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PDBsum entry 1zmd
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Oxidoreductase
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PDB id
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1zmd
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References listed in PDB file
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Key reference
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Title
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Crystal structure of human dihydrolipoamide dehydrogenase: NAD+/nadh binding and the structural basis of disease-Causing mutations.
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Authors
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C.A.Brautigam,
J.L.Chuang,
D.R.Tomchick,
M.Machius,
D.T.Chuang.
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Ref.
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J Mol Biol, 2005,
350,
543-552.
[DOI no: ]
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PubMed id
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Abstract
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Human dihydrolipoamide dehydrogenase (hE3) is an enzymatic component common to
the mitochondrial alpha-ketoacid dehydrogenase and glycine decarboxylase
complexes. Mutations to this homodimeric flavoprotein cause the often-fatal
human disease known as E3 deficiency. To catalyze the oxidation of
dihydrolipoamide, hE3 uses two molecules: non-covalently bound FAD and a
transiently bound substrate, NAD+. To address the catalytic mechanism of hE3 and
the structural basis for E3 deficiency, the crystal structures of hE3 in the
presence of NAD+ or NADH have been determined at resolutions of 2.5A and 2.1A,
respectively. Although the overall fold of the enzyme is similar to that of
yeast E3, these two structures differ at two loops that protrude from the
proteins and at their FAD-binding sites. The structure of oxidized hE3 with NAD+
bound demonstrates that the nicotinamide moiety is not proximal to the FAD. When
NADH is present, however, the nicotinamide base stacks directly on the
isoalloxazine ring system of the FAD. This is the first time that this
mechanistically requisite conformation of NAD+ or NADH has been observed in E3
from any species. Because E3 structures were previously available only from
unicellular organisms, speculations regarding the molecular mechanisms of E3
deficiency were based on homology models. The current hE3 structures show
directly that the disease-causing mutations occur at three locations in the
human enzyme: the dimer interface, the active site, and the FAD and
NAD(+)-binding sites. The mechanisms by which these mutations impede the
function of hE3 are discussed.
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Figure 1.
Figure 1. The crystal structure of the hE3 homodimer. Shown
is a stereo ribbon diagram of the dimer. The atoms from the FAD
and NADH are shown as spheres. In the left monomer, the domains
are differently colored: the FAD-binding domain is green; the
NAD^+-binding domain, purple; the central domain, blue; the
interface domain, orange. The other monomer is colored tan.
Bound molecules of FAD and NADH are colored brown and cyan,
respectively, for the left monomer, and tan in the right monomer.
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Figure 6.
Figure 6. Residues whose mutation causes E3 deficiency.
Stereo representations of disease-causing mutations that occur
(a) at the homodimer interface, (b) near to the
disulfide-exchange site, or (c) near to the bound FAD or NADH
molecules. The coordinates represented here come from the G
(blue) and H (tan) monomers of hE3-Lip-NADH. Mutation to V188 is
not known to cause disease; it is included to show its proximity
to I358. The section of electron density in (b) is a 2F[o] -F[c]
map contoured at the 1s level. In (b), the N3 atom of FAD is
labeled. Secondary structure is shown semi-transparently to
allow all atoms to be viewed. Atoms and secondary structural
features are colored as in Figure 2 and Figure 3.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2005,
350,
543-552)
copyright 2005.
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