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PDBsum entry 1qho
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Contents |
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* Residue conservation analysis
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PDB id:
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Hydrolase
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Title:
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Five-domain alpha-amylase from bacillus stearothermophilus, maltose/acarbose complex
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Structure:
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Alpha-amylase. Chain: a. Fragment: intact protein, all 5 domains. Synonym: "maltogenic" alpha amylase. Engineered: yes. Other_details: contains an acarbose-derived hexasaccharide and maltose
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Source:
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Geobacillus stearothermophilus. Organism_taxid: 1422. Expressed in: bacillus subtilis. Expression_system_taxid: 1423
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Resolution:
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1.70Å
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R-factor:
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0.151
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R-free:
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0.175
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Authors:
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Z.Dauter,M.Dauter,A.M.Brzozowski,S.Christensen,T.V.Borchert,L.Beier, K.S.Wilson,G.J.Davies
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Key ref:
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Z.Dauter
et al.
(1999).
X-ray structure of Novamyl, the five-domain "maltogenic" alpha-amylase from Bacillus stearothermophilus: maltose and acarbose complexes at 1.7A resolution.
Biochemistry,
38,
8385-8392.
PubMed id:
DOI:
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Date:
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25-May-99
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Release date:
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31-May-00
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PROCHECK
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Headers
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References
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P19531
(AMYM_GEOSE) -
Maltogenic alpha-amylase from Geobacillus stearothermophilus
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Seq:
Struc:
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719 a.a.
686 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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Enzyme class:
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E.C.3.2.1.133
- glucan 1,4-alpha-maltohydrolase.
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Reaction:
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Hydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides so as to remove successive alpha-maltose residues from the non-reducing ends of the chains.
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DOI no:
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Biochemistry
38:8385-8392
(1999)
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PubMed id:
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X-ray structure of Novamyl, the five-domain "maltogenic" alpha-amylase from Bacillus stearothermophilus: maltose and acarbose complexes at 1.7A resolution.
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Z.Dauter,
M.Dauter,
A.M.Brzozowski,
S.Christensen,
T.V.Borchert,
L.Beier,
K.S.Wilson,
G.J.Davies.
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ABSTRACT
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The three-dimensional structure of the Bacillus stearothermophilus "maltogenic"
alpha-amylase, Novamyl, has been determined by X-ray crystallography at a
resolution of 1.7 A. Unlike conventional alpha-amylases from glycoside hydrolase
family 13, Novamyl exhibits the five-domain structure more usually associated
with cyclodextrin glycosyltransferase. Complexes of the enzyme with both maltose
and the inhibitor acarbose have been characterized. In the maltose complex, two
molecules of maltose are found in the -1 to -2 and +2 to +3 subsites of the
active site, with two more on the C and E domains. The C-domain maltose occupies
a position identical to one previously observed in the Bacillus circulans CGTase
structure [Lawson, C. L., et al. (1994) J. Mol. Biol. 236, 590-600], suggesting
that the C-domain plays a genuine biological role in saccharide binding. In the
acarbose-maltose complex, the tetrasaccharide inhibitor acarbose is found as an
extended hexasaccharide species, bound in the -3 to +3 subsites. The transition
state mimicking pseudosaccharide is bound in the -1 subsite of the enzyme in a
2H3 half-chair conformation, as expected. The active site of Novamyl lies in an
open gully, fully consistent with its ability to perform internal cleavage via
an endo as opposed to an exo activity.
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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.
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J Struct Biol,
174,
196-202.
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PDB codes:
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C.Christiansen,
M.Abou Hachem,
S.Janecek,
A.Viksø-Nielsen,
A.Blennow,
and
B.Svensson
(2009).
The carbohydrate-binding module family 20--diversity, structure, and function.
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FEBS J,
276,
5006-5029.
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R.M.Kelly,
L.Dijkhuizen,
and
H.Leemhuis
(2009).
The evolution of cyclodextrin glucanotransferase product specificity.
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Appl Microbiol Biotechnol,
84,
119-133.
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A.Cartmell,
E.Topakas,
V.M.Ducros,
M.D.Suits,
G.J.Davies,
and
H.J.Gilbert
(2008).
The Cellvibrio japonicus Mannanase CjMan26C Displays a Unique exo-Mode of Action That Is Conferred by Subtle Changes to the Distal Region of the Active Site.
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J Biol Chem,
283,
34403-34413.
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PDB codes:
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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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S.Rana,
B.Kundu,
and
S.Durani
(2007).
A mixed-alpha,beta miniprotein stereochemically reprogrammed to high-binding affinity for acetylcholine.
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Biopolymers,
87,
231-243.
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M.Machovic,
B.Svensson,
E.A.MacGregor,
and
S.Janecek
(2005).
A new clan of CBM families based on bioinformatics of starch-binding domains from families CBM20 and CBM21.
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FEBS J,
272,
5497-5513.
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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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D.Hoffmeister,
and
J.S.Thorson
(2004).
Mechanistic implications of Escherichia coli galactokinase structure-based engineering.
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Chembiochem,
5,
989-992.
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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.
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J Biol Chem,
279,
10093-10102.
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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.R.Mott,
D.Nietlispach,
L.J.Hopkins,
G.Mirey,
J.H.Camonis,
and
D.Owen
(2003).
Structure of the GTPase-binding domain of Sec5 and elucidation of its Ral binding site.
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J Biol Chem,
278,
17053-17059.
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PDB code:
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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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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.
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Eur J Biochem,
270,
635-645.
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H.Kamasaka,
K.Sugimoto,
H.Takata,
T.Nishimura,
and
T.Kuriki
(2002).
Bacillus stearothermophilus neopullulanase selective hydrolysis of amylose to maltose in the presence of amylopectin.
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Appl Environ Microbiol,
68,
1658-1664.
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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.
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Eur J Biochem,
269,
5377-5390.
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L.K.Skov,
O.Mirza,
D.Sprogøe,
I.Dar,
M.Remaud-Simeon,
C.Albenne,
P.Monsan,
and
M.Gajhede
(2002).
Oligosaccharide and sucrose complexes of amylosucrase. Structural implications for the polymerase activity.
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J Biol Chem,
277,
47741-47747.
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PDB codes:
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M.J.Kim,
H.S.Lee,
J.S.Cho,
T.J.Kim,
T.W.Moon,
S.T.Oh,
J.W.Kim,
B.H.Oh,
and
K.H.Park
(2002).
Preparation and characterization of alpha-D-glucopyranosyl-alpha-acarviosinyl-D-glucopyranose, a novel inhibitor specific for maltose-producing amylase.
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Biochemistry,
41,
9099-9108.
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O.Kirk,
T.V.Borchert,
and
C.C.Fuglsang
(2002).
Industrial enzyme applications.
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Curr Opin Biotechnol,
13,
345-351.
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T.P.Frandsen,
M.M.Palcic,
and
B.Svensson
(2002).
Substrate recognition by three family 13 yeast alpha-glucosidases.
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Eur J Biochem,
269,
728-734.
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B.Höcker,
C.Jürgens,
M.Wilmanns,
and
R.Sterner
(2001).
Stability, catalytic versatility and evolution of the (beta alpha)(8)-barrel fold.
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Curr Opin Biotechnol,
12,
376-381.
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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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S.Fort,
A.Varrot,
M.Schülein,
S.Cottaz,
H.Driguez,
and
G.J.Davies
(2001).
Mixed-linkage cellooligosaccharides: a new class of glycoside hydrolase inhibitors.
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Chembiochem,
2,
319-325.
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PDB code:
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A.M.Brzozowski,
D.M.Lawson,
J.P.Turkenburg,
H.Bisgaard-Frantzen,
A.Svendsen,
T.V.Borchert,
Z.Dauter,
K.S.Wilson,
and
G.J.Davies
(2000).
Structural analysis of a chimeric bacterial alpha-amylase. High-resolution analysis of native and ligand complexes.
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Biochemistry,
39,
9099-9107.
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PDB codes:
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I.Przylas,
Y.Terada,
K.Fujii,
T.Takaha,
W.Saenger,
and
N.Sträter
(2000).
X-ray structure of acarbose bound to amylomaltase from Thermus aquaticus. Implications for the synthesis of large cyclic glucans.
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Eur J Biochem,
267,
6903-6913.
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PDB code:
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J.E.Nielsen,
and
T.V.Borchert
(2000).
Protein engineering of bacterial alpha-amylases.
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Biochim Biophys Acta,
1543,
253-274.
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K.Ohdan,
T.Kuriki,
H.Takata,
H.Kaneko,
and
S.Okada
(2000).
Introduction of raw starch-binding domains into Bacillus subtilis alpha-amylase by fusion with the starch-binding domain of Bacillus cyclomaltodextrin glucanotransferase.
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Appl Environ Microbiol,
66,
3058-3064.
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N.Ichikawa,
R.Fujisaka,
and
R.Kuribayashi
(2000).
Requirement for lysine-19 of the yeast mitochondrial ATPase inhibitor for the stability of the inactivated inhibitor-F1Fo complex at higher pH.
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Biosci Biotechnol Biochem,
64,
89-95.
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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
