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PDBsum entry 1dp0
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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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High resolution refinement of beta-Galactosidase in a new crystal form reveals multiple metal-Binding sites and provides a structural basis for alpha-Complementation.
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Authors
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D.H.Juers,
R.H.Jacobson,
D.Wigley,
X.J.Zhang,
R.E.Huber,
D.E.Tronrud,
B.W.Matthews.
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Ref.
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Protein Sci, 2000,
9,
1685-1699.
[DOI no: ]
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PubMed id
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Abstract
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The unrefined fold of Escherichia coli beta-galactosidase based on a monoclinic
crystal form with four independent tetramers has been reported previously. Here,
we describe a new, orthorhombic form with one tetramer per asymmetric unit that
has permitted refinement of the structure at 1.7 A resolution. This
high-resolution analysis has confirmed the original description of the structure
and revealed new details. An essential magnesium ion, identified at the active
site in the monoclinic crystals, is also seen in the orthorhombic form.
Additional putative magnesium binding sites are also seen. Sodium ions are also
known to affect catalysis, and five putative binding sites have been identified,
one close to the active site. In a crevice on the protein surface, five linked
five-membered solvent rings form a partial clathrate-like structure. Some other
unusual aspects of the structure include seven apparent cis-peptide bonds, four
of which are proline, and several internal salt-bridge networks. Deep
solvent-filled channels and tunnels extend across the surface of the molecule
and pass through the center of the tetramer. Because of these departures from a
compact globular shape, the molecule is not well characterized by prior
empirical relationships between the mass and surface area of proteins. The 50 or
so residues at the amino terminus have a largely extended conformation and
mostly lie across the surface of the protein. At the same time, however, segment
13-21 contributes to a subunit interface, and residues 29-33 pass through a
"tunnel" formed by a domain interface. Taken together, the overall arrangement
provides a structural basis for the phenomenon of alpha-complementation.
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Secondary reference #1
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Title
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Structural comparisons of tim barrel proteins suggest functional and evolutionary relationships between beta-Galactosidase and other glycohydrolases.
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Authors
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D.H.Juers,
R.E.Huber,
B.W.Matthews.
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Ref.
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Protein Sci, 1999,
8,
122-136.
[DOI no: ]
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PubMed id
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Secondary reference #2
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Title
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Three-Dimensional structure of beta-Galactosidase from e. Coli.
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Authors
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R.H.Jacobson,
X.J.Zhang,
R.F.Dubose,
B.W.Matthews.
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Ref.
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Nature, 1994,
369,
761-766.
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PubMed id
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Secondary reference #3
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Title
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Crystallization of beta-Galactosidase from escherichia coli.
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Authors
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R.H.Jacobson,
B.W.Matthews.
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Ref.
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J Mol Biol, 1992,
223,
1177-1182.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1. Diffraction pattern of the monoclinic rystals recorded at CHESS. The inset shows an enlarged view of the
iffraction pattern aboe the beam stop. The cale is arked in millimeters. The blackening of the film to the left of the
beam stop is not due to misalignment but to he very igh intensity of the (0,0,6) reflection. 2'' oscillation photograph;
exposure time 2.5 min; rystal-to-film distance 400 mm; I = 0.908'' 8; film size 8 inches x 10 inches; crystal size
0% mm x 02 mm x @2 mm. The diffraction limit at thtop ad bottom edge of the film is 30 d.
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Figure 3.
Figure 3. Section = 180'' of the locked rotation fuction (Tong & Rossmann, 1990). Resolution 190 to 5.5 8. This
Figure displays the result of the calculation as a stereographic projection. The directions in space are plotted in spherical
polar co-ordinates where the axial tilt of the rotation vector away from the c axis of the crystal co-ordinate ystem ($) is
plotted latitudinaly and the rotation within the a*b* plane (4) longitudinally. The 3 crosses indicate 1 choice f a set f 3
orthogonal axes of Z-fold ymmetry (see the ext). Contours are drawn at increments of 1 with the lowest contour
drawn at 1.3 0 (see legend to Fig. 2).
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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