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PDBsum entry 1kxh
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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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Biochemistry
41:4273-4280
(2002)
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PubMed id:
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Crystallographic evidence of a transglycosylation reaction: ternary complexes of a psychrophilic alpha-amylase.
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N.Aghajari,
M.Roth,
R.Haser.
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ABSTRACT
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The psychrophilic Pseudoalteromonas haloplanctis alpha-amylase is shown to form
ternary complexes with two alpha-amylase inhibitors present in the active site
region, namely, a molecule of Tris and a trisaccharide inhibitor or
heptasaccharide inhibitor, respectively. The crystal structures of these
complexes have been determined by X-ray crystallography to 1.80 and 1.74 A
resolution, respectively. In both cases, the prebound inhibitor Tris is expelled
from the active site by the incoming oligosaccharide inhibitor substrate
analogue, but stays linked to it, forming well-defined ternary complexes with
the enzyme. These results illustrate competition in the crystalline state
between two inhibitors, an oligosaccharide substrate analogue and a Tris
molecule, bound at the same time in the active site region. Taken together,
these structures show that the enzyme performs transglycosylation in the complex
with the pseudotetrasaccharide acarbose (confirmed by a mutant structure),
leading to a well-defined heptasaccharide, considered as a more potent
inhibitor. Furthermore, the substrate-induced ordering of water molecules within
a channel highlights a possible pathway used for hydrolysis of starch and
related poly- and oligosaccharides.
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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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L.C.Tsai,
C.H.Hsiao,
W.Y.Liu,
L.M.Yin,
and
L.F.Shyur
(2011).
Structural basis for the inhibition of 1,3-1,4-β-d-glucanase by noncompetitive calcium ion and competitive Tris inhibitors.
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Biochem Biophys Res Commun,
407,
593-598.
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K.Yamamoto,
H.Miyake,
M.Kusunoki,
and
S.Osaki
(2010).
Crystal structures of isomaltase from Saccharomyces cerevisiae and in complex with its competitive inhibitor maltose.
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FEBS J,
277,
4205-4214.
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PDB codes:
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B.Khemakhem,
M.B.Ali,
N.Aghajari,
M.Juy,
R.Haser,
and
S.Bejar
(2009).
Engineering of the alpha-amylase from Geobacillus stearothermophilus US100 for detergent incorporation.
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Biotechnol Bioeng,
102,
380-389.
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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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J.Y.Damián-Almazo,
A.Moreno,
A.López-Munguía,
X.Soberón,
F.González-Muñoz,
and
G.Saab-Rincón
(2008).
Enhancement of the alcoholytic activity of alpha-amylase AmyA from Thermotoga maritima MSB8 (DSM 3109) by site-directed mutagenesis.
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Appl Environ Microbiol,
74,
5168-5177.
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N.Nagano,
T.Noguchi,
and
Y.Akiyama
(2007).
Systematic comparison of catalytic mechanisms of hydrolysis and transfer reactions classified in the EzCatDB database.
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Proteins,
66,
147-159.
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G.J.Davies,
A.M.Brzozowski,
Z.Dauter,
M.D.Rasmussen,
T.V.Borchert,
and
K.S.Wilson
(2005).
Structure of a Bacillus halmapalus family 13 alpha-amylase, BHA, in complex with an acarbose-derived nonasaccharide at 2.1 A resolution.
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Acta Crystallogr D Biol Crystallogr,
61,
190-193.
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PDB code:
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X.Robert,
R.Haser,
H.Mori,
B.Svensson,
and
N.Aghajari
(2005).
Oligosaccharide binding to barley alpha-amylase 1.
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J Biol Chem,
280,
32968-32978.
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PDB codes:
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A.Hoyoux,
V.Blaise,
T.Collins,
S.D'Amico,
E.Gratia,
A.L.Huston,
J.C.Marx,
G.Sonan,
Y.Zeng,
G.Feller,
and
C.Gerday
(2004).
Extreme catalysts from low-temperature environments.
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J Biosci Bioeng,
98,
317-330.
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N.Ramasubbu,
C.Ragunath,
P.J.Mishra,
L.M.Thomas,
G.Gyémánt,
and
L.Kandra
(2004).
Human salivary alpha-amylase Trp58 situated at subsite -2 is critical for enzyme activity.
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Eur J Biochem,
271,
2517-2529.
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PDB codes:
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S.B.Gabelli,
M.A.Bianchet,
H.F.Azurmendi,
Z.Xia,
V.Sarawat,
A.S.Mildvan,
and
L.M.Amzel
(2004).
Structure and mechanism of GDP-mannose glycosyl hydrolase, a Nudix enzyme that cleaves at carbon instead of phosphorus.
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Structure,
12,
927-935.
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PDB code:
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A.Linden,
O.Mayans,
W.Meyer-Klaucke,
G.Antranikian,
and
M.Wilmanns
(2003).
Differential regulation of a hyperthermophilic alpha-amylase with a novel (Ca,Zn) two-metal center by zinc.
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J Biol Chem,
278,
9875-9884.
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PDB codes:
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H.Leemhuis,
B.W.Dijkstra,
and
L.Dijkhuizen
(2003).
Thermoanaerobacterium thermosulfurigenes cyclodextrin glycosyltransferase.
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Eur J Biochem,
270,
155-162.
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M.Kagawa,
Z.Fujimoto,
M.Momma,
K.Takase,
and
H.Mizuno
(2003).
Crystal structure of Bacillus subtilis alpha-amylase in complex with acarbose.
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J Bacteriol,
185,
6981-6984.
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PDB code:
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N.Aghajari,
G.Feller,
C.Gerday,
and
R.Haser
(2002).
Structural basis of alpha-amylase activation by chloride.
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Protein Sci,
11,
1435-1441.
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PDB codes:
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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
