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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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6 terms
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DOI no:
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J Mol Biol
278:617-628
(1998)
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PubMed id:
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Crystal structure of yellow meal worm alpha-amylase at 1.64 A resolution.
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S.Strobl,
K.Maskos,
M.Betz,
G.Wiegand,
R.Huber,
F.X.Gomis-Rüth,
R.Glockshuber.
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ABSTRACT
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The three-dimensional structure of the alpha-amylase from Tenebrio molitor
larvae (TMA) has been determined by molecular replacement techniques using
diffraction data of a crystal of space group P212121 (a=51.24 A; b=93.46 A;
c=96.95 A). The structure has been refined to a crystallographic R-factor of
17.7% for 58,219 independent reflections in the 7.0 to 1.64 A resolution range,
with root-mean-square deviations of 0.008 A for bond lengths and 1.482 degrees
for bond angles. The final model comprises all 471 residues of TMA, 261 water
molecules, one calcium cation and one chloride anion. The electron density
confirms that the N-terminal glutamine residue has undergone a post-transitional
modification resulting in a stable 5-oxo-proline residue. The X-ray structure of
TMA provides the first three-dimensional model of an insect alpha-amylase.The
monomeric enzyme exhibits an elongated shape approximately 75 Ax46 Ax40 A and
consists of three distinct domains, in line with models for alpha-amylases from
microbial, plant and mammalian origin. However, the structure of TMA reflects in
the substrate and inhibitor binding region a remarkable difference from
mammalian alpha-amylases: the lack of a highly flexible, glycine-rich loop,
which has been proposed to be involved in a "trap-release" mechanism
of substrate hydrolysis by mammalian alpha-amylases. The structural differences
between alpha-amylases of various origins might explain the specificity of
inhibitors directed exclusively against insect alpha-amylases.
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Selected figure(s)
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Figure 3.
Figure 3. Superposition of the domain A/domain C interface
of TMA (green) and barley α-amylase (BAA) (red). Only the trace
of the TMA residues 251 to 326 and 359 to 471 and of the BAA
residues 251 to 403 are shown. TMA residues 263 to 266, 304 to
315, 366 to 377, 390 to 406 and 460 to 467 were superimposed on
BAA residues 262 to 265, 303 to 314, 333 to 344, 359 to 375 and
395 to 402.
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Figure 5.
Figure 5. Coordination of the calcium ion in the TMA
structure. The calcium ion is represented by a yellow sphere and
water molecules by blue spheres. B domain residues are depicted
in red and the A domain residue in green. Coordinating
interactions are shown as blue lines.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1998,
278,
617-628)
copyright 1998.
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Figures were
selected
by an automated process.
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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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F.M.Reyes-Sosa,
F.P.Molina-Heredia,
and
M.A.De la Rosa
(2010).
A novel alpha-amylase from the cyanobacterium Nostoc sp. PCC 7119.
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Appl Microbiol Biotechnol, 86,
131-141.
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J.Pytelková,
J.Hubert,
M.Lepsík,
J.Sobotník,
R.Sindelka,
I.Krízková,
M.Horn,
and
M.Mares
(2009).
Digestive alpha-amylases of the flour moth Ephestia kuehniella--adaptation to alkaline environment and plant inhibitors.
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FEBS J, 276,
3531-3546.
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J.C.Marx,
J.Poncin,
J.P.Simorre,
P.W.Ramteke,
and
G.Feller
(2008).
The noncatalytic triad of alpha-amylases: a novel structural motif involved in conformational stability.
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Proteins, 70,
320-328.
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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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A.J.Plested,
and
M.L.Mayer
(2007).
Structure and mechanism of kainate receptor modulation by anions.
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Neuron, 53,
829-841.
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PDB code:
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K.F.Lin,
T.R.Lee,
P.H.Tsai,
M.P.Hsu,
C.S.Chen,
and
P.C.Lyu
(2007).
Structure-based protein engineering for alpha-amylase inhibitory activity of plant defensin.
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Proteins, 68,
530-540.
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PDB code:
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F.Maczkowiak,
and
J.L.Da Lage
(2006).
Origin and evolution of the Amyrel gene in the alpha-amylase multigene family of Diptera.
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Genetica, 128,
145-158.
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P.B.Pelegrini,
A.M.Murad,
M.F.Grossi-de-Sá,
L.V.Mello,
L.A.Romeiro,
E.F.Noronha,
R.A.Caldas,
and
O.L.Franco
(2006).
Structure and enzyme properties of Zabrotes subfasciatus alpha-amylase.
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Arch Insect Biochem Physiol, 61,
77-86.
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Y.J.Liu,
C.S.Cheng,
S.M.Lai,
M.P.Hsu,
C.S.Chen,
and
P.C.Lyu
(2006).
Solution structure of the plant defensin VrD1 from mung bean and its possible role in insecticidal activity against bruchids.
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Proteins, 63,
777-786.
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PDB code:
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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.
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Biopolymers, 75,
95.
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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.
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Structure, 11,
973-984.
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PDB codes:
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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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O.L.Franco,
D.J.Rigden,
F.R.Melo,
and
M.F.Grossi-De-Sá
(2002).
Plant alpha-amylase inhibitors and their interaction with insect alpha-amylases.
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Eur J Biochem, 269,
397-412.
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E.A.MacGregor,
S.Janecek,
and
B.Svensson
(2001).
Relationship of sequence and structure to specificity in the alpha-amylase family of enzymes.
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Biochim Biophys Acta, 1546,
1.
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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.
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Eur J Biochem, 268,
6545-6558.
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J.C.Martins,
M.Enassar,
R.Willem,
J.M.Wieruzeski,
G.Lippens,
and
S.J.Wodak
(2001).
Solution structure of the main alpha-amylase inhibitor from amaranth seeds.
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Eur J Biochem, 268,
2379-2389.
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PDB code:
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J.Iulek,
O.L.Franco,
M.Silva,
C.T.Slivinski,
C.Bloch,
D.J.Rigden,
and
M.F.Grossi de Sá
(2000).
Purification, biochemical characterisation and partial primary structure of a new alpha-amylase inhibitor from Secale cereale (rye).
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Int J Biochem Cell Biol, 32,
1195-1204.
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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.
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Eur J Biochem, 267,
1019-1029.
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P.J.Pereira,
V.Lozanov,
A.Patthy,
R.Huber,
W.Bode,
S.Pongor,
and
S.Strobl
(1999).
Specific inhibition of insect alpha-amylases: yellow meal worm alpha-amylase in complex with the amaranth alpha-amylase inhibitor at 2.0 A resolution.
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Structure, 7,
1079-1088.
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PDB code:
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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.
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Structure, 6,
1503-1516.
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PDB code:
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S.Strobl,
K.Maskos,
G.Wiegand,
R.Huber,
F.X.Gomis-Rüth,
and
R.Glockshuber
(1998).
A novel strategy for inhibition of alpha-amylases: yellow meal worm alpha-amylase in complex with the Ragi bifunctional inhibitor at 2.5 A resolution.
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Structure, 6,
911-921.
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PDB code:
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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
code is
shown on the right.
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Links
