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2016 ; 89
(6
): 645-51
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Using Cryo-EM to Map Small Ligands on Dynamic Metabolic Enzymes: Studies with
Glutamate Dehydrogenase
#MMPMID27036132
Borgnia MJ
; Banerjee S
; Merk A
; Matthies D
; Bartesaghi A
; Rao P
; Pierson J
; Earl LA
; Falconieri V
; Subramaniam S
; Milne JL
Mol Pharmacol
2016[Jun]; 89
(6
): 645-51
PMID27036132
show ga
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.