9HUZ

CryoEM map of the large glutamate dehydrogenase composed of 180 kDa subunits from Mycobacterium smegmatis obtained in the presence of NAD+ and L-glutamate. Closed2 tetramer

Summary for 9HUZ

• Entry DOI: 10.2210/pdb9huz/pdb
• EMDB information: 52419 52420 52421
• Descriptor: NAD-specific glutamate dehydrogenase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE (2 entities in total)
• Functional Keywords: large glutamate dehydrogenase, tetramer, oxidoreductase
• Biological source: Mycolicibacterium smegmatis
• Total number of polymer chains: 4
• Total formula weight: 708021.14

Authors

Lazaro, M.,Chamorro, N.,Lopez-Alonso, J.P.,Charro, D.,Rasia, R.M.,Jimenez-Oses, G.,Valle, M.,Lisa, M.N. (deposition date: 2024-12-23, release date: 2026-01-14, Last modification date: 2026-04-08)

Primary citation

Lazaro, M.,Chamorro, N.,Lopez-Alonso, J.P.,Charro, D.,Rasia, R.M.,Jimenez-Oses, G.,Valle, M.,Lisa, M.N.
Tertiary and quaternary structure remodeling by occupancy of the substrate binding pocket in a large glutamate dehydrogenase.
Protein Sci., 35:e70544-e70544, 2026

PubMed Abstract: Glutamate dehydrogenases (GDHs) catalyze the oxidative deamination of L-glutamate to 2-oxoglutarate using NAD(P) as a cofactor. The large type of GDHs (L-GDHs) displays a dynamic homotetrameric architecture that alternates between open and closed states. However, the catalytic mechanism and the functional relevance of the large conformational changes in L-GDHs remain poorly understood. Here, we use cryo-EM to investigate the structure and the conformational landscape of the mycobacterial L-GDH composed of 180 kDa subunits (mL-GDH) when incubated with L-glutamate and NAD. Classification of the heterogeneous population of tetramers reveals opening-closing motions and sorting of individual subunits resolves the occupancy of the cofactor and substrate binding pockets. Cryo-EM maps show that ligand binding to the glutamate binding pocket is accompanied by structural changes in a region approximately two nanometers away from the active site, leading to the formation of a previously undetected interaction between the catalytic domains of neighboring subunits in mL-GDH closed tetrameric states. Our findings indicate that the occupancy of the substrate binding site of mL-GDH is linked to a remodeling of both the tertiary and quaternary structure of the enzyme.

PubMed: 41877587
DOI: 10.1002/pro.70544

Experimental method

ELECTRON MICROSCOPY (3.57 Å)