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Atomic resolution structure of Escherichia coli dUTPase determined ab initio

González, A; Larsson, G; Persson, R and Cedergren, Eila LU (2001) In Acta Crystallographica. Section D: Biological Crystallography 57(Part 6). p.767-774
Abstract
Cryocooled crystals of a mercury complex of Escherichia coli dUTPase diffract to atomic resolution. Data to 1.05 Å resolution were collected from a derivative crystal and the structure model was derived from a Fourier map with phases calculated from the coordinates of the Hg atom (one site per subunit of the trimeric enzyme) using the program ARP/wARP. After refinement with anisotropic temperature factors a highly accurate model of the bacterial dUTPase was obtained. Data to 1.45 Å from a native crystal were also collected and the 100 K structures were compared. Inspection of the refined models reveals that a large part of the dUTPase remains rather mobile upon freezing, with 14% of the main chain being totally disordered and with numerous... (More)
Cryocooled crystals of a mercury complex of Escherichia coli dUTPase diffract to atomic resolution. Data to 1.05 Å resolution were collected from a derivative crystal and the structure model was derived from a Fourier map with phases calculated from the coordinates of the Hg atom (one site per subunit of the trimeric enzyme) using the program ARP/wARP. After refinement with anisotropic temperature factors a highly accurate model of the bacterial dUTPase was obtained. Data to 1.45 Å from a native crystal were also collected and the 100 K structures were compared. Inspection of the refined models reveals that a large part of the dUTPase remains rather mobile upon freezing, with 14% of the main chain being totally disordered and with numerous side chains containing disordered atoms in multiple discrete conformations. A large number of those residues surround the active-site cavity. Two glycerol molecules (the cryosolvent) occupy the deoxyribose-binding site. Comparison between the native enzyme and the mercury complex shows that the active site is not adversely affected by the binding of mercury. An unexpected effect seems to be a stabilization of the crystal lattice by means of long-range interactions, making derivatization a potentially useful tool for further studies of inhibitor-substrate-analogue complexes of this protein at very high resolution. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
dUTPase.
in
Acta Crystallographica. Section D: Biological Crystallography
volume
57
issue
Part 6
pages
767 - 774
publisher
John Wiley and Sons Inc.
external identifiers
  • scopus:0034979897
ISSN
1399-0047
DOI
10.1107/S0907444901004255
language
English
LU publication?
yes
id
6073dd0d-dc5f-48fb-bcfa-6bcedcbed5cb (old id 124978)
date added to LUP
2007-07-04 17:13:53
date last changed
2018-05-29 10:06:01
@article{6073dd0d-dc5f-48fb-bcfa-6bcedcbed5cb,
  abstract     = {Cryocooled crystals of a mercury complex of Escherichia coli dUTPase diffract to atomic resolution. Data to 1.05 Å resolution were collected from a derivative crystal and the structure model was derived from a Fourier map with phases calculated from the coordinates of the Hg atom (one site per subunit of the trimeric enzyme) using the program ARP/wARP. After refinement with anisotropic temperature factors a highly accurate model of the bacterial dUTPase was obtained. Data to 1.45 Å from a native crystal were also collected and the 100 K structures were compared. Inspection of the refined models reveals that a large part of the dUTPase remains rather mobile upon freezing, with 14% of the main chain being totally disordered and with numerous side chains containing disordered atoms in multiple discrete conformations. A large number of those residues surround the active-site cavity. Two glycerol molecules (the cryosolvent) occupy the deoxyribose-binding site. Comparison between the native enzyme and the mercury complex shows that the active site is not adversely affected by the binding of mercury. An unexpected effect seems to be a stabilization of the crystal lattice by means of long-range interactions, making derivatization a potentially useful tool for further studies of inhibitor-substrate-analogue complexes of this protein at very high resolution.},
  author       = {González, A and Larsson, G and Persson, R and Cedergren, Eila},
  issn         = {1399-0047},
  keyword      = {dUTPase.},
  language     = {eng},
  number       = {Part 6},
  pages        = {767--774},
  publisher    = {John Wiley and Sons Inc.},
  series       = {Acta Crystallographica. Section D: Biological Crystallography},
  title        = {Atomic resolution structure of Escherichia coli dUTPase determined ab initio},
  url          = {http://dx.doi.org/10.1107/S0907444901004255},
  volume       = {57},
  year         = {2001},
}