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PDBsum entry 2g7f
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References listed in PDB file
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Key reference
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Title
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The structure of vibrio cholerae extracellular endonuclease i reveals the presence of a buried chloride ion.
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Authors
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B.Altermark,
A.O.Smalås,
N.P.Willassen,
R.Helland.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2006,
62,
1387-1391.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structure of a periplasmic/extracellular endonuclease from Vibrio
cholerae has been solved at low and at neutral pH. Crystals grown at pH 4.6 and
6.9 diffracted to 1.6 A (on BM01A at the ESRF) and 1.95 A (on a rotating-anode
generator), respectively. The structures of the endonuclease were compared with
the structure of a homologous enzyme in V. vulnificus. The structures of the V.
cholerae enzyme at different pH values are essentially identical to each other
and to the V. vulnificus enzyme. However, interesting features were observed in
the solvent structures. Both V. cholerae structures reveal the presence of a
chloride ion completely buried within the core of the protein, with the nearest
solvent molecule approximately 7 A away. Magnesium, which is essential for
catalysis, is present in the structure at neutral pH, but is absent at low pH,
and may partly explain the inactivity of the enzyme at lower pH.
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Figure 2.
Figure 2 (a) Stereo plot illustrating the anomalous difference
map (red) contoured at 4.5  surrounding
the buried chloride (green) in the interior of the protein and
the S atoms (yellow). Magnesium is displayed as an orange
sphere. (b) Stereo plot of the interactions between the chloride
ion (green sphere) and the protein main-chain N atoms of Tyr43,
Cys44, Ile123 and the O^  atom
of Ser41. Two disulfide bridges in the vicinity of the
chloride-binding site are also displayed. This figure was
prepared with PyMOL (DeLano, 2002[DeLano, W. L. (2002). The
PyMOL Molecular Visualization System. http://www.pymol.org .])
and MOLSCRIPT (Kraulis, 1991[Kraulis, P. J. (1991). J. Appl.
Cryst. 24, 946-950.]).
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The above figure is
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2006,
62,
1387-1391)
copyright 2006.
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