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PDBsum entry 1ee6
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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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The first structure of pectate lyase belonging to polysaccharide lyase family 3.
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Authors
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M.Akita,
A.Suzuki,
T.Kobayashi,
S.Ito,
T.Yamane.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2001,
57,
1786-1792.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structure of a highly alkaline low molecular weight pectate lyase
(Pel-15) was determined at 1.5 A resolution by the multiple isomorphous
replacement (MIR) method. This is the first pectate lyase structure from
polysaccharide lyase family 3. The overall structure is a simple eight-turn
right-handed parallel beta-helix domain with one long loop protruding from one
side of the beta-helix. The low molecular weight of Pel-15 derives from the lack
of N- and C-terminal extensions that are found in many beta-helix proteins.
Although the structure has one calcium ion at pH 6.7, raising the pH to 9.5
results in the binding of an additional calcium ion. The common calcium ion
found in both the pH 6.5 and 9.5 structures seems to stabilize both the
beta-helix structure and the long protruding loop. The additional calcium ion
found in the pH 9.5 structure alone may neutralize the acidic substrate. The
region around the additional calcium ion is thought to bind to the substrate, as
this region is rich in charged amino-acid residues which are required in
catalysis.
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Figure 3.
Figure 3 Stereoview of the Pel-15 unique calcium-binding site
formed by Asp80, Val81, Lys103 and three water molecules. One
calcium-bound water molecule is bound to the O atom of Gly34 on
the first T3. The location of this region is shown in Fig. 1-.
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Figure 5.
Figure 5 Stereoviews of the T3-PB1 groove regions of (a) Pel-15
and (b) Ech-PelC (PDB entry [202]1air ). The location of this
region is shown in Fig. 1[203] [link]-[204][turqarr.gif] .
Amino-acid side chains are represented by stick models. The
calcium ion and amino-acid side chains in the pH 9.5 structure
are represented by a yellow sphere and red sticks, respectively.
The conformations of those amino-acid side chains are changed by
attachment of the calcium ion.
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2001,
57,
1786-1792)
copyright 2001.
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