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PDBsum entry 1kcc
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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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Active-Site architecture of endopolygalacturonase i from stereum purpureum revealed by crystal structures in native and ligand-Bound forms at atomic resolution.
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Authors
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T.Shimizu,
T.Nakatsu,
K.Miyairi,
T.Okuno,
H.Kato.
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Ref.
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Biochemistry, 2002,
41,
6651-6659.
[DOI no: ]
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PubMed id
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Abstract
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Crystal structures of endopolygalacturonase from Stereum purpureum were solved
in native and two galacturonic acid complex states at atomic resolution.
Endopolygalacturonase catalyzes the hydrolysis of alpha-1,4-glycosidic linkage
of polygalacturonate in pectin. The native structure was determined by the
multiple wavelength anomalous dispersion method and was refined anisotropically
with SHELXL-97, with an R factor of 11.4% and an R(free) factor of 14.0% at 0.96
A resolution. The enzyme folds into a right-handed parallel beta-helix with 10
complete turns. The crystal structures of its binary complex with one
D-galacturonate and its ternary complex with two D-galacturonates were also
determined to identify the substrate binding site at 1.0 and 1.15 A resolutions,
respectively. In the binary complex, one beta-D-galactopyranuronate was found in
the +1 subsite, thus proving the strong affinity of the +1 subsite expected from
the bond cleavage frequency on oligogalacturonates. In the ternary complex, an
additional beta-D-galactofuranuronate was found in the -1 subsite. In both
subsites, the recognition of the galacturonate carboxy group is important in
galacturonate binding. In the +1 subsite, the carboxy group interacts with three
basic residues, His195, Arg226, and Lys228, which were conserved in all
endopolygalacturonases. In the -1 subsite, the unique nonprolyl cis-peptide bond
is believed to be involved in binding the carboxy group of the substrate. The
active site architecture of the complexes provides insight into the mechanism of
inverting glycosyl hydrolases and also sheds light on the basis of the
differences between the family 28 and the other inverting glycosyl hydrolases.
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Secondary reference #1
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Title
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Crystallization and preliminary X-Ray study of endopolygalacturonase from the pathogenic fungus stereum purpureum.
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Authors
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T.Shimizu,
T.Nakatsu,
K.Miyairi,
T.Okuno,
H.Kato.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2001,
57,
1171-1173.
[DOI no: ]
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PubMed id
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Figure 2.
Figure 2 Detail from the diffraction pattern of deglycosylated
endopolygalacturonase I with synchrotron radiation at cryogenic
temperature (100 K). The detector edge corresponds to 0.96 Å
resolution.
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The above figure is
reproduced from the cited reference
with permission from the IUCr
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Secondary reference #2
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Title
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Determination of glycosylation sites, Disulfide bridges, And the c-Terminus of stereum purpureum mature endopolygalacturonase i by electrospray ionization mass spectrometry.
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Authors
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T.Shimizu,
K.Miyairi,
T.Okuno.
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Ref.
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Eur J Biochem, 2000,
267,
2380-2389.
[DOI no: ]
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PubMed id
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Figure 6.
Fig. 6. Covalent structure of endoPG I. The deleted
C-terminal sequence is shown in lower case letters. Sugar chain
1, M5 sugar chain; Sugar chain 2, M5 sugar chain and the higher
homologues. Sugar chain 3, M5 sugar chain; Sugar chain 4, M5
sugar chain and the higher homologues. EndoPG Ia, sugar chain 1
+ 2; endoPG Ib, sugar chain 1 + 2 + (3 or 4); and endoPG Ic,
sugar chain 1 + 2 + 3 + 4.
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Figure 7.
Fig. 7. Alignment of endoPG I and otherfungal, plant, and
bacterial endoPGs with emphasis on cysteine residues. Conserved
cysteine residues are indicated by a  .
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The above figures are
reproduced from the cited reference
with permission from the Federation of European Biochemical Societies
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Secondary reference #3
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Title
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Isolation, Characterization, And sugar chain structure of endopg ia, Ib and ic from stereum purpureum.
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Authors
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Y.Hasui,
Y.Fukui,
J.Kikuchi,
N.Kato,
K.Miyairi,
T.Okuno.
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Ref.
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Biosci Biotechnol Biochem, 1998,
62,
852-857.
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PubMed id
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