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PDBsum entry 1deh
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Oxidoreductase
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PDB id
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1deh
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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X-Ray structure of human beta3beta3 alcohol dehydrogenase. The contribution of ionic interactions to coenzyme binding.
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Authors
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G.J.Davis,
W.F.Bosron,
C.L.Stone,
K.Owusu-Dekyi,
T.D.Hurley.
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Ref.
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J Biol Chem, 1996,
271,
17057-17061.
[DOI no: ]
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PubMed id
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Abstract
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The three-dimensional structure of the human beta3beta3 dimeric alcohol
dehydrogenase (beta3) was determined to 2.4-A resolution. beta3 was crystallized
as a ternary complex with the coenzyme NAD+ and the competitive inhibitor
4-iodopyrazole. beta3 is a polymorphic variant at ADH2 that differs from beta1
by a single amino acid substitution of Arg-369 --> Cys. The available x-ray
structures of mammalian alcohol dehydrogenases show that the side chain of
Arg-369 forms an ion pair with the NAD(H) pyrophosphate to stabilize the
E.NAD(H) complex. The Cys-369 side chain of beta3 cannot form this interaction.
The three-dimensional structures of beta3 and beta1 are virtually identical,
with the exception that Cys-369 and two water molecules in beta3 occupy the
position of Arg-369 in beta1. The two waters occupy the same positions as two
guanidino nitrogens of Arg-369. Hence, the number of hydrogen bonding
interactions between the enzyme and NAD(H) are the same for both isoenzymes.
However, beta3 differs from beta1 by the loss of the electrostatic interaction
between the NAD(H) pyrophosphate and the Arg-369 side chain. The equilibrium
dissociation constants of beta3 for NAD+ and NADH are 350-fold and 4000-fold
higher, respectively, than those for beta1. These changes correspond to binding
free energy differences of 3.5 kcal/mol for NAD+ and 4.9 kcal/mol for NADH.
Thus, the Arg-369 --> Cys substitution of beta3 isoenzyme destabilizes the
interaction between coenzyme and beta3 alcohol dehydrogenase.
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Figure 1.
Fig. 1. Electron density in the vicinity of residue 369. Omit
2F[o]  F[c]
electron density maps for (A)  [3] ADH and
(B) [1] ADH.
Waters which occur between the amino acid at position 369 and
coenzyme molecule are also displayed. The electron density maps
were calculated after first removing those atoms displayed in
the figure from the structure factor calculation. The maps are
contoured at 1 S.D. of their respective electron density.
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Figure 2.
Fig. 2. Aligned active sites of human [1] and [3] ADH. A
stereo diagram of human [3] (thick
lines) and [1] (thin
lines) structures in the vicinity of amino acid 369. The
structures were aligned by superposition of all their respective
C  atoms.
R.m.s differences for alignment of [3] to [1] are 0.25
Å for all C atoms.
Alignments of individual subunits or domains yielded r.m.s
values of 0.19 Å for the C atoms
within subunit A, 0.17 Å for the C atoms
within the coenzyme domain, and 0.20 Å for the catalytic
domain of the A subunits; the corresponding values for alignment
of the B subunits are 0.25, 0.19, and 0.24 Å.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(1996,
271,
17057-17061)
copyright 1996.
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Secondary reference #1
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Title
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Structures of three human beta alcohol dehydrogenase variants. Correlations with their functional differences.
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Authors
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T.D.Hurley,
W.F.Bosron,
C.L.Stone,
L.M.Amzel.
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Ref.
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J Mol Biol, 1994,
239,
415-429.
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PubMed id
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