5GP4

Lactobacillus brevis CGMCC 1306 Glutamate decarboxylase

Summary for 5GP4

• Entry DOI: 10.2210/pdb5gp4/pdb
• Descriptor: Glutamate decarboxylase, PYRIDOXAL-5'-PHOSPHATE (3 entities in total)
• Functional Keywords: glutamate decarboxylase lactobacillus brevis cgmcc 1306 gamma-aminobutyric acid pyridoxal phosphate (plp), lyase
• Biological source: Lactobacillus brevis
• Total number of polymer chains: 3
• Total formula weight: 161579.42

Authors

Mei, L.,Huang, J. (deposition date: 2016-07-31, release date: 2017-08-02, Last modification date: 2023-11-08)

Primary citation

Huang, J.,Fang, H.,Gai, Z.C.,Mei, J.Q.,Li, J.N.,Hu, S.,Lv, C.J.,Zhao, W.R.,Mei, L.H.
Lactobacillus brevis CGMCC 1306 glutamate decarboxylase: Crystal structure and functional analysis.
Biochem. Biophys. Res. Commun., 503:1703-1709, 2018

PubMed Abstract: Glutamate decarboxylase (GAD), which is a unique pyridoxal 5-phosphate (PLP)-dependent enzyme, can catalyze α-decarboxylation of l-glutamate (L-Glu) to γ-aminobutyrate (GABA). The crystal structure of GAD in complex with PLP from Lactobacillus brevis CGMCC 1306 was successfully solved by molecular-replacement, and refined at 2.2 Å resolution to an R factor of 18.76% (R = 23.08%). The coenzyme pyridoxal 5-phosphate (PLP) forms a Schiff base with the active-site residue Lys279 by continuous electron density map, which is critical for catalysis by PLP-dependent decarboxylase. Gel filtration showed that the active (pH 4.8) and inactive (pH 7.0) forms of GAD are all dimer. The residues (Ser126, Ser127, Cys168, Ile211, Ser276, His278 and Ser321) play important roles in anchoring PLP cofactor inside the active site and supporting its catalytic reactivity. The mutant T215A around the putative substrate pocket displayed an 1.6-fold improvement in catalytic efficiency (k/K) compared to the wild-type enzyme (1.227 mM S versus 0.777 mM S), which was the highest activity among all variants tested. The flexible loop (Tyr308-Glu312), which is positioned near the substrate-binding site, is involved in the catalytic reaction, and the conserved residue Tyr308 plays a vital role in decarboxylation of L-Glu.

PubMed: 30049439
DOI: 10.1016/j.bbrc.2018.07.102

Experimental method

X-RAY DIFFRACTION (2.16 Å)