8S3D

Crystal structure of Medicago truncatula glutamate dehydrogenase 2 in complex with 2-amino-2-hydroxyglutarate (reaction intermediate) and NAD

8S3D の概要

• エントリーDOI: 10.2210/pdb8s3d/pdb
• 分子名称: Glutamate dehydrogenase, TRIETHYLENE GLYCOL, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, ... (11 entities in total)
• 機能のキーワード: complex with reaction intermediate, glutamate dehydrogenase, oxidoreductase
• 由来する生物種: Arabidopsis thaliana (thale cress)
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 278853.49

構造登録者

Grzechowiak, M.,Ruszkowski, M. (登録日: 2024-02-19, 公開日: 2024-09-04)

主引用文献

Grzechowiak, M.,Sliwiak, J.,Link, A.,Ruszkowski, M.
Legume-type glutamate dehydrogenase: Structure, activity, and inhibition studies.
Int.J.Biol.Macromol., 278:134648-134648, 2024

PubMed Abstract: Glutamate dehydrogenases (GDHs) are key enzymes at the crossroads of N and C metabolism in plants. Legumes, whose N metabolism is particularly intricate, possess a unique type of GDH. This study presents an analysis of a legume-type GDH (isoform 2) from Medicago truncatula (MtGDH2). We measured MtGDH2 activity in both the Glu → 2-oxoglutarate (2OG) and 2OG → Glu reaction directions and obtained kinetic parameters for Glu, 2OG, NAD, and NADH. Inhibition assays revealed that compounds possessing di- or tricarboxylates act as inhibitors of plant GDHs. Interestingly, 2,6-pyridinedicarboxylate (PYR) weakly inhibits MtGDH2 compared to Arabidopsis thaliana homologs. Furthermore, we explored tetrazole derivatives to discover 3-(1H-tetrazol-5-yl)benzoic acid (TBA) as an MtGDH2 inhibitor. The kinetic experiments are supported by six crystal structures, solved as: (i) unliganded enzyme, (ii) trapping the reaction intermediate 2-amino-2-hydroxyglutarate and NAD, and also complexed with NAD and inhibitors such as (iii) citrate, (iv) PYR, (v) isophthalate, and (vi) TBA. The complex with TBA revealed a new mode of action that, in contrast to other inhibitors, prevents domain closure. This discovery points to TBA as a starting point for the development of novel GDH inhibitors to study the functions of GDH in plants and potentially boost biomass production.

PubMed: 39142482
DOI: 10.1016/j.ijbiomac.2024.134648

実験手法

X-RAY DIFFRACTION (1.65 Å)