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PDBsum entry 1dib
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Oxidoreductase,hydrolase
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PDB id
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1dib
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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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Structures of three inhibitor complexes provide insight into the reaction mechanism of the human methylenetetrahydrofolate dehydrogenase/cyclohydrolase.
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Authors
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A.Schmidt,
H.Wu,
R.E.Mackenzie,
V.J.Chen,
J.R.Bewly,
J.E.Ray,
J.E.Toth,
M.Cygler.
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Ref.
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Biochemistry, 2000,
39,
6325-6335.
[DOI no: ]
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PubMed id
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Abstract
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Enzymes involved in tetrahydrofolate metabolism are of particular pharmaceutical
interest, as their function is crucial for amino acid and DNA biosynthesis. The
crystal structure of the human cytosolic methylenetetrahydrofolate
dehydrogenase/cyclohydrolase (DC301) domain of a trifunctional enzyme has been
determined previously with a bound NADP cofactor. While the substrate binding
site was identified to be localized in a deep and rather hydrophobic cleft at
the interface between two protein domains, the unambiguous assignment of
catalytic residues was not possible. We succeeded in determining the crystal
structures of three ternary DC301/NADP/inhibitor complexes. Investigation of
these structures followed by site-directed mutagenesis studies allowed
identification of the amino acids involved in catalysis by both enzyme
activities. The inhibitors bind close to Lys56 and Tyr52, residues of a strictly
conserved motif for active sites in dehydrogenases. While Lys56 is in a good
position for chemical interaction with the substrate analogue, Tyr52 was found
stacking against the inhibitors' aromatic rings and hence seems to be more
important for proper positioning of the ligand than for catalysis. Also, Ser49
and/or Cys147 were found to possibly act as an activator for water in the
cyclohydrolase step. These and the other residues (Gln100 and Asp125), with
which contacts are made, are strictly conserved in THF dehydrogenases. On the
basis of structural and mutagenesis data, we propose a reaction mechanism for
both activities, the dehydrogenase and the cyclohydrolase.
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Secondary reference #1
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Title
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The 3-D structure of a folate-Dependent dehydrogenase/cyclohydrolase bifunctional enzyme at 1.5 a resolution.
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Authors
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M.Allaire,
Y.Li,
R.E.Mackenzie,
M.Cygler.
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Ref.
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Structure, 1998,
6,
173-182.
[DOI no: ]
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PubMed id
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Figure 8.
Figure 8. Hydrogen-bonding network near the YXXXK motif.
The trace of residues 46-56 is shown as thick lines. Residues
99-103, as well as the sidechain of residues 49, 52 and 56 are
shown in ball-and-stick representation. The water molecule is
labeled with the letter W. Hydrogen bonds are shown in dashed
lines.
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The above figure is
reproduced from the cited reference
with permission from Cell Press
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