1KGT

Crystal Structure of Tetrahydrodipicolinate N-Succinyltransferase in Complex with Pimelate and Succinyl-CoA

1KGT の概要

• エントリーDOI: 10.2210/pdb1kgt/pdb
• 関連するPDBエントリー: 1KGQ 1TDT 2TDT 3TDT
• 分子名称: 2,3,4,5-TETRAHYDROPYRIDINE-2-CARBOXYLATE N-SUCCINYLTRANSFERASE, PIMELIC ACID, SUCCINYL-COENZYME A, ... (4 entities in total)
• 機能のキーワード: left-handed parallel beta helix, transferase
• 由来する生物種: Mycobacterium bovis
• 細胞内の位置: Cytoplasm: P56220
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 30946.77

構造登録者

Beaman, T.W.,Vogel, K.W.,Drueckhammer, D.G.,Blanchard, J.S.,Roderick, S.L. (登録日: 2001-11-28, 公開日: 2002-04-03, 最終更新日: 2024-02-14)

主引用文献

Beaman, T.W.,Vogel, K.W.,Drueckhammer, D.G.,Blanchard, J.S.,Roderick, S.L.
Acyl group specificity at the active site of tetrahydridipicolinate N-succinyltransferase.
Protein Sci., 11:974-979, 2002

PubMed Abstract: Tetrahydrodipicolinate N-succinyltransferase (DapD) catalyzes the succinyl-CoA-dependent acylation of L-2-amino-6-oxopimelate to 2-N-succinyl-6-oxopimelate as part of the succinylase branch of the meso-diaminopimelate/lysine biosynthetic pathway of bacteria, blue-green algae, and plants. This pathway provides meso-diaminopimelate as a building block for cell wall peptidoglycan in most bacteria, and is regarded as a target pathway for antibacterial agents. We have solved the X-ray crystal structures of DapD in ternary complexes with pimelate/succinyl-CoA and L-2-aminopimelate with the nonreactive cofactor analog, succinamide-CoA. These structures define the binding conformation of the cofactor succinyl group and its interactions with the enzyme and place its thioester carbonyl carbon in close proximity to the nucleophilic 2-amino group of the acceptor, in support of a direct attack ternary complex mechanism. The acyl group specificity differences between homologous tetrahydrodipicolinate N-acetyl- and N-succinyltransferases can be rationalized with reference to at least three amino acids that interact with or give accessible active site volume to the cofactor succinyl group. These residues account at least in part for the substrate specificity that commits metabolic intermediates to either the succinylase or acetylase branches of the meso-diaminopimelate/lysine biosynthetic pathway.

PubMed: 11910040
DOI: 10.1110/ps.4310102

実験手法

X-RAY DIFFRACTION (2.3 Å)