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Hydrolase (o-glycosyl)
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PDB id
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1amy
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Contents |
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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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Gene Ontology (GO) functional annotation
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Biological process
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metabolic process
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2 terms
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Biochemical function
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catalytic activity
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7 terms
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DOI no:
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J Mol Biol
239:104-121
(1994)
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PubMed id:
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Crystal and molecular structure of barley alpha-amylase.
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A.Kadziola,
J.Abe,
B.Svensson,
R.Haser.
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ABSTRACT
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The three-dimensional structure of barley malt alpha-amylase (isoform AMY2-2)
was determined by multiple isomorphous replacement using three heavy-atom
derivatives and solvent flattening. The model was refined using a combination of
simulated annealing and conventional restrained least-squares crystallographic
refinement to an R-factor of 0.153 based on 18,303 independent reflections with
F(o) > sigma(F(o)) between 10 and 2.8 A resolution, with root-mean-square
deviations of 0.016 A and 3.3 degrees from ideal bond lengths and bond angles,
respectively. The final model consists of 403 amino acid residues, three calcium
ions and 153 water molecules. The polypeptide chain folds into three domains: a
central domain forming a (beta alpha)8-barrel of 286 residues, with a protruding
irregular structured loop domain of 64 residues (domain B) connecting strand
beta 3 and helix alpha 3 of the barrel, and a C-terminal domain of 53 residues
forming a five stranded anti-parallel beta-sheet. Unlike the previously known
alpha-amylase structures, AMY2-2 contains three Ca2+ binding sites co-ordinated
by seven or eight oxygen atoms from carboxylate groups, main-chain carbonyl
atoms and water molecules, all calcium ions being bound to domain B and
therefore essential for the structural integrity of that domain. Two of the Ca2+
sites are located only 7.0 A apart with one Asp residue serving as ligand for
both. One Ca2+ site located at about 20 A from the other two was found to be
exchangeable with Eu3+. By homology with other alpha-amylases, some important
active site residues are identified as Asp179, Glu204 and Asp289, and are
situated at the C-terminal end of the central beta-barrel. A starch granule
binding site, previously identified as Trp276 and Trp277, is situated on
alpha-helix 6 in the central (beta alpha)8-barrel, at the surface of the enzyme.
This binding site region is associated with a considerable disruption of the
(beta alpha)8-barrel 8-fold symmetry.
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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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X.Qin,
L.Ren,
X.Yang,
F.Bai,
L.Wang,
P.Geng,
G.Bai,
and
Y.Shen
(2011).
Structures of human pancreatic α-amylase in complex with acarviostatins: Implications for drug design against type II diabetes.
|
| |
J Struct Biol, 174,
196-202.
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|
|
PDB codes:
|
|
|
|
|
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|
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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.
|
| |
FEBS J, 277,
4205-4214.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
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.
|
| |
Appl Environ Microbiol, 74,
5168-5177.
|
|
|
|
|
|
|
I.Matsui,
and
K.Harata
(2007).
Implication for buried polar contacts and ion pairs in hyperthermostable enzymes.
|
| |
FEBS J, 274,
4012-4022.
|
|
|
|
|
|
|
K.S.Bak-Jensen,
S.Laugesen,
O.Ostergaard,
C.Finnie,
P.Roepstorff,
and
B.Svensson
(2007).
Spatio-temporal profiling and degradation of alpha-amylase isozymes during barley seed germination.
|
| |
FEBS J, 274,
2552-2565.
|
|
|
|
|
|
|
R.Buckow,
U.Weiss,
V.Heinz,
and
D.Knorr
(2007).
Stability and catalytic activity of alpha-amylase from barley malt at different pressure-temperature conditions.
|
| |
Biotechnol Bioeng, 97,
1.
|
|
|
|
|
|
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R.Maurus,
A.Begum,
H.H.Kuo,
A.Racaza,
S.Numao,
C.Andersen,
J.W.Tams,
J.Vind,
C.M.Overall,
S.G.Withers,
and
G.D.Brayer
(2005).
Structural and mechanistic studies of chloride induced activation of human pancreatic alpha-amylase.
|
| |
Protein Sci, 14,
743-755.
|
|
|
PDB codes:
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|
|
G.André,
and
V.Tran
(2004).
Putative implication of alpha-amylase loop 7 in the mechanism of substrate binding and reaction products release.
|
| |
Biopolymers, 75,
95.
|
|
|
|
|
|
|
J.Allouch,
W.Helbert,
B.Henrissat,
and
M.Czjzek
(2004).
Parallel substrate binding sites in a beta-agarase suggest a novel mode of action on double-helical agarose.
|
| |
Structure, 12,
623-632.
|
|
|
PDB code:
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|
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K.S.Bak-Jensen,
G.André,
T.E.Gottschalk,
G.Paës,
V.Tran,
and
B.Svensson
(2004).
Tyrosine 105 and threonine 212 at outermost substrate binding subsites -6 and +4 control substrate specificity, oligosaccharide cleavage patterns, and multiple binding modes of barley alpha-amylase 1.
|
| |
J Biol Chem, 279,
10093-10102.
|
|
|
|
|
|
|
S.Numao,
I.Damager,
C.Li,
T.M.Wrodnigg,
A.Begum,
C.M.Overall,
G.D.Brayer,
and
S.G.Withers
(2004).
In situ extension as an approach for identifying novel alpha-amylase inhibitors.
|
| |
J Biol Chem, 279,
48282-48291.
|
|
|
PDB codes:
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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.
|
| |
J Biol Chem, 278,
9875-9884.
|
|
|
PDB codes:
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A.Tanaka,
and
E.Hoshino
(2003).
Secondary calcium-binding parameter of Bacillus amyloliquefaciens alpha-amylase obtained from inhibition kinetics.
|
| |
J Biosci Bioeng, 96,
262-267.
|
|
|
|
|
|
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H.B.Fritzsche,
T.Schwede,
and
G.E.Schulz
(2003).
Covalent and three-dimensional structure of the cyclodextrinase from Flavobacterium sp. no. 92.
|
| |
Eur J Biochem, 270,
2332-2341.
|
|
|
PDB code:
|
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|
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|
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N.Oudjeriouat,
Y.Moreau,
M.Santimone,
B.Svensson,
G.Marchis-Mouren,
and
V.Desseaux
(2003).
On the mechanism of alpha-amylase.
|
| |
Eur J Biochem, 270,
3871-3879.
|
|
|
|
|
|
|
S.Janecek,
B.Svensson,
and
E.A.MacGregor
(2003).
Relation between domain evolution, specificity, and taxonomy of the alpha-amylase family members containing a C-terminal starch-binding domain.
|
| |
Eur J Biochem, 270,
635-645.
|
|
|
|
|
|
|
S.S.Mar,
H.Mori,
J.H.Lee,
K.Fukuda,
W.Saburi,
A.Fukuhara,
M.Okuyama,
S.Chiba,
and
A.Kimura
(2003).
Purification, characterization, and sequence analysis of two alpha-amylase isoforms from azuki bean, Vigna angularis, showing different affinity towards beta-cyclodextrin sepharose.
|
| |
Biosci Biotechnol Biochem, 67,
1080-1093.
|
|
|
|
|
|
|
T.Nonaka,
M.Fujihashi,
A.Kita,
H.Hagihara,
K.Ozaki,
S.Ito,
and
K.Miki
(2003).
Crystal structure of calcium-free alpha-amylase from Bacillus sp. strain KSM-K38 (AmyK38) and its sodium ion binding sites.
|
| |
J Biol Chem, 278,
24818-24824.
|
|
|
PDB codes:
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|
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|
|
X.Robert,
R.Haser,
T.E.Gottschalk,
F.Ratajczak,
H.Driguez,
B.Svensson,
and
N.Aghajari
(2003).
The structure of barley alpha-amylase isozyme 1 reveals a novel role of domain C in substrate recognition and binding: a pair of sugar tongs.
|
| |
Structure, 11,
973-984.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
G.Parsiegla,
A.Belaïch,
J.P.Belaïch,
and
R.Haser
(2002).
Crystal structure of the cellulase Cel9M enlightens structure/function relationships of the variable catalytic modules in glycoside hydrolases.
|
| |
Biochemistry, 41,
11134-11142.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
H.Mori,
K.S.Bak-Jensen,
and
B.Svensson
(2002).
Barley alpha-amylase Met53 situated at the high-affinity subsite -2 belongs to a substrate binding motif in the beta-->alpha loop 2 of the catalytic (beta/alpha)8-barrel and is critical for activity and substrate specificity.
|
| |
Eur J Biochem, 269,
5377-5390.
|
|
|
|
|
|
|
X.Robert,
T.E.Gottschalk,
R.Haser,
B.Svensson,
and
N.Aghajari
(2002).
Expression, purification and preliminary crystallographic studies of alpha-amylase isozyme 1 from barley seeds.
|
| |
Acta Crystallogr D Biol Crystallogr, 58,
683-686.
|
|
|
|
|
|
|
E.A.MacGregor,
S.Janecek,
and
B.Svensson
(2001).
Relationship of sequence and structure to specificity in the alpha-amylase family of enzymes.
|
| |
Biochim Biophys Acta, 1546,
1.
|
|
|
|
|
|
|
H.Mori,
K.S.Bak-Jensen,
T.E.Gottschalk,
M.S.Motawia,
I.Damager,
B.L.Møller,
and
B.Svensson
(2001).
Modulation of activity and substrate binding modes by mutation of single and double subsites +1/+2 and -5/-6 of barley alpha-amylase 1.
|
| |
Eur J Biochem, 268,
6545-6558.
|
|
|
|
|
|
|
J.H.Lebbink,
C.Bertoldo,
G.Tibbelin,
J.T.Andersen,
F.Duffner,
G.Antranikian,
and
R.Ladenstein
(2000).
Crystallization and preliminary X-ray crystallographic studies of the thermoactive pullulanase type I, hydrolyzing alpha-1,6 glycosidic linkages, from Fervidobacterium pennivorans Ven5.
|
| |
Acta Crystallogr D Biol Crystallogr, 56,
1470-1472.
|
|
|
|
|
|
|
K.W.Rodenburg,
F.Vallée,
N.Juge,
N.Aghajari,
X.Guo,
R.Haser,
and
B.Svensson
(2000).
Specific inhibition of barley alpha-amylase 2 by barley alpha-amylase/subtilisin inhibitor depends on charge interactions and can be conferred to isozyme 1 by mutation.
|
| |
Eur J Biochem, 267,
1019-1029.
|
|
|
|
|
|
|
L.Janda,
J.Damborský,
M.Petrícek,
J.Spízek,
and
P.Tichý
(2000).
Molecular characterization of the Thermomonospora curvata aglA gene encoding a thermotolerant alpha-1,4-glucosidase.
|
| |
J Appl Microbiol, 88,
773-783.
|
|
|
|
|
|
|
T.Wegrzyn,
K.Reilly,
G.Cipriani,
P.Murphy,
R.Newcomb,
R.Gardner,
and
E.MacRae
(2000).
A novel alpha-amylase gene is transiently upregulated during low temperature exposure in apple fruit.
|
| |
Eur J Biochem, 267,
1313-1322.
|
|
|
|
|
|
|
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.
|
| |
Protein Sci, 8,
635-643.
|
|
|
PDB code:
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|
|
|
|
|
|
|
G.André,
A.Buléon,
R.Haser,
and
V.Tran
(1999).
Amylose chain behavior in an interacting context. III. Complete occupancy of the AMY2 barley alpha-amylase cleft and comparison with biochemical data.
|
| |
Biopolymers, 50,
751-762.
|
|
|
|
|
|
|
R.A.Jones,
L.S.Jermiin,
S.Easteal,
B.K.Patel,
and
I.R.Beacham
(1999).
Amylase and 16S rRNA genes from a hyperthermophilic archaebacterium.
|
| |
J Appl Microbiol, 86,
93.
|
|
|
|
|
|
|
R.Abe,
K.Yoshida,
M.Aoyagi,
S.Kasahara,
E.Ichishima,
and
T.Nakajima
(1999).
Characterization of chimeric enzymes constructed between two distinct alpha-amylase cDNAs from cultured rice cells.
|
| |
Biosci Biotechnol Biochem, 63,
1329-1335.
|
|
|
|
|
|
|
A.K.Schmidt,
S.Cottaz,
H.Driguez,
and
G.E.Schulz
(1998).
Structure of cyclodextrin glycosyltransferase complexed with a derivative of its main product beta-cyclodextrin.
|
| |
Biochemistry, 37,
5909-5915.
|
|
|
PDB code:
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|
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|
|
F.Vallée,
A.Kadziola,
Y.Bourne,
M.Juy,
K.W.Rodenburg,
B.Svensson,
and
R.Haser
(1998).
Barley alpha-amylase bound to its endogenous protein inhibitor BASI: crystal structure of the complex at 1.9 A resolution.
|
| |
Structure, 6,
649-659.
|
|
|
PDB code:
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|
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|
|
|
G.Parsiegla,
M.Juy,
C.Reverbel-Leroy,
C.Tardif,
J.P.Belaïch,
H.Driguez,
and
R.Haser
(1998).
The crystal structure of the processive endocellulase CelF of Clostridium cellulolyticum in complex with a thiooligosaccharide inhibitor at 2.0 A resolution.
|
| |
EMBO J, 17,
5551-5562.
|
|
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PDB code:
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|
|
M.J.Cho,
S.S.Cha,
J.H.Park,
H.J.Cha,
H.S.Lee,
K.H.Park,
and
B.H.Oh
(1998).
Preliminary X-ray crystallographic analysis of a novel maltogenic amylase from Bacillus stearothermophilus ET1.
|
| |
Acta Crystallogr D Biol Crystallogr, 54,
416-418.
|
|
|
|
|
|
|
M.Machius,
N.Declerck,
R.Huber,
and
G.Wiegand
(1998).
Activation of Bacillus licheniformis alpha-amylase through a disorder-->order transition of the substrate-binding site mediated by a calcium-sodium-calcium metal triad.
|
| |
Structure, 6,
281-292.
|
|
|
PDB code:
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|
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|
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|
|
N.Aghajari,
G.Feller,
C.Gerday,
and
R.Haser
(1998).
Crystal structures of the psychrophilic alpha-amylase from Alteromonas haloplanctis in its native form and complexed with an inhibitor.
|
| |
Protein Sci, 7,
564-572.
|
|
|
PDB codes:
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|
|
|
|
|
|
|
N.Aghajari,
G.Feller,
C.Gerday,
and
R.Haser
(1998).
Structures of the psychrophilic Alteromonas haloplanctis alpha-amylase give insights into cold adaptation at a molecular level.
|
| |
Structure, 6,
1503-1516.
|
|
|
PDB code:
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|
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|
|
B.X.Yan,
and
Y.Q.Sun
(1997).
Glycine residues provide flexibility for enzyme active sites.
|
| |
J Biol Chem, 272,
3190-3194.
|
|
|
|
|
|
|
C.Spiess,
H.P.Happersberger,
M.O.Glocker,
E.Spiess,
K.Rippe,
and
M.Ehrmann
(1997).
Biochemical characterization and mass spectrometric disulfide bond mapping of periplasmic alpha-amylase MalS of Escherichia coli.
|
| |
J Biol Chem, 272,
22125-22133.
|
|
|
|
|
|
|
I.Matsui,
and
B.Svensson
(1997).
Improved activity and modulated action pattern obtained by random mutagenesis at the fourth beta-alpha loop involved in substrate binding to the catalytic (beta/alpha)8-barrel domain of barley alpha-amylase 1.
|
| |
J Biol Chem, 272,
22456-22463.
|
|
|
|
|
|
|
K.S.Devulapalle,
S.D.Goodman,
Q.Gao,
A.Hemsley,
and
G.Mooser
(1997).
Knowledge-based model of a glucosyltransferase from the oral bacterial group of mutans streptococci.
|
| |
Protein Sci, 6,
2489-2493.
|
|
|
|
|
|
|
M.E.Himmel,
P.A.Karplus,
J.Sakon,
W.S.Adney,
J.O.Baker,
and
S.R.Thomas
(1997).
Polysaccharide hydrolase folds diversity of structure and convergence of function.
|
| |
Appl Biochem Biotechnol, 63,
315-325.
|
|
|
|
|
|
|
T.Suganuma,
Y.Maeda,
K.Kitahara,
and
T.Nagahama
(1997).
Study of the action of human salivary alpha-amylase on 2-chloro-4-nitrophenyl alpha-maltotrioside in the presence of potassium thiocyanate.
|
| |
Carbohydr Res, 303,
219-227.
|
|
|
|
|
|
|
C.Gilles,
J.P.Astier,
G.Marchis-Mouren,
C.Cambillau,
and
F.Payan
(1996).
Crystal structure of pig pancreatic alpha-amylase isoenzyme II, in complex with the carbohydrate inhibitor acarbose.
|
| |
Eur J Biochem, 238,
561-569.
|
|
|
PDB code:
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|
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|
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|
|
|
G.Feller,
O.Bussy,
C.Houssier,
and
C.Gerday
(1996).
Structural and functional aspects of chloride binding to Alteromonas haloplanctis alpha-amylase.
|
| |
J Biol Chem, 271,
23836-23841.
|
|
|
|
|
|
|
M.Alkazaz,
V.Desseaux,
G.Marchis-Mouren,
F.Payan,
E.Forest,
and
M.Santimone
(1996).
The mechanism of porcine pancreatic alpha-amylase. Kinetic evidence for two additional carbohydrate-binding sites.
|
| |
Eur J Biochem, 241,
787-796.
|
|
|
|
|
|
|
M.Terashima,
and
S.Katoh
(1996).
Modification of alpha-amylase functions by protein engineering.
|
| |
Ann N Y Acad Sci, 799,
65-69.
|
|
|
|
|
|
|
T.Suganuma,
M.Ohnishi,
K.Hiromi,
and
T.Nagahama
(1996).
Elucidation of the subsite structure of bacterial saccharifying alpha-amylase and its mode of degradation of maltose.
|
| |
Carbohydr Res, 282,
171-180.
|
|
|
|
|
|
|
C.Wiesmann,
G.Beste,
W.Hengstenberg,
and
G.E.Schulz
(1995).
The three-dimensional structure of 6-phospho-beta-galactosidase from Lactococcus lactis.
|
| |
Structure, 3,
961-968.
|
|
|
PDB code:
|
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|
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|
|
|
F.Casset,
A.Imberty,
R.Haser,
F.Payan,
and
S.Perez
(1995).
Molecular modelling of the interaction between the catalytic site of pig pancreatic alpha-amylase and amylose fragments.
|
| |
Eur J Biochem, 232,
284-293.
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G.D.Brayer,
Y.Luo,
and
S.G.Withers
(1995).
The structure of human pancreatic alpha-amylase at 1.8 A resolution and comparisons with related enzymes.
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| |
Protein Sci, 4,
1730-1742.
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PDB code:
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M.Qian,
R.Haser,
and
F.Payan
(1995).
Carbohydrate binding sites in a pancreatic alpha-amylase-substrate complex, derived from X-ray structure analysis at 2.1 A resolution.
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Protein Sci, 4,
747-755.
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S.Knapp,
A.Rüdiger,
G.Antranikian,
P.L.Jorgensen,
and
R.Ladenstein
(1995).
Crystallization and preliminary crystallographic analysis of an amylopullulanase from the hyperthermophilic archaeon Pyrococcus woesei.
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Proteins, 23,
595-597.
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J.D.McCarter,
and
S.G.Withers
(1994).
Mechanisms of enzymatic glycoside hydrolysis.
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| |
Curr Opin Struct Biol, 4,
885-892.
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M.Terashima,
A.Kubo,
M.Suzawa,
Y.Itoh,
and
S.Katoh
(1994).
The roles of the N-linked carbohydrate chain of rice alpha-amylase in thermostability and enzyme kinetics.
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Eur J Biochem, 226,
249-254.
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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
