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PDBsum entry 1ud3
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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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Crystal structure of calcium-Free alpha-Amylase from bacillus sp. Strain ksm-K38 (amyk38) and its sodium ion binding sites.
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Authors
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T.Nonaka,
M.Fujihashi,
A.Kita,
H.Hagihara,
K.Ozaki,
S.Ito,
K.Miki.
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Ref.
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J Biol Chem, 2003,
278,
24818-24824.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structure of a calcium-free alpha-amylase (AmyK38) from Bacillus sp.
strain KSM-K38, which resists chelating reagents and chemical oxidants, has been
determined by the molecular replacement method and refined to a crystallographic
R-factor of 19.9% (R-free of 23.2%) at 2.13-A resolution. The main chain folding
of AmyK38 is almost homologous to that of Bacillus licheniformis alpha-amylase.
However, neither a highly conserved calcium ion, which is located at the
interface between domains A and B, nor any other calcium ions appear to exist in
the AmyK38 molecule, although three sodium ions were found, one of which is
located at the position corresponding to that of a highly conserved calcium ion
of other alpha-amylases. The existence of these sodium ions was
crystallographically confirmed by the structures of three metal-exchanged and
mutated enzymes. This is the first case in which the structure of the
calcium-free alpha-amylase has been determined by crystallography, and it was
suggested that these sodium ions, instead of calcium ions, are used to retain
the structure and function of AmyK38.
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Figure 2.
FIG. 2. Stereo view of the ribbon model of the overall
structure of AmyK38. Three domains (A, B, and C) are shown in
red, blue, and green, respectively. Three sodium ions, Na I, Na
II, and Na III, are shown as yellow spheres. The N and C termini
of AmyK38 are in the domains A and C, respectively. Domain A is
the most well conserved (  /  )[8]-barrel domain in
-amylases. Domain C,
which is composed of -strands with the
socalled Greek key motif, is also conserved in amylolytic
enzymes, except in barley -amylase. Na I and Na
II are located at the sites corresponding to the Ca^2^+ ions (Ca
I and Ca III) in the BLA structure. These figures were drawn by
MOLSCRIPT and Raster3D (34, 35).
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Figure 3.
FIG. 3. Stereo views of three sodium ions binding sites of
AmyK38 and BLA (Protein Data Bank accession code 1bli [PDB]
(1)). Pentagonal and quadrilateral bipyramidal cages surrounding
metal ions are drawn by solid or broken lines. Sodium and
calcium ions are drawn as yellow and sky-blue spheres,
respectively. These figures were drawn by MOLSCRIPT, Raster3D,
and Conscript (34-36). In a, the  [A] weighted omit map
(lightblue; contoured at 4.0 ) is shown, and refined
models of the Na I site of wild-type AmyK38 are shown in the
upper section. The model in the lower section is the
calcium-sodium-calcium triad containing the Ca I site of BLA
corresponding to the Na I site of AmyK38. In b, the [A]
weighted omit map (light blue; contoured at 4.0 ) is
shown, and refined models of the Na II site of wild-type AmyK38
are shown in the upper section. The model in the lower section
is the Ca III site of BLA corresponding to the Na II site of
AmyK38. In c, the [A] weighted omit map
(light blue; contoured at 4.0 ) is shown, and the
refined model of the Na III site of wild-type AmyK38 is shown in
the upper section. The model in the lower section is the site of
BLA corresponding to the Na III site of AmyK38. d, the
superimposition of the refined structure of N289H AmyK38 on BLA
around the corresponding site of the Na III site in wild-type
AmyK38. The model of BLA is drawn transparently.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2003,
278,
24818-24824)
copyright 2003.
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