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PDBsum entry 1euw
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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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Atomic resolution structure of escherichia coli dutpase determined ab initio.
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Authors
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A.González,
G.Larsson,
R.Persson,
E.Cedergren-Zeppezauer.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2001,
57,
767-774.
[DOI no: ]
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PubMed id
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Abstract
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Cryocooled crystals of a mercury complex of Escherichia coli dUTPase diffract to
atomic resolution. Data to 1.05 A 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 A 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.
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Figure 4.
Figure 4 Detail of the 1.05 Å structure, showing parts of the
polypeptide chain at the active site, including Tyr93 and one
molecule of glycerol (Glyc139). The 2mF[o] - DF[c]
electron-density map is contoured at 2  (in
blue) and 4 (coral).
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Figure 5.
Figure 5 View of the mercury-binding site in a 2mF[o] - DF[c]
electron-density map contoured at 3 and 10 (in
blue and orange, respectively) showing clearly the multiple
conformations of the Hg atom (red spheres) bound to the S  of
Cys36.
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2001,
57,
767-774)
copyright 2001.
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