Using Cryo-EM to Map Small Ligands on Dynamic Metabolic Enzymes: Studies with Glutamate Dehydrogenase.

Journal Article (Journal Article)

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.

Full Text

Duke Authors

Cited Authors

  • Borgnia, MJ; Banerjee, S; Merk, A; Matthies, D; Bartesaghi, A; Rao, P; Pierson, J; Earl, LA; Falconieri, V; Subramaniam, S; Milne, JLS

Published Date

  • June 2016

Published In

Volume / Issue

  • 89 / 6

Start / End Page

  • 645 - 651

PubMed ID

  • 27036132

Pubmed Central ID

  • PMC4885502

Electronic International Standard Serial Number (EISSN)

  • 1521-0111

Digital Object Identifier (DOI)

  • 10.1124/mol.116.103382


  • eng

Conference Location

  • United States