5E3R

Crystal structure of DapD in complex with 2-aminopimelate from Corynebacterium glutamicum

5E3R の概要

• エントリーDOI: 10.2210/pdb5e3r/pdb
• 関連するPDBエントリー: 5E3P 5E3Q
• 分子名称: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, (2S)-2-aminoheptanedioic acid (3 entities in total)
• 機能のキーワード: transferase, corynebacterium glutamicum, l-lysine
• 由来する生物種: Corynebacterium glutamicum
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 32085.03

構造登録者

Sagong, H.-Y.,Kim, K.-J. (登録日: 2015-10-03, 公開日: 2015-11-04, 最終更新日: 2023-11-08)

主引用文献

Sagong, H.Y.,Kim, K.J.
Crystal Structure and Biochemical Characterization of Tetrahydrodipicolinate N-Succinyltransferase from Corynebacterium glutamicum.
J.Agric.Food Chem., 63:10641-10646, 2015

PubMed Abstract: Tetrahydrodipicolinate N-succinyltransferase (DapD) is an enzyme involved in the biosynthesis of l-lysine by converting tetrahydrodipicolinate into N-succinyl-l-2-amino-6-oxopimelate, using succinyl-CoA as a cofactor. We determined the crystal structure of DapD from Corynebacterium glutamicum (CgDapD). CgDapD functions as a trimer, and each monomer consists of three domains: an N-terminal helical domain (NTD), a left-handed β-helix (LβH) domain, and a β C-terminal domain (CTD). The mode of cofactor binding to CgDapD, elucidated by determining the structure in complex with succinyl-CoA, reveals that the position of the CTD changes slightly as the cofactor binds to the enzyme. The superposition of this structure with that of Mycobacterium tuberculosis shows differences in residues that make up cofactor-binding sites. Moreover, we determined the structure of CgDapD in complex with the substrate analogue 2-aminopimelate and revealed that the analogue was stabilized by conserved residues. The catalytic and substrate binding sites of CgDapD were confirmed by site-directed mutagenesis experiments.

PubMed: 26602189
DOI: 10.1021/acs.jafc.5b04785

実験手法

X-RAY DIFFRACTION (1.85 Å)