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PDBsum entry 3jd0
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Oxidoreductase
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PDB id
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3jd0
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References listed in PDB file
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Key reference
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Title
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Using cryo-Em to map small ligands on dynamic metabolic enzymes: studies with glutamate dehydrogenase.
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Authors
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M.J.Borgnia,
S.Banerjee,
A.Merk,
D.Matthies,
A.Bartesaghi,
P.Rao,
J.Pierson,
L.A.Earl,
V.Falconieri,
S.Subramaniam,
J.L.Milne.
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Ref.
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Mol Pharmacol, 2016,
89,
645-651.
[DOI no: ]
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PubMed id
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Abstract
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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.
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