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PDBsum entry 2myr
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Structure
5:663-675
(1997)
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PubMed id:
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The crystal structures of Sinapis alba myrosinase and a covalent glycosyl-enzyme intermediate provide insights into the substrate recognition and active-site machinery of an S-glycosidase.
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W.P.Burmeister,
S.Cottaz,
H.Driguez,
R.Iori,
S.Palmieri,
B.Henrissat.
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ABSTRACT
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BACKGROUND: Myrosinase is the enzyme responsible for the hydrolysis of a variety
of plant anionic 1-thio-beta-D-glucosides called glucosinolates. Myrosinase and
glucosinolates, which are stored in different tissues of the plant, are mixed
during mastication generating toxic by-products that are believed to play a role
in the plant defence system. Whilst O-glycosidases are extremely widespread in
nature, myrosinase is the only known S-glycosidase. This intriguing enzyme,
which shows sequence similarities with O-glycosidases, offers the opportunity to
analyze the similarities and differences between enzymes hydrolyzing S- and
O-glycosidic bonds. RESULTS: The structures of native myrosinase from white
mustard seed (Sinapis alba) and of a stable glycosyl-enzyme intermediate have
been solved at 1.6 A resolution. The protein folds into a (beta/alpha)8-barrel
structure, very similar to that of the cyanogenic beta-glucosidase from white
clover. The enzyme forms a dimer stabilized by a Zn2+ ion and is heavily
glycosylated. At one glycosylation site the complete structure of a
plant-specific heptasaccharide is observed. The myrosinase structure reveals a
hydrophobic pocket, ideally situated for the binding of the hydrophobic
sidechain of glucosinolates, and two arginine residues positioned for
interaction with the sulphate group of the substrate. With the exception of the
replacement of the general acid/base glutamate by a glutamine residue, the
catalytic machinery of myrosinase is identical to that of the cyanogenic
beta-glucosidase. The structure of the glycosyl-enzyme intermediate shows that
the sugar ring is bound via an alpha-glycosidic linkage to Glu409, the catalytic
nucleophile of myrosinase. CONCLUSIONS: The structure of myrosinase shows
features which illustrate the adaptation of the plant enzyme to the dehydrated
environment of the seed. The catalytic mechanism of myrosinase is explained by
the excellent leaving group properties of the substrate aglycons, which do not
require the assistance of an enzymatic acid catalyst. The replacement of the
general acid/base glutamate of O-glycosidases by a glutamine residue in
myrosinase suggests that for hydrolysis of the glycosyl-enzyme, the role of this
residue is to ensure a precise positioning of a water molecule rather than to
provide general base assistance.
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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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N.Agerbirk,
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Characterization of a novel β-thioglucosidase CpTGG1 in Carica papaya and its substrate-dependent and ascorbic acid-independent O-β-glucosidase activity.
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J.R.Ketudat Cairns,
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Protein J,
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PDB code:
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B.A.Halkier,
and
J.Gershenzon
(2006).
Biology and biochemistry of glucosinolates.
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Annu Rev Plant Biol,
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Family 4 glycosidases carry out efficient hydrolysis of thioglycosides by an alpha,beta-elimination mechanism.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
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A.Bourderioux,
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and
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The glucosinolate-myrosinase system. New insights into enzyme-substrate interactions by use of simplified inhibitors.
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Org Biomol Chem,
3,
1872-1879.
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PDB codes:
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B.E.Stranger,
and
T.Mitchell-Olds
(2005).
Nucleotide variation at the myrosinase-encoding locus, TGG1, and quantitative myrosinase enzyme activity variation in Arabidopsis thaliana.
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Mol Ecol,
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E.J.Taylor,
A.Goyal,
C.I.Guerreiro,
J.A.Prates,
V.A.Money,
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How family 26 glycoside hydrolases orchestrate catalysis on different polysaccharides: structure and activity of a Clostridium thermocellum lichenase, CtLic26A.
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J Biol Chem,
280,
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PDB codes:
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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.
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Structure,
12,
623-632.
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PDB code:
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J.K.McCarthy,
A.Uzelac,
D.F.Davis,
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Improved catalytic efficiency and active site modification of 1,4-beta-D-glucan glucohydrolase A from Thermotoga neapolitana by directed evolution.
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J Biol Chem,
279,
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S.R.Marana,
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Investigation of the substrate specificity of a beta-glycosidase from Spodoptera frugiperda using site-directed mutagenesis and bioenergetics analysis.
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Eur J Biochem,
271,
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T.Akiba,
M.Nishio,
I.Matsui,
and
K.Harata
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X-ray structure of a membrane-bound beta-glycosidase from the hyperthermophilic archaeon Pyrococcus horikoshii.
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Proteins,
57,
422-431.
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PDB code:
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Z.Xu,
L.Escamilla-Treviño,
L.Zeng,
M.Lalgondar,
D.Bevan,
B.Winkel,
A.Mohamed,
C.L.Cheng,
M.C.Shih,
J.Poulton,
and
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Functional genomic analysis of Arabidopsis thaliana glycoside hydrolase family 1.
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Plant Mol Biol,
55,
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E.Bismuto,
F.Febbraio,
S.Limongelli,
R.Briante,
and
R.Nucci
(2003).
Dynamic fluorescence studies of beta-glycosidase mutants from Sulfolobus solfataricus: effects of single mutations on protein thermostability.
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Proteins,
51,
10-20.
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S.R.Marana,
L.M.Mendonça,
E.H.Andrade,
W.R.Terra,
and
C.Ferreira
(2003).
The role of residues R97 and Y331 in modulating the pH optimum of an insect beta-glycosidase of family 1.
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Eur J Biochem,
270,
4866-4875.
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X.Wang,
X.He,
S.Yang,
X.An,
W.Chang,
and
D.Liang
(2003).
Structural basis for thermostability of beta-glycosidase from the thermophilic eubacterium Thermus nonproteolyticus HG102.
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J Bacteriol,
185,
4248-4255.
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PDB code:
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B.Cobucci-Ponzano,
M.Moracci,
B.Di Lauro,
M.Ciaramella,
R.D'Avino,
and
M.Rossi
(2002).
Ionic network at the C-terminus of the beta-glycosidase from the hyperthermophilic archaeon Sulfolobus solfataricus: Functional role in the quaternary structure thermal stabilization.
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Proteins,
48,
98.
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J.G.Berrin,
W.R.McLauchlan,
P.Needs,
G.Williamson,
A.Puigserver,
P.A.Kroon,
and
N.Juge
(2002).
Functional expression of human liver cytosolic beta-glucosidase in Pichia pastoris. Insights into its role in the metabolism of dietary glucosides.
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Eur J Biochem,
269,
249-258.
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J.Zhang,
B.Pontoppidan,
J.Xue,
L.Rask,
and
J.Meijer
(2002).
The third myrosinase gene TGG3 in Arabidopsis thaliana is a pseudogene specifically expressed in stamen and petal.
|
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Physiol Plant,
115,
25-34.
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S.R.Marana,
W.R.Terra,
and
C.Ferreira
(2002).
The role of amino-acid residues Q39 and E451 in the determination of substrate specificity of the Spodoptera frugiperda beta-glycosidase.
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Eur J Biochem,
269,
3705-3714.
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T.Kaper,
H.H.van Heusden,
B.van Loo,
A.Vasella,
J.van der Oost,
and
W.M.de Vos
(2002).
Substrate specificity engineering of beta-mannosidase and beta-glucosidase from Pyrococcus by exchange of unique active site residues.
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Biochemistry,
41,
4147-4155.
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B.Pontoppidan,
B.Ekbom,
S.Eriksson,
and
J.Meijer
(2001).
Purification and characterization of myrosinase from the cabbage aphid (Brevicoryne brassicae), a brassica herbivore.
|
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Eur J Biochem,
268,
1041-1048.
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M.Hrmova,
J.N.Varghese,
R.De Gori,
B.J.Smith,
H.Driguez,
and
G.B.Fincher
(2001).
Catalytic mechanisms and reaction intermediates along the hydrolytic pathway of a plant beta-D-glucan glucohydrolase.
|
| |
Structure,
9,
1005-1016.
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PDB codes:
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S.Eriksson,
B.Ek,
J.Xue,
L.Rask,
and
J.Meijer
(2001).
Identification and characterization of soluble and insoluble myrosinase isoenzymes in different organs of Sinapis alba.
|
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Physiol Plant,
111,
353-364.
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S.R.Marana,
M.Jacobs-Lorena,
W.R.Terra,
and
C.Ferreira
(2001).
Amino acid residues involved in substrate binding and catalysis in an insect digestive beta-glycosidase.
|
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Biochim Biophys Acta,
1545,
41-52.
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X.Y.He,
X.Q.Wang,
S.J.Yang,
W.R.Chang,
and
D.C.Liang
(2001).
Overexpression, purification, crystallization and preliminary crystallographic studies on a thermostable beta-glycosidase from Thermus nonproteolyticus HG102.
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Acta Crystallogr D Biol Crystallogr,
57,
1650-1651.
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C.S.Rye,
and
S.G.Withers
(2000).
Glycosidase mechanisms.
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Curr Opin Chem Biol,
4,
573-580.
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G.P.Connelly,
S.G.Withers,
and
L.P.McIntosh
(2000).
Analysis of the dynamic properties of Bacillus circulans xylanase upon formation of a covalent glycosyl-enzyme intermediate.
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Protein Sci,
9,
512-524.
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M.Czjzek,
M.Cicek,
V.Zamboni,
D.R.Bevan,
B.Henrissat,
and
A.Esen
(2000).
The mechanism of substrate (aglycone) specificity in beta -glucosidases is revealed by crystal structures of mutant maize beta -glucosidase-DIMBOA, -DIMBOAGlc, and -dhurrin complexes.
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Proc Natl Acad Sci U S A,
97,
13555-13560.
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PDB codes:
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O.Leoni,
R.Iori,
and
S.Palmieri
(2000).
Hydrolysis of glucosinolates using nylon-immobilized myrosinase to produce pure bioactive molecules.
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Biotechnol Bioeng,
68,
660-664.
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T.Kaper,
J.H.Lebbink,
J.Pouwels,
J.Kopp,
G.E.Schulz,
J.van der Oost,
and
W.M.de Vos
(2000).
Comparative structural analysis and substrate specificity engineering of the hyperthermostable beta-glucosidase CelB from Pyrococcus furiosus.
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Biochemistry,
39,
4963-4970.
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W.P.Burmeister
(2000).
Structural changes in a cryo-cooled protein crystal owing to radiation damage.
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Acta Crystallogr D Biol Crystallogr,
56,
328-341.
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PDB codes:
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Z.Marković-Housley,
G.Miglierini,
L.Soldatova,
P.J.Rizkallah,
U.Müller,
and
T.Schirmer
(2000).
Crystal structure of hyaluronidase, a major allergen of bee venom.
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Structure,
8,
1025-1035.
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PDB codes:
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A.Guasch,
M.Vallmitjana,
R.Pérez,
E.Querol,
J.A.Pérez-Pons,
and
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Cloning, overexpression, crystallization and preliminary X-ray analysis of a family 1 beta--glucosidase from Streptomyces.
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Acta Crystallogr D Biol Crystallogr,
55,
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D.H.Juers,
R.E.Huber,
and
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(1999).
Structural comparisons of TIM barrel proteins suggest functional and evolutionary relationships between beta-galactosidase and other glycohydrolases.
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Protein Sci,
8,
122-136.
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E.Sabini,
G.Sulzenbacher,
M.Dauter,
Z.Dauter,
P.L.Jørgensen,
M.Schülein,
C.Dupont,
G.J.Davies,
and
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Catalysis and specificity in enzymatic glycoside hydrolysis: a 2,5B conformation for the glycosyl-enzyme intermediate revealed by the structure of the Bacillus agaradhaerens family 11 xylanase.
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Chem Biol,
6,
483-492.
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PDB codes:
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G.Sidhu,
S.G.Withers,
N.T.Nguyen,
L.P.McIntosh,
L.Ziser,
and
G.D.Brayer
(1999).
Sugar ring distortion in the glycosyl-enzyme intermediate of a family G/11 xylanase.
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Biochemistry,
38,
5346-5354.
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PDB codes:
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G.Sulzenbacher,
L.F.Mackenzie,
K.S.Wilson,
S.G.Withers,
C.Dupont,
and
G.J.Davies
(1999).
The crystal structure of a 2-fluorocellotriosyl complex of the Streptomyces lividans endoglucanase CelB2 at 1.2 A resolution.
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Biochemistry,
38,
4826-4833.
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PDB code:
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J.U.Flanagan,
J.Rossjohn,
M.W.Parker,
P.G.Board,
and
G.Chelvanayagam
(1999).
Mutagenic analysis of conserved arginine residues in and around the novel sulfate binding pocket of the human Theta class glutathione transferase T2-2.
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Protein Sci,
8,
2205-2212.
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P.R.Jones,
B.L.Moller,
and
P.B.Hoj
(1999).
The UDP-glucose:p-hydroxymandelonitrile-O-glucosyltransferase that catalyzes the last step in synthesis of the cyanogenic glucoside dhurrin in Sorghum bicolor. Isolation, cloning, heterologous expression, and substrate specificity.
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J Biol Chem,
274,
35483-35491.
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S.J.Charnock,
and
G.J.Davies
(1999).
Structure of the nucleotide-diphospho-sugar transferase, SpsA from Bacillus subtilis, in native and nucleotide-complexed forms.
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| |
Biochemistry,
38,
6380-6385.
|
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PDB codes:
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G.J.Davies,
L.Mackenzie,
A.Varrot,
M.Dauter,
A.M.Brzozowski,
M.Schülein,
and
S.G.Withers
(1998).
Snapshots along an enzymatic reaction coordinate: analysis of a retaining beta-glycoside hydrolase.
|
| |
Biochemistry,
37,
11707-11713.
|
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PDB codes:
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G.J.Davies,
M.Dauter,
A.M.Brzozowski,
M.E.Bjørnvad,
K.V.Andersen,
and
M.Schülein
(1998).
Structure of the Bacillus agaradherans family 5 endoglucanase at 1.6 A and its cellobiose complex at 2.0 A resolution.
|
| |
Biochemistry,
37,
1926-1932.
|
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PDB codes:
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I.L.Alberts,
K.Nadassy,
and
S.J.Wodak
(1998).
Analysis of zinc binding sites in protein crystal structures.
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| |
Protein Sci,
7,
1700-1716.
|
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V.Notenboom,
C.Birsan,
M.Nitz,
D.R.Rose,
R.A.Warren,
and
S.G.Withers
(1998).
Insights into transition state stabilization of the beta-1,4-glycosidase Cex by covalent intermediate accumulation in active site mutants.
|
| |
Nat Struct Biol,
5,
812-818.
|
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PDB code:
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B.Henrissat,
and
G.Davies
(1997).
Structural and sequence-based classification of glycoside hydrolases.
|
| |
Curr Opin Struct Biol,
7,
637-644.
|
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
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Where a reference describes a PDB structure, the PDB
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shown on the right.
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