21FT

GABA aminotransferase from Arabidopsis thaliana

Summary for 21FT

• Entry DOI: 10.2210/pdb21ft/pdb
• Descriptor: Gamma-aminobutyrate transaminase POP2, mitochondrial (2 entities in total)
• Functional Keywords: gaba, plant protein
• Biological source: Arabidopsis thaliana (thale cress)
• Total number of polymer chains: 4
• Total formula weight: 208665.88

Authors

Okoda, N.,Okuda, S.,Tsutsumi, K.,Sano, K.,Kobata, K.,Nagata, K. (deposition date: 2025-12-12, release date: 2026-06-03, Last modification date: 2026-06-10)

Primary citation

Okoda, N.,Okuda, S.,Tsutsumi, K.,Itoh, H.,Okamoto, K.,Kawakami, H.,Sano, K.,Kobata, K.,Nagata, K.
Crystal structure of the plant GABA aminotransferase AtGABA-T from Arabidopsis thaliana.
Acta Crystallogr.,Sect.F, 82:208-215, 2026

PubMed Abstract: γ-Aminobutyric acid aminotransferase (GABA-T) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes γ-aminobutyric acid (GABA) degradation in the mitochondrial GABA shunt. Plant GABA-Ts correspond to EC 2.6.1.96 and differ from mammalian and bacterial GABA-Ts (EC 2.6.1.19) in substrate specificity; however, their structural basis has remained unclear. Here, we report the crystal structure of GABA aminotransferase from Arabidopsis thaliana (AtGABA-T) at 2.0 Å resolution. Structural comparison using Foldseek indicates that AtGABA-T belongs to the class III aminotransferase family. Comparison with a class III ω-aminotransferase suggests that Arg423 located in the C-terminal region of AtGABA-T functions as the primary anchor for the carboxyl group of GABA, together with residues forming a tunnel-shaped substrate-access pathway. In contrast to nonplant GABA aminotransferases, which utilize a conserved N-terminal arginine for substrate recognition, AtGABA-T employs a distinct C-terminal arginine. These findings provide direct structural evidence for the classification of AtGABA-T as a class III aminotransferase and reveal a distinct mode of substrate recognition in AtGABA-T.

PubMed: 42065129
DOI: 10.1107/S2053230X26003456

Experimental method

X-RAY DIFFRACTION (2 Å)