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PDBsum entry 1ebf
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Oxidoreductase
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PDB id
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1ebf
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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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Crystal structures of homoserine dehydrogenase suggest a novel catalytic mechanism for oxidoreductases.
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Authors
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B.Delabarre,
P.R.Thompson,
G.D.Wright,
A.M.Berghuis.
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Ref.
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Nat Struct Biol, 2000,
7,
238-244.
[DOI no: ]
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PubMed id
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Abstract
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The structure of the antifungal drug target homoserine dehydrogenase (HSD) was
determined from Saccharomyces cerevisiae in apo and holo forms, and as a ternary
complex with bound products, by X-ray diffraction. The three forms show that the
enzyme is a dimer, with each monomer composed of three regions, the
nucleotide-binding region, the dimerization region and the catalytic region. The
dimerization and catalytic regions have novel folds, whereas the fold of the
nucleotide-binding region is a variation on the Rossmann fold. The novel folds
impose a novel composition and arrangement of active site residues when compared
to all other currently known oxidoreductases. This observation, in conjunction
with site-directed mutagenesis of active site residues and steady-state kinetic
measurements, suggest that HSD exhibits a new variation on dehydrogenase
chemistry.
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Figure 1.
Figure 1. Electron density maps for the two crystal forms of
HSD. a, Stereo view of a 2F[o]- F[c] electron density map
calculated with coefficients from the final tetragonal crystal
form model and contoured at 1  .
The portion of the molecule shown here is the dimer interfacial
region of the extended  -sheet
and is composed of residues 320 -335 from monomer A, and
residues 332 -335 and 319 -325 from monomer B. b, Stereo view of
the F[o]- F[c] simulated annealing omit map for the NAD^+
molecule in the tetragonal crystal form, contoured at 2 .
c, Stereo view of the F[o]- F[c] simulated annealing omit map
for the NADA and l-Hse molecules in the monoclinic crystal form,
contoured at 2 .
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Figure 5.
Figure 5. Proposed reaction mechanisms of hydride transfer for
HSD. a, Probable reaction mechanism for the forward direction
with the substrate in the aldehyde form. Asp 214, Glu 208 and
Wat460 serve to bind the substrate, whereas Lys 223, oriented by
Asp 219, donates a proton to the C4 oxygen of l-ASA. The
cofactor NADH delivers its pro-S hydride to the C4 carbon of
l-ASA. Arrows indicate electron flow. b, Alternative reaction
mechanism for the forward direction with the substrate in the
gem-diol form. The main difference from the reaction proposed
for the aldehyde form is that Lys 223 donates a proton to the
hydroxyl group, which departs as a water molecule, and Asp 219
hydrogen bonds to the hydroxyl group, which remains in the
product alcohol.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Biol
(2000,
7,
238-244)
copyright 2000.
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Secondary reference #1
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Title
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Crystallization and preliminary X-Ray diffraction studies of homoserine dehydrogenase from saccharomyces cerevisiae.
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Authors
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B.Delabarre,
S.L.Jacques,
C.E.Pratt,
D.A.Ruth,
G.D.Wright,
A.M.Berghuis.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 1998,
54,
413-415.
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PubMed id
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