Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Tertiary and quaternary structure remodeling by occupancy of the substrate binding pocket in a large glutamate dehydrogenase.
Journal, issue, pages	Protein Sci, Vol. 35, Issue 4, Page e70544, Year 2026
Publish date	Mar 25, 2026
Authors	Melisa Lázaro / Nicolás Chamorro / Jorge P López-Alonso / Diego Charro / Rodolfo M Rasia / Gonzalo Jiménez-Osés / Mikel Valle / María-Natalia Lisa /
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 ...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.
External links	Protein Sci / PubMed:41877587
Methods	EM (single particle)
Resolution	2.63 - 4.1 Å
Structure data	52419 9hux EMDB-52419: CryoEM map of the large glutamate dehydrogenase composed of 180 kDa subunits from Mycobacterium smegmatis obtained in the presence of NAD+ and L-glutamate. Open Tetramer PDB-9hux: CryoEM map of the large glutamate dehydrogenase composed of 180 kDa subunits from Mycobacterium smegmatis obtained in the presence of NAD+ and L-glutamate. Open Tetramer. Method: EM (single particle) / Resolution: 3.88 Å 52420 9huy EMDB-52420, PDB-9huy: CryoEM map of the large glutamate dehydrogenase composed of 180 kDa subunits from Mycobacterium smegmatis obtained in the presence of NAD+ and L-glutamate. Closed1 tetramer. Method: EM (single particle) / Resolution: 3.54 Å 52421 9huz EMDB-52421, PDB-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 Method: EM (single particle) / Resolution: 3.57 Å 52422 9hv0 EMDB-52422, PDB-9hv0: CryoEM map of the large glutamate dehydrogenase composed of 180 kDa subunits from Mycobacterium smegmatis obtained in the presence of NAD+ and L-glutamate. Empty monomer. Method: EM (single particle) / Resolution: 3.07 Å 52423 9hv4 EMDB-52423, PDB-9hv4: CryoEM map of the large glutamate dehydrogenase composed of 180 kDa subunits from Mycobacterium smegmatis obtained in the presence of NAD+ and L-glutamate. cofactor-monomer. Method: EM (single particle) / Resolution: 2.95 Å 52424 9hv5 EMDB-52424, PDB-9hv5: CryoEM map of the large glutamate dehydrogenase composed of 180 kDa subunits from Mycobacterium smegmatis obtained in the presence of NAD+ and L-glutamate. Cofactor/ligand-monomer Method: EM (single particle) / Resolution: 3.12 Å EMDB-52425: CryoEM map of the large glutamate dehydrogenase composed of 180 kDa subunits from Mycobacterium smegmatis obtained in the presence of NAD+ and L-glutamate. cofactor/ligand-monomer in Open tetramer. Method: EM (single particle) / Resolution: 3.23 Å EMDB-52426: CryoEM map of the large glutamate dehydrogenase composed of 180 kDa subunits from Mycobacterium smegmatis obtained in the presence of NAD+ and L-glutamate. cofactor/ligand-monomer in Closed1 tetramer. Method: EM (single particle) / Resolution: 3.11 Å EMDB-52427: CryoEM map of the large glutamate dehydrogenase composed of 180 kDa subunits from Mycobacterium smegmatis obtained in the presence of NAD+ and L-glutamate. cofactor/ligand-monomer in Closed2 tetramer. Method: EM (single particle) / Resolution: 3.18 Å 52428 9hv6 EMDB-52428, PDB-9hv6: CryoEM map of the large glutamate dehydrogenase composed of 180 kDa subunits from Mycobacterium smegmatis obtained in the presence of NAD+ and L-glutamate. Total-monomer Method: EM (single particle) / Resolution: 2.63 Å EMDB-52429: 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 with cofactor/ligand-monomer. Method: EM (single particle) / Resolution: 4.1 Å
Chemicals	ChemComp-NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NADYM ChemComp-GLU*: GLUTAMIC ACID
Source	mycolicibacterium smegmatis (bacteria)
Keywords	OXIDOREDUCTASE / Large glutamate dehydrogenase / Tetramer