1q5u
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HUMAN DUTP PYROPHOSPHATASE
OverviewOverview
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.
About this StructureAbout this Structure
1Q5U is a Single protein structure of sequence from Homo sapiens. Full crystallographic information is available from OCA.
ReferenceReference
Human dUTP pyrophosphatase: uracil recognition by a beta hairpin and active sites formed by three separate subunits., Mol CD, Harris JM, McIntosh EM, Tainer JA, Structure. 1996 Sep 15;4(9):1077-92. PMID:8805593
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