8KAR image
Deposition Date 2023-08-03
Release Date 2024-08-07
Last Version Date 2025-08-06
Entry Detail
PDB ID:
8KAR
Keywords:
Title:
Glutamate dehydrogenase-AKG
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.73 Å
R-Value Free:
0.23
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
C 1 2 1
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Glutamate dehydrogenase
Chain IDs:A, B, C
Chain Length:419
Number of Molecules:3
Biological Source:Saccharolobus solfataricus
Primary Citation
Structural insight into the unique substrate specificity of glutamate dehydrogenase from Saccharolobus solfataricus.
Extremophiles 29 32 32 (2025)
PMID: 40705132 DOI: 10.1007/s00792-025-01395-1

Abstact

The gene (SSO1457) encoding a L-glutamate dehydrogenase (GDH) homolog from the thermoacidophilic archaeon Saccharolobus solfataricus P2 was overexpressed in Escherichia coli. At a substrate concentration of 50 mM, the enzyme (SSO1457) produced exhibited much higher specific activity toward L-norvaline than L-glutamate at temperatures between 55 and 75°C, whereas the enzyme showed higher activity for L-glutamate than L-norvaline at 85°C. The crystal structures of both NAD+/2-oxovalerate-bound and NAD+/2-oxoglutarate-bound SSO1457 were determined. Comparison of the two structures showed that the positioning of the substrate molecules and the surrounding residues is nearly identical in the two complexes. In the 2-oxoglutarate-bound structure, the C5-carboxylate group of 2-oxoglutarate is hydrogen-bonded with the side chains of Lys72, Arg188, and Ser351, as observed in other GDHs. By contrast, in the 2-oxovalerate-bound structure, the C01, C02, and C03 atoms of 2-oxovalerate are anchored via hydrophobic interactions to the side chains of Met93 and Val348. Site-directed mutagenesis shows that the side chain of Met93 mainly mediates the reactivity of SSO1457 towards L-norvaline and contributes to high specific activities for L-norvaline.

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Primary Citation of related structures