3JD4

Glutamate dehydrogenase in complex with NADH and GTP, closed conformation

Summary for 3JD4

• Entry DOI: 10.2210/pdb3jd4/pdb
• Related: 3JCZ 3JD0 3JD1 3JD2 3JD3
• EMDB information: 6630 6631 6632 6633 6634 6635
• Descriptor: Glutamate dehydrogenase 1, mitochondrial, 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE, GUANOSINE-5'-TRIPHOSPHATE (3 entities in total)
• Functional Keywords: glutamate metabolism, mitochondria, oxidoreductase
• Biological source: Bos taurus (bovine)
• Total number of polymer chains: 6
• Total formula weight: 345937.92

Authors

Borgnia, M.J.,Banerjee, S.,Merk, A.,Matthies, D.,Bartesaghi, A.,Rao, P.,Pierson, J.,Earl, L.A.,Falconieri, V.,Subramaniam, S.,Milne, J.L.S. (deposition date: 2016-03-28, release date: 2016-04-27, Last modification date: 2025-06-11)

Primary citation

Borgnia, M.J.,Banerjee, S.,Merk, A.,Matthies, D.,Bartesaghi, A.,Rao, P.,Pierson, J.,Earl, L.A.,Falconieri, V.,Subramaniam, S.,Milne, J.L.
Using Cryo-EM to Map Small Ligands on Dynamic Metabolic Enzymes: Studies with Glutamate Dehydrogenase.
Mol.Pharmacol., 89:645-651, 2016

PubMed Abstract: Cryo-electron microscopy (cryo-EM) methods are now being used to determine structures at near-atomic resolution and have great promise in molecular pharmacology, especially in the context of mapping the binding of small-molecule ligands to protein complexes that display conformational flexibility. We illustrate this here using glutamate dehydrogenase (GDH), a 336-kDa metabolic enzyme that catalyzes the oxidative deamination of glutamate. Dysregulation of GDH leads to a variety of metabolic and neurologic disorders. Here, we report near-atomic resolution cryo-EM structures, at resolutions ranging from 3.2 Å to 3.6 Å for GDH complexes, including complexes for which crystal structures are not available. We show that the binding of the coenzyme NADH alone or in concert with GTP results in a binary mixture in which the enzyme is in either an "open" or "closed" state. Whereas the structure of NADH in the active site is similar between the open and closed states, it is unexpectedly different at the regulatory site. Our studies thus demonstrate that even in instances when there is considerable structural information available from X-ray crystallography, cryo-EM methods can provide useful complementary insights into regulatory mechanisms for dynamic protein complexes.

PubMed: 27036132
DOI: 10.1124/mol.116.103382

Experimental method

ELECTRON MICROSCOPY (3.4 Å)