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PDBsum entry 1jfh
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* Residue conservation analysis
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Enzyme class:
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E.C.3.2.1.1
- alpha-amylase.
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Reaction:
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Endohydrolysis of 1,4-alpha-glucosidic linkages in oligosaccharides and polysaccharides.
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DOI no:
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Protein Sci
6:2285-2296
(1997)
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PubMed id:
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Structure of a pancreatic alpha-amylase bound to a substrate analogue at 2.03 A resolution.
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M.Qian,
S.Spinelli,
H.Driguez,
F.Payan.
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ABSTRACT
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The structure of pig pancreatic alpha-amylase in complex with carbohydrate
inhibitor and proteinaceous inhibitors is known but the successive events
occurring at the catalytic center still remain to be elucidated. The X-ray
structure analysis of a crystal of pig pancreatic alpha-amylase (PPA, EC
3.2.1.1.) soaked with an enzyme-resistant substrate analogue, methyl
4,4'-dithio-alpha-maltotrioside, showed electron density corresponding to the
binding of substrate analogue molecules at the active site and at the "second
binding site." The electron density observed at the active site was interpreted
in terms of overlapping networks of oligosaccharides, which show binding of
substrate analogue molecules at subsites prior to and subsequent to the cleavage
site. A weaker patch of density observed at subsite -1 (using a nomenclature
where the site of hydrolysis is taken to be between subsites -1 and +1) was
modeled with water molecules. Conformational changes take place upon substrate
analogue binding and the "flexible loop" that constitutes the surface edge of
the active site is observed in a specific conformation. This confirms that this
loop plays an important role in the recognition and binding of the ligand. The
crystal structure was refined at 2.03 A resolution, to an R-factor of 16.0
(Rfree, 18.5).
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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S.B.Larson,
J.S.Day,
and
A.McPherson
(2010).
X-ray crystallographic analyses of pig pancreatic alpha-amylase with limit dextrin, oligosaccharide, and alpha-cyclodextrin.
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Biochemistry,
49,
3101-3115.
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PDB codes:
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C.Ragunath,
S.G.Manuel,
V.Venkataraman,
H.B.Sait,
C.Kasinathan,
and
N.Ramasubbu
(2008).
Probing the role of aromatic residues at the secondary saccharide-binding sites of human salivary alpha-amylase in substrate hydrolysis and bacterial binding.
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J Mol Biol,
384,
1232-1248.
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W.C.Obiro,
T.Zhang,
and
B.Jiang
(2008).
The nutraceutical role of the Phaseolus vulgaris alpha-amylase inhibitor.
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Br J Nutr,
100,
1.
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J.R.Rich,
W.W.Wakarchuk,
and
D.R.Bundle
(2006).
Chemical and chemoenzymatic synthesis of S-linked ganglioside analogues and their protein conjugates for use as immunogens.
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Chemistry,
12,
845-858.
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S.Jacques,
J.R.Rich,
C.C.Ling,
and
D.R.Bundle
(2006).
Chemoenzymatic synthesis of GM3 and GM2 gangliosides containing a truncated ceramide functionalized for glycoconjugate synthesis and solid phase applications.
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Org Biomol Chem,
4,
142-154.
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H.Baumann,
S.Ohrman,
Y.Shinohara,
O.Ersoy,
D.Choudhury,
A.Axén,
U.Tedebark,
and
E.Carredano
(2003).
Rational design, synthesis, and verification of affinity ligands to a protein surface cleft.
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Protein Sci,
12,
784-793.
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M.Westerfors,
U.Tedebark,
H.O.Andersson,
S.Ohrman,
D.Choudhury,
O.Ersoy,
Y.Shinohara,
A.Axén,
E.Carredano,
and
H.Baumann
(2003).
Structure-based discovery of a new affinity ligand to pancreatic alpha-amylase.
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J Mol Recognit,
16,
396-405.
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V.König,
L.Vértesy,
and
T.R.Schneider
(2003).
Structure of the alpha-amylase inhibitor tendamistat at 0.93 A.
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Acta Crystallogr D Biol Crystallogr,
59,
1737-1743.
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PDB code:
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G.Gyémánt,
G.Hovánszki,
and
L.Kandra
(2002).
Subsite mapping of the binding region of alpha-amylases with a computer program.
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Eur J Biochem,
269,
5157-5162.
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T.R.Schneider
(2002).
A genetic algorithm for the identification of conformationally invariant regions in protein molecules.
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Acta Crystallogr D Biol Crystallogr,
58,
195-208.
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A.P.Demchenko
(2001).
Recognition between flexible protein molecules: induced and assisted folding.
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J Mol Recognit,
14,
42-61.
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R.Koukiekolo,
V.Desseaux,
Y.Moreau,
G.Marchis-Mouren,
and
M.Santimone
(2001).
Mechanism of porcine pancreatic alpha-amylase. Inhibition of amylose and maltopentaose hydrolysis by alpha-, beta- and gamma-cyclodextrins.
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Eur J Biochem,
268,
841-848.
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E.H.Rydberg,
G.Sidhu,
H.C.Vo,
J.Hewitt,
H.C.Côte,
Y.Wang,
S.Numao,
R.T.MacGillivray,
C.M.Overall,
G.D.Brayer,
and
S.G.Withers
(1999).
Cloning, mutagenesis, and structural analysis of human pancreatic alpha-amylase expressed in Pichia pastoris.
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Protein Sci,
8,
635-643.
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PDB code:
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R.Koukiekolo,
V.Le Berre-Anton,
V.Desseaux,
Y.Moreau,
P.Rougé,
G.Marchis-Mouren,
and
M.Santimone
(1999).
Mechanism of porcine pancreatic alpha-amylase inhibition of amylose and maltopentaose hydrolysis by kidney bean (Phaseolus vulgaris) inhibitor and comparison with that by acarbose.
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Eur J Biochem,
265,
20-26.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
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Links
