Structural and mutational studies on the unusual substrate specificity of meso-diaminopimelate dehydrogenase from Symbiobacterium thermophilum.
Chembiochem, 15:217-222, 2014

PubMed Abstract: Wild-type meso-diaminopimelate dehydrogenase (DAPDH) is usually specific to the native substrate, meso-2,6-diaminopimelate. Recently, a DAPDH from Symbiobacterium thermophilum (StDAPDH) was found to exhibit expanded substrate specificity. As such, its crystal structures in apo form and in complex with NADP(+) and both NADPH and meso-DAP were investigated to reveal the structural basis of its unique catalytic properties. Structural analysis results show that StDAPDH should prefer an ordered kinetic catalytic mechanism. A second substrate entrance tunnel with Met152 at its bottleneck was found, through which pyruvate/D-alanine might bind and enter the catalytic cavity, providing some structural insights into its high activity toward pyruvate. The side chain of Met152 might interact with Asp92 and Asn253, thus affecting the domain motion and catalysis. These results offer useful information for understanding the unique catalytic properties of StDAPDH and guiding further engineering of this enzyme.

PubMed: 24339368
DOI: 10.1002/cbic.201300691

実験手法

X-RAY DIFFRACTION (2.12 Å)