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The Refined Structure of dUTPase from Escherichia coli

Dauter, Z; Wilson, K S; Larsson, G; Nyman, Per-Olof LU and Cedergren-Zeppezauer, E S (1998) In Acta Crystallographica. Section D: Biological Crystallography D54(5). p.735-749
Abstract
Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase, E.C. 3.6.1.23) catalyzes the hydrolysis of dUTP to dUMP and pyrophosphate and is involved in nucleotide metabolism and DNA synthesis. A crystal of the recombinant E. coli enzyme, precipitated from polyethylene glycol mixtures in the presence of succinate at pH 4.2, was used to collect synchrotron diffraction data to 1.9 Å resolution, in space group R3, a = b = 86.62, c = 62.23 Å. Mercury and platinum derivative data were collected at wavelengths to optimize the anomalous contribution. The resulting 2.2 Å MIRAS phases differed from the final set by 40° on average and produced an excellent map which was easy to interpret. The model contains 132 water molecules and refined to an R... (More)
Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase, E.C. 3.6.1.23) catalyzes the hydrolysis of dUTP to dUMP and pyrophosphate and is involved in nucleotide metabolism and DNA synthesis. A crystal of the recombinant E. coli enzyme, precipitated from polyethylene glycol mixtures in the presence of succinate at pH 4.2, was used to collect synchrotron diffraction data to 1.9 Å resolution, in space group R3, a = b = 86.62, c = 62.23 Å. Mercury and platinum derivative data were collected at wavelengths to optimize the anomalous contribution. The resulting 2.2 Å MIRAS phases differed from the final set by 40° on average and produced an excellent map which was easy to interpret. The model contains 132 water molecules and refined to an R value of 13.7%. 136 residues have clear electron density out of 152 expected from the gene sequence. The 16 C-terminal residues are presumably disordered in the crystal lattice. The monomer is a `jelly-roll' type, containing mostly -sheet and only one short helix. The molecule is a tight trimer. A long C-terminal arm extends from one subunit and encompasses the next one within the trimer contributing to its -sheet. Conserved sequence motifs common among dUTPases, previously suggested to compose the active site and confirmed in a recent study of the dUDP complex, are located at subunit-subunit interfaces along the threefold axis, in parts of the -sheet and in loop regions. A similar molecular architecture has recently been found in two other trimeric dUTPases. (Less)
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publication status
published
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in
Acta Crystallographica. Section D: Biological Crystallography
volume
D54
issue
5
pages
735 - 749
publisher
International Union of Crystallography
external identifiers
  • scopus:0032167573
ISSN
1399-0047
DOI
10.1107/S0907444997016223
language
English
LU publication?
yes
id
9b304292-f41f-4b6c-98eb-ed7a915007f4 (old id 125499)
date added to LUP
2007-07-04 16:04:17
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2017-01-01 06:59:26
@article{9b304292-f41f-4b6c-98eb-ed7a915007f4,
  abstract     = {Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase, E.C. 3.6.1.23) catalyzes the hydrolysis of dUTP to dUMP and pyrophosphate and is involved in nucleotide metabolism and DNA synthesis. A crystal of the recombinant E. coli enzyme, precipitated from polyethylene glycol mixtures in the presence of succinate at pH 4.2, was used to collect synchrotron diffraction data to 1.9 Å resolution, in space group R3, a = b = 86.62, c = 62.23 Å. Mercury and platinum derivative data were collected at wavelengths to optimize the anomalous contribution. The resulting 2.2 Å MIRAS phases differed from the final set by 40° on average and produced an excellent map which was easy to interpret. The model contains 132 water molecules and refined to an R value of 13.7%. 136 residues have clear electron density out of 152 expected from the gene sequence. The 16 C-terminal residues are presumably disordered in the crystal lattice. The monomer is a `jelly-roll' type, containing mostly -sheet and only one short helix. The molecule is a tight trimer. A long C-terminal arm extends from one subunit and encompasses the next one within the trimer contributing to its -sheet. Conserved sequence motifs common among dUTPases, previously suggested to compose the active site and confirmed in a recent study of the dUDP complex, are located at subunit-subunit interfaces along the threefold axis, in parts of the -sheet and in loop regions. A similar molecular architecture has recently been found in two other trimeric dUTPases.},
  author       = {Dauter, Z and Wilson, K S and Larsson, G and Nyman, Per-Olof and Cedergren-Zeppezauer, E S},
  issn         = {1399-0047},
  language     = {eng},
  number       = {5},
  pages        = {735--749},
  publisher    = {International Union of Crystallography},
  series       = {Acta Crystallographica. Section D: Biological Crystallography},
  title        = {The Refined Structure of dUTPase from Escherichia coli},
  url          = {http://dx.doi.org/10.1107/S0907444997016223},
  volume       = {D54},
  year         = {1998},
}