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PDBsum entry 1q5h
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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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Human dutp pyrophosphatase: uracil recognition by a beta hairpin and active sites formed by three separate subunits.
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Authors
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C.D.Mol,
J.M.Harris,
E.M.Mcintosh,
J.A.Tainer.
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Ref.
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Structure, 1996,
4,
1077-1092.
[DOI no: ]
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PubMed id
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Abstract
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BACKGROUND. The essential enzyme dUTP pyrophosphatase (dUTPase) is exquisitely
specific for dUTP and is critical for the fidelity of DNA replication and
repair. dUTPase hydrolyzes dUTP to dUMP and pyrophosphate, simultaneously
reducing dUTP levels and providing the dUMP for dTTP biosynthesis. A high
cellular dTTP: dUTP ratio is essential to avoid uracil incorporation into DNA,
which would lead to strand breaks and cell death. We report the first detailed
atomic-resolution structure of a eukaryotic dUTPase, human dUTPase, and
complexes with the uracil-containing deoxyribonucleotides, dUMP, dUDP and dUTP.
RESULTS. The crystal structure reveals that each subunit of the dUTPase trimer
folds into an eight-stranded jelly-roll beta barrel, with the C-terminal beta
strands interchanged among the subunits. The structure is similar to that of the
E. coli enzyme, despite low sequence homology between the two enzymes. The
nucleotide complexes reveal a simple and elegant way for a beta hairpin to
recognize specific nucleic acids: uracil is inserted into a distorted
antiparallel beta hairpin and hydrogen bonds entirely to main-chain atoms. This
interaction mimics DNA base pairing, selecting uracil over cytosine and
sterically precluding thymine and ribose binding. Residues from the second
subunit interact with the phosphate groups and a glycine-rich C-terminal tail of
the third subunit caps the substrate-bound active site, causing total
complementary enclosure of substrate. To our knowledge, this is the first
documented instance of all three subunits of a trimeric enzyme supplying
residues that are critical to enzyme function and catalysis. CONCLUSIONS. The
dUTPase nucleotide-binding sites incorporate some features of other
nucleotide-binding proteins and protein kinases, but seem distinct in sequence
and architecture. The novel nucleic acid base recognition motif appears ancient;
higher order structures, such as the ribosome, may have evolved from a motif of
this kind. These uracil-beta-hairpin interactions are an obvious way for
peptides to become early coenzymes in an RNA world, providing a plausible link
to the protein-DNA world. Within the beta hairpin, there is a tyrosine corner
motif that normally specifies beta-arch connections; this tyrosine motif was
apparently recruited to discriminate against ribonucleotides, more recently than
the evolution of the beta hairpin itself.
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Figure 8.
Figure 8. Schematic of dUTPase-substrate interactions
showing the structural basis for the exquisite specificity for
dUTP that requires all three subunits. Hydrogen bonds (<3.4 å )
are shown (dashed lines) with the donor-acceptor atom distance
beneath the protein atom label. Hydrophobic interactions (wavy
lines) are shown only for the key residues Tyr82, which packs
against the deoxyribose, and Phe135, which stacks above the
bound uracil base. Uracil and deoxyribose are primarily
recognized by one subunit (gold rectangles), phosphate groups by
the adjacent subunit (purple rectangles), whereas the bound
substrate is capped by residues from the C-terminal tail of a
third subunit (blue rectangles).
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The above figure is
reprinted
by permission from Cell Press:
Structure
(1996,
4,
1077-1092)
copyright 1996.
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