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PDBsum entry 6cel
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Contents |
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* Residue conservation analysis
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Enzyme class:
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E.C.3.2.1.91
- cellulose 1,4-beta-cellobiosidase (non-reducing end).
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Reaction:
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Hydrolysis of 1,4-beta-D-glucosidic linkages in cellulose and cellotetraose, releasing cellobiose from the non-reducing ends of the chains.
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DOI no:
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J Mol Biol
275:309-325
(1998)
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PubMed id:
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High-resolution crystal structures reveal how a cellulose chain is bound in the 50 A long tunnel of cellobiohydrolase I from Trichoderma reesei.
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C.Divne,
J.Ståhlberg,
T.T.Teeri,
T.A.Jones.
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ABSTRACT
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Detailed information has been obtained, by means of protein X-ray
crystallography, on how a cellulose chain is bound in the cellulose-binding
tunnel of cellobiohydrolase I (CBHI), the major cellulase in the hydrolysis of
native, crystalline cellulose by the fungus Trichoderma reesei. Three
high-resolution crystal structures of different catalytically deficient mutants
of CBHI in complex with cellotetraose, cellopentaose and cellohexaose have been
refined at 1.9, 1.7 and 1.9 A resolution, respectively. The observed binding of
cellooligomers in the tunnel allowed unambiguous identification of ten
well-defined subsites for glucosyl units that span a length of approximately 50
A. All bound oligomers have the same directionality and orientation, and the
positions of the glucosyl units in each binding site agree remarkably well
between the different complexes. The binding mode observed here corresponds to
that expected during productive binding of a cellulose chain. The structures
support the hypothesis that hydrolysis by CBHI proceeds from the reducing
towards the non-reducing end of a cellulose chain, and they provide a structural
explanation for the observed distribution of initial hydrolysis products.
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Selected figure(s)
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Figure 1.
Figure 1. Schematic representation of the CBHI catalytic
domain with a cellooligomer bound in sites −7 to +2.
Secondary-structure elements are coloured as follows: β
strands, blue arrows; α helices, red spirals; loop regions,
yellow coils. The cellooligomer is shown in pink as a
ball-and-stick object. The illustration was created with
MOLSCRIPT (Kraulis, 1991).
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Figure 5.
Figure 5. Tryptophan residues from T. reesei CBHI (yellow)
and CBHII (red) aligned with respect to a single glucose
residue. Tryptophan-indole rings interacting with the more
hydrophobic β face a shown “above” the glucosyl unit, and
those interacting with the α face “below”.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1998,
275,
309-325)
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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G.T.Beckham,
Y.J.Bomble,
E.A.Bayer,
M.E.Himmel,
and
M.F.Crowley
(2011).
Applications of computational science for understanding enzymatic deconstruction of cellulose.
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Curr Opin Biotechnol,
22,
231-238.
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J.Jalak,
and
P.Väljamäe
(2010).
Mechanism of initial rapid rate retardation in cellobiohydrolase catalyzed cellulose hydrolysis.
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Biotechnol Bioeng,
106,
871-883.
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L.J.Yin,
S.T.Jiang,
S.H.Pon,
and
H.H.Lin
(2010).
Hydrolysis of Chlorella by Cellulomonas sp. YJ5 cellulases and its biofunctional properties.
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J Food Sci,
75,
H317-H323.
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N.Todaka,
C.M.Lopez,
T.Inoue,
K.Saita,
J.Maruyama,
M.Arioka,
K.Kitamoto,
T.Kudo,
and
S.Moriya
(2010).
Heterologous expression and characterization of an endoglucanase from a symbiotic protist of the lower termite, Reticulitermes speratus.
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Appl Biochem Biotechnol,
160,
1168-1178.
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O.Danot
(2010).
The inducer maltotriose binds in the central cavity of the tetratricopeptide-like sensor domain of MalT, a bacterial STAND transcription factor.
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Mol Microbiol,
77,
628-641.
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S.P.Voutilainen,
P.G.Murray,
M.G.Tuohy,
and
A.Koivula
(2010).
Expression of Talaromyces emersonii cellobiohydrolase Cel7A in Saccharomyces cerevisiae and rational mutagenesis to improve its thermostability and activity.
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Protein Eng Des Sel,
23,
69-79.
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C.L.Ting,
D.E.Makarov,
and
Z.G.Wang
(2009).
A kinetic model for the enzymatic action of cellulase.
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J Phys Chem B,
113,
4970-4977.
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H.Zakariassen,
B.B.Aam,
S.J.Horn,
K.M.Vårum,
M.Sørlie,
and
V.G.Eijsink
(2009).
Aromatic Residues in the Catalytic Center of Chitinase A from Serratia marcescens Affect Processivity, Enzyme Activity, and Biomass Converting Efficiency.
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J Biol Chem,
284,
10610-10617.
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M.Dashtban,
H.Schraft,
and
W.Qin
(2009).
Fungal bioconversion of lignocellulosic residues; opportunities & perspectives.
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Int J Biol Sci,
5,
578-595.
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M.Maki,
K.T.Leung,
and
W.Qin
(2009).
The prospects of cellulase-producing bacteria for the bioconversion of lignocellulosic biomass.
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Int J Biol Sci,
5,
500-516.
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R.Gupta,
and
Y.Y.Lee
(2009).
Mechanism of cellulase reaction on pure cellulosic substrates.
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Biotechnol Bioeng,
102,
1570-1581.
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R.Suzuki,
Z.Fujimoto,
S.Ito,
S.Kawahara,
S.Kaneko,
K.Taira,
T.Hasegawa,
and
A.Kuno
(2009).
Crystallographic snapshots of an entire reaction cycle for a retaining xylanase from Streptomyces olivaceoviridis E-86.
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J Biochem,
146,
61-70.
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PDB codes:
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S.P.Voutilainen,
H.Boer,
M.Alapuranen,
J.Jänis,
J.Vehmaanperä,
and
A.Koivula
(2009).
Improving the thermostability and activity of Melanocarpus albomyces cellobiohydrolase Cel7B.
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Appl Microbiol Biotechnol,
83,
261-272.
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A.Zen,
V.Carnevale,
A.M.Lesk,
and
C.Micheletti
(2008).
Correspondences between low-energy modes in enzymes: dynamics-based alignment of enzymatic functional families.
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Protein Sci,
17,
918-929.
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S.P.Voutilainen,
T.Puranen,
M.Siika-Aho,
A.Lappalainen,
M.Alapuranen,
J.Kallio,
S.Hooman,
L.Viikari,
J.Vehmaanperä,
and
A.Koivula
(2008).
Cloning, expression, and characterization of novel thermostable family 7 cellobiohydrolases.
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Biotechnol Bioeng,
101,
515-528.
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T.Parkkinen,
A.Koivula,
J.Vehmaanperä,
and
J.Rouvinen
(2008).
Crystal structures of Melanocarpus albomyces cellobiohydrolase Cel7B in complex with cello-oligomers show high flexibility in the substrate binding.
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Protein Sci,
17,
1383-1394.
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PDB codes:
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E.C.Stanca-Kaposta,
D.P.Gamblin,
J.Screen,
B.Liu,
L.C.Snoek,
B.G.Davis,
and
J.P.Simons
(2007).
Carbohydrate molecular recognition: a spectroscopic investigation of carbohydrate-aromatic interactions.
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Phys Chem Chem Phys,
9,
4444-4451.
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K.Igarashi,
M.Wada,
and
M.Samejima
(2007).
Activation of crystalline cellulose to cellulose III(I) results in efficient hydrolysis by cellobiohydrolase.
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FEBS J,
274,
1785-1792.
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T.Jeoh,
C.I.Ishizawa,
M.F.Davis,
M.E.Himmel,
W.S.Adney,
and
D.K.Johnson
(2007).
Cellulase digestibility of pretreated biomass is limited by cellulose accessibility.
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Biotechnol Bioeng,
98,
112-122.
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T.Parkkinen,
A.Koivula,
J.Vehmaanperä,
and
J.Rouvinen
(2007).
Preliminary X-ray analysis of cellobiohydrolase Cel7B from Melanocarpus albomyces.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
63,
754-757.
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J.Alvarado,
A.Ghosh,
T.Janovitz,
A.Jauregui,
M.S.Hasson,
and
D.A.Sanders
(2006).
Origin of exopolyphosphatase processivity: Fusion of an ASKHA phosphotransferase and a cyclic nucleotide phosphodiesterase homolog.
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Structure,
14,
1263-1272.
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PDB code:
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K.Igarashi,
M.Wada,
R.Hori,
and
M.Samejima
(2006).
Surface density of cellobiohydrolase on crystalline celluloses. A critical parameter to evaluate enzymatic kinetics at a solid-liquid interface.
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FEBS J,
273,
2869-2878.
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R.Stern,
and
M.J.Jedrzejas
(2006).
Hyaluronidases: their genomics, structures, and mechanisms of action.
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Chem Rev,
106,
818-839.
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S.J.Horn,
P.Sikorski,
J.B.Cederkvist,
G.Vaaje-Kolstad,
M.Sørlie,
B.Synstad,
G.Vriend,
K.M.Vårum,
and
V.G.Eijsink
(2006).
Costs and benefits of processivity in enzymatic degradation of recalcitrant polysaccharides.
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Proc Natl Acad Sci U S A,
103,
18089-18094.
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C.Mulakala,
and
P.J.Reilly
(2005).
Hypocrea jecorina (Trichoderma reesei) Cel7A as a molecular machine: A docking study.
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Proteins,
60,
598-605.
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C.Mulakala,
and
P.J.Reilly
(2005).
Force calculations in automated docking: enzyme-substrate interactions in Fusarium oxysporum Cel7B.
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Proteins,
61,
590-596.
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M.J.Jedrzejas,
and
R.Stern
(2005).
Structures of vertebrate hyaluronidases and their unique enzymatic mechanism of hydrolysis.
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Proteins,
61,
227-238.
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M.Yamada,
Y.Amano,
E.Horikawa,
K.Nozaki,
and
T.Kanda
(2005).
Mode of action of cellulases on dyed cotton with a reactive dye.
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Biosci Biotechnol Biochem,
69,
45-50.
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S.A.Douthit,
M.Dlakic,
D.E.Ohman,
and
M.J.Franklin
(2005).
Epimerase active domain of Pseudomonas aeruginosa AlgG, a protein that contains a right-handed beta-helix.
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J Bacteriol,
187,
4573-4583.
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S.Fushinobu,
M.Hidaka,
Y.Honda,
T.Wakagi,
H.Shoun,
and
M.Kitaoka
(2005).
Structural basis for the specificity of the reducing end xylose-releasing exo-oligoxylanase from Bacillus halodurans C-125.
|
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J Biol Chem,
280,
17180-17186.
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PDB codes:
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W.Ubhayasekera,
I.G.Muñoz,
A.Vasella,
J.Ståhlberg,
and
S.L.Mowbray
(2005).
Structures of Phanerochaete chrysosporium Cel7D in complex with product and inhibitors.
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FEBS J,
272,
1952-1964.
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PDB codes:
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Z.Dai,
B.S.Hooker,
R.D.Quesenberry,
and
S.R.Thomas
(2005).
Optimization of Acidothermus cellulolyticus endoglucanase (E1) production in transgenic tobacco plants by transcriptional, post-transcription and post-translational modification.
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Transgenic Res,
14,
627-643.
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A.Grassick,
P.G.Murray,
R.Thompson,
C.M.Collins,
L.Byrnes,
G.Birrane,
T.M.Higgins,
and
M.G.Tuohy
(2004).
Three-dimensional structure of a thermostable native cellobiohydrolase, CBH IB, and molecular characterization of the cel7 gene from the filamentous fungus, Talaromyces emersonii.
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Eur J Biochem,
271,
4495-4506.
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PDB code:
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A.Miyanaga,
T.Koseki,
H.Matsuzawa,
T.Wakagi,
H.Shoun,
and
S.Fushinobu
(2004).
Crystal structure of a family 54 alpha-L-arabinofuranosidase reveals a novel carbohydrate-binding module that can bind arabinose.
|
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J Biol Chem,
279,
44907-44914.
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PDB codes:
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M.Gruno,
P.Väljamäe,
G.Pettersson,
and
G.Johansson
(2004).
Inhibition of the Trichoderma reesei cellulases by cellobiose is strongly dependent on the nature of the substrate.
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Biotechnol Bioeng,
86,
503-511.
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A.Grassick,
G.Birrane,
M.Tuohy,
P.Murray,
and
T.Higgins
(2003).
Crystallization and preliminary crystallographic analysis of the catalytic domain cellobiohydrolase I from Talaromyces emersonii.
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Acta Crystallogr D Biol Crystallogr,
59,
1283-1284.
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A.M.Larsson,
R.Andersson,
J.Ståhlberg,
L.Kenne,
and
T.A.Jones
(2003).
Dextranase from Penicillium minioluteum: reaction course, crystal structure, and product complex.
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Structure,
11,
1111-1121.
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PDB codes:
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H.Boer,
and
A.Koivula
(2003).
The relationship between thermal stability and pH optimum studied with wild-type and mutant Trichoderma reesei cellobiohydrolase Cel7A.
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Eur J Biochem,
270,
841-848.
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H.Jung,
D.B.Wilson,
and
L.P.Walker
(2003).
Binding and reversibility of Thermobifida fusca Cel5A, Cel6B, and Cel48A and their respective catalytic domains to bacterial microcrystalline cellulose.
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Biotechnol Bioeng,
84,
151-159.
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I.G.Muñoz,
S.L.Mowbray,
and
J.Ståhlberg
(2003).
The catalytic module of Cel7D from Phanerochaete chrysosporium as a chiral selector: structural studies of its complex with the beta blocker (R)-propranolol.
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Acta Crystallogr D Biol Crystallogr,
59,
637-643.
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PDB code:
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P.Väljamäe,
K.Kipper,
G.Pettersson,
and
G.Johansson
(2003).
Synergistic cellulose hydrolysis can be described in terms of fractal-like kinetics.
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Biotechnol Bioeng,
84,
254-257.
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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.
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Biochemistry,
41,
11134-11142.
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PDB codes:
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I.Kwon,
K.Ekino,
T.Oka,
M.Goto,
and
K.Furukawa
(2002).
Effects of amino acid alterations on the transglycosylation reaction of endoglucanase I from Trichoderma viride HK-75.
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Biosci Biotechnol Biochem,
66,
110-116.
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A.Varrot,
M.Schülein,
S.Fruchard,
H.Driguez,
and
G.J.Davies
(2001).
Atomic resolution structure of endoglucanase Cel5A in complex with methyl 4,4II,4III,4IV-tetrathio-alpha-cellopentoside highlights the alternative binding modes targeted by substrate mimics.
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Acta Crystallogr D Biol Crystallogr,
57,
1739-1742.
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PDB code:
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C.Boisset,
C.Pétrequin,
H.Chanzy,
B.Henrissat,
and
M.Schülein
(2001).
Optimized mixtures of recombinant Humicola insolens cellulases for the biodegradation of crystalline cellulose.
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Biotechnol Bioeng,
72,
339-345.
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G.Michel,
L.Chantalat,
E.Duee,
T.Barbeyron,
B.Henrissat,
B.Kloareg,
and
O.Dideberg
(2001).
The kappa-carrageenase of P. carrageenovora features a tunnel-shaped active site: a novel insight in the evolution of Clan-B glycoside hydrolases.
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Structure,
9,
513-525.
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PDB code:
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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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C.Boisset,
C.Fraschini,
M.Schülein,
B.Henrissat,
and
H.Chanzy
(2000).
Imaging the enzymatic digestion of bacterial cellulose ribbons reveals the endo character of the cellobiohydrolase Cel6A from Humicola insolens and its mode of synergy with cellobiohydrolase Cel7A.
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Appl Environ Microbiol,
66,
1444-1452.
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G.Parsiegla,
C.Reverbel-Leroy,
C.Tardif,
J.P.Belaich,
H.Driguez,
and
R.Haser
(2000).
Crystal structures of the cellulase Cel48F in complex with inhibitors and substrates give insights into its processive action.
|
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Biochemistry,
39,
11238-11246.
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PDB codes:
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H.Boer,
T.T.Teeri,
and
A.Koivula
(2000).
Characterization of Trichoderma reesei cellobiohydrolase Cel7A secreted from Pichia pastoris using two different promoters.
|
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Biotechnol Bioeng,
69,
486-494.
|
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L.L.Leggio,
J.Jenkins,
G.W.Harris,
and
R.W.Pickersgill
(2000).
X-ray crystallographic study of xylopentaose binding to Pseudomonas fluorescens xylanase A.
|
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Proteins,
41,
362-373.
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PDB code:
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S.R.Herron,
J.A.Benen,
R.D.Scavetta,
J.Visser,
and
F.Jurnak
(2000).
Structure and function of pectic enzymes: virulence factors of plant pathogens.
|
| |
Proc Natl Acad Sci U S A,
97,
8762-8769.
|
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S.Zhang,
D.C.Irwin,
and
D.B.Wilson
(2000).
Site-directed mutation of noncatalytic residues of Thermobifida fusca exocellulase Cel6B.
|
| |
Eur J Biochem,
267,
3101-3115.
|
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A.Varrot,
M.Schülein,
and
G.J.Davies
(1999).
Structural changes of the active site tunnel of Humicola insolens cellobiohydrolase, Cel6A, upon oligosaccharide binding.
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| |
Biochemistry,
38,
8884-8891.
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PDB code:
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D.J.Cosgrove,
and
D.J.Cosgrove
(1999).
Enzymes and other agents that enhance cell wall extensibility.
|
| |
Annu Rev Plant Physiol Plant Mol Biol,
50,
391-417.
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G.Henriksson,
A.Nutt,
H.Henriksson,
B.Pettersson,
J.Ståhlberg,
G.Johansson,
and
G.Pettersson
(1999).
Endoglucanase 28 (Cel12A), a new Phanerochaete chrysosporium cellulase.
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| |
Eur J Biochem,
259,
88-95.
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|
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H.Palonen,
M.Tenkanen,
and
M.Linder
(1999).
Dynamic interaction of Trichoderma reesei cellobiohydrolases Cel6A and Cel7A and cellulose at equilibrium and during hydrolysis.
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| |
Appl Environ Microbiol,
65,
5229-5233.
|
|
|
|
|
|
|
J.Zou,
G.J.Kleywegt,
J.Ståhlberg,
H.Driguez,
W.Nerinckx,
M.Claeyssens,
A.Koivula,
T.T.Teeri,
and
T.A.Jones
(1999).
Crystallographic evidence for substrate ring distortion and protein conformational changes during catalysis in cellobiohydrolase Ce16A from trichoderma reesei.
|
| |
Structure,
7,
1035-1045.
|
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|
PDB codes:
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M.Hedeland,
S.Holmin,
M.Nygård,
and
C.Pettersson
(1999).
Chromatographic evaluation of structure selective and enantioselective retention of amines and acids on cellobiohydrolase I wild type and its mutant D214N.
|
| |
J Chromatogr A,
864,
1.
|
|
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|
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N.Hamada,
N.Fuse,
M.Shimosaka,
R.Kodaira,
Y.Amano,
T.Kanda,
and
M.Okazaki
(1999).
Cloning and characterization of a new exo-cellulase gene, cel3, in Irpex lacteus.
|
| |
FEMS Microbiol Lett,
172,
231-237.
|
|
|
|
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|
P.Väljamäe,
V.Sild,
A.Nutt,
G.Pettersson,
and
G.Johansson
(1999).
Acid hydrolysis of bacterial cellulose reveals different modes of synergistic action between cellobiohydrolase I and endoglucanase I.
|
| |
Eur J Biochem,
266,
327-334.
|
|
|
|
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|
E.A.Bayer,
H.Chanzy,
R.Lamed,
and
Y.Shoham
(1998).
Cellulose, cellulases and cellulosomes.
|
| |
Curr Opin Struct Biol,
8,
548-557.
|
|
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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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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
