PDBsum entry 1q5h

Hydrolase

PDB id: 1q5h

Contents

Protein chains

127 a.a. *

136 a.a. *

Ligands

DUD ×3

Metals

_MG

Waters ×238

* Residue conservation analysis

PDB id:

1q5h

Name:

Hydrolase

Title:

Human dutp pyrophosphatase complex with dudp

Structure:

Dutp pyrophosphatase. Chain: a, b, c. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Trimer (from PQS)

Resolution:

2.00Å R-factor: 0.179 R-free: 0.214

Authors:

C.D.Mol,J.M.Harris,E.M.Mcintosh,J.A.Tainer

Key ref:

C.D.Mol et al. (1996). Human dUTP pyrophosphatase: uracil recognition by a beta hairpin and active sites formed by three separate subunits. Structure, 4, 1077-1092. PubMed id: 8805593 DOI: 10.1016/S0969-2126(96)00114-1

Date:

07-Aug-03 Release date: 19-Aug-03

Protein chain

P33316  (DUT_HUMAN) -  Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial from Homo sapiens

Seq: 252 a.a.

Struc: 127 a.a.

Protein chains

P33316  (DUT_HUMAN) -  Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial from Homo sapiens

Seq: 252 a.a.

Struc: 136 a.a.

Enzyme reactions

• Enzyme class: Chains A, B, C: E.C.3.6.1.23 - dUTP diphosphatase.
• Reaction: dUTP + H2O = dUMP + diphosphate + H⁺

dUTP (Bound ligand (Het Group name = DUD) matches with 85.71% similarity) + H2O = dUMP + diphosphate + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/S0969-2126(96)00114-1

Structure 4:1077-1092 (1996)

PubMed id: 8805593

Human dUTP pyrophosphatase: uracil recognition by a beta hairpin and active sites formed by three separate subunits.

C.D.Mol, J.M.Harris, E.M.McIntosh, J.A.Tainer.

ABSTRACT

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.

Selected figure(s)

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).

The above figure is reprinted by permission from Cell Press: Structure (1996, 4, 1077-1092) copyright 1996.

Figure was selected by an automated process.