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PDBsum entry 1f9d
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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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Crystal structure of the cellulase cel48f from c. Cellulolyticum in complex with cellotetraose
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Structure:
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Endo-1,4-beta-glucanase f. Chain: a. Fragment: catalytic module. Synonym: cellulase cel48f, cellulase f, egccf. Engineered: yes. Mutation: yes
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Source:
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Clostridium cellulolyticum. Organism_taxid: 1521. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_organelle: bl21 de3.
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Resolution:
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2.30Å
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R-factor:
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0.151
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R-free:
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0.189
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Authors:
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G.Parsiegla,C.Reverbel-Leroy,C.Tardif,J.P.Belaich,H.Driguez,R.Haser
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Key ref:
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G.Parsiegla
et al.
(2000).
Crystal structures of the cellulase Cel48F in complex with inhibitors and substrates give insights into its processive action.
Biochemistry,
39,
11238-11246.
PubMed id:
DOI:
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Date:
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10-Jul-00
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Release date:
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02-Aug-00
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PROCHECK
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Headers
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References
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P37698
(GUNF_CLOCE) -
Endoglucanase F from Ruminiclostridium cellulolyticum (strain ATCC 35319 / DSM 5812 / JCM 6584 / H10)
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Seq:
Struc:
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722 a.a.
629 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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*
PDB and UniProt seqs differ
at 1 residue position (black
cross)
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Enzyme class:
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E.C.3.2.1.4
- cellulase.
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Reaction:
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Endohydrolysis of 1,4-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans.
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DOI no:
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Biochemistry
39:11238-11246
(2000)
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PubMed id:
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Crystal structures of the cellulase Cel48F in complex with inhibitors and substrates give insights into its processive action.
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G.Parsiegla,
C.Reverbel-Leroy,
C.Tardif,
J.P.Belaich,
H.Driguez,
R.Haser.
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ABSTRACT
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Cellulase Cel48F from Clostridium cellulolyticum was described as a processive
endo-cellulase. The active site is composed of a 25 A long tunnel which is
followed by an open cleft. During the processive action, the cellulose substrate
has to slide through the tunnel to continuously supply the leaving group site
with sugar residues after the catalytic cleavage. To study this processive
action in the tunnel, the native catalytic module of Cel48F and the inactive
mutant E55Q, have been cocrystallized with cellobiitol, two thio-oligosaccharide
inhibitors (PIPS-IG3 and IG4) and the cello-oligosaccharides cellobiose,
-tetraose and -hexaose. Seven sub-sites in the tunnel section of the active
center could be identified and three of the four previously reported sub-sites
in the open cleft section were reconfirmed. The sub-sites observed for the
thio-oligosaccharide inhibitors and oligosaccharides, respectively, were located
at two different positions in the tunnel corresponding to a shift in the chain
direction of about a half sugar subunit. These two positions have different
patterns of stacking interactions with aromatic residues present in the tunnel.
Multiple patterns are not observed in nonprocessive endo-cellulases, where only
one sugar position is favored by aromatic stacking. It is therefore proposed
that the aromatic residues serve as lubricating agents to reduce the sliding
barrier in the processive action.
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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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M.Saharay,
H.Guo,
and
J.C.Smith
(2010).
Catalytic mechanism of cellulose degradation by a cellobiohydrolase, CelS.
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PLoS One,
5,
e12947.
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T.C.Freeman,
and
W.C.Wimley
(2010).
A highly accurate statistical approach for the prediction of transmembrane beta-barrels.
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Bioinformatics,
26,
1965-1974.
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T.Ishida,
S.Fushinobu,
R.Kawai,
M.Kitaoka,
K.Igarashi,
and
M.Samejima
(2009).
Crystal structure of glycoside hydrolase family 55 {beta}-1,3-glucanase from the basidiomycete Phanerochaete chrysosporium.
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J Biol Chem,
284,
10100-10109.
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PDB codes:
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C.D.Putnam,
M.Hammel,
G.L.Hura,
and
J.A.Tainer
(2007).
X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution.
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Q Rev Biophys,
40,
191-285.
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M.Nagae,
A.Tsuchiya,
T.Katayama,
K.Yamamoto,
S.Wakatsuki,
and
R.Kato
(2007).
Structural basis of the catalytic reaction mechanism of novel 1,2-alpha-L-fucosidase from Bifidobacterium bifidum.
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J Biol Chem,
282,
18497-18509.
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PDB codes:
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C.Regni,
A.M.Schramm,
and
L.J.Beamer
(2006).
The reaction of phosphohexomutase from Pseudomonas aeruginosa: structural insights into a simple processive enzyme.
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J Biol Chem,
281,
15564-15571.
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PDB codes:
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M.Desvaux
(2006).
Unravelling carbon metabolism in anaerobic cellulolytic bacteria.
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Biotechnol Prog,
22,
1229-1238.
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A.L.Demain,
M.Newcomb,
and
J.H.Wu
(2005).
Cellulase, clostridia, and ethanol.
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Microbiol Mol Biol Rev,
69,
124-154.
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J.Jänis,
J.Hakanpää,
N.Hakulinen,
F.M.Ibatullin,
A.Hoxha,
P.J.Derrick,
J.Rouvinen,
and
P.Vainiotalo
(2005).
Determination of thioxylo-oligosaccharide binding to family 11 xylanases using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry and X-ray crystallography.
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FEBS J,
272,
2317-2333.
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PDB code:
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M.Desvaux
(2005).
Clostridium cellulolyticum: model organism of mesophilic cellulolytic clostridia.
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FEMS Microbiol Rev,
29,
741-764.
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D.B.Wilson
(2004).
Studies of Thermobifida fusca plant cell wall degrading enzymes.
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Chem Rec,
4,
72-82.
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E.Devillard,
D.B.Goodheart,
S.K.Karnati,
E.A.Bayer,
R.Lamed,
J.Miron,
K.E.Nelson,
and
M.Morrison
(2004).
Ruminococcus albus 8 mutants defective in cellulose degradation are deficient in two processive endocellulases, Cel48A and Cel9B, both of which possess a novel modular architecture.
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J Bacteriol,
186,
136-145.
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H.Maamar,
O.Valette,
H.P.Fierobe,
A.Bélaich,
J.P.Bélaich,
and
C.Tardif
(2004).
Cellulolysis is severely affected in Clostridium cellulolyticum strain cipCMut1.
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Mol Microbiol,
51,
589-598.
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T.Itoh,
S.Akao,
W.Hashimoto,
B.Mikami,
and
K.Murata
(2004).
Crystal structure of unsaturated glucuronyl hydrolase, responsible for the degradation of glycosaminoglycan, from Bacillus sp. GL1 at 1.8 A resolution.
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J Biol Chem,
279,
31804-31812.
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PDB code:
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A.Varrot,
T.P.Frandsen,
I.von Ossowski,
V.Boyer,
S.Cottaz,
H.Driguez,
M.Schülein,
and
G.J.Davies
(2003).
Structural basis for ligand binding and processivity in cellobiohydrolase Cel6A from Humicola insolens.
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Structure,
11,
855-864.
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PDB codes:
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D.Mandelman,
A.Belaich,
J.P.Belaich,
N.Aghajari,
H.Driguez,
and
R.Haser
(2003).
X-Ray crystal structure of the multidomain endoglucanase Cel9G from Clostridium cellulolyticum complexed with natural and synthetic cello-oligosaccharides.
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J Bacteriol,
185,
4127-4135.
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PDB codes:
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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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K.Murashima,
A.Kosugi,
and
R.H.Doi
(2002).
Synergistic effects on crystalline cellulose degradation between cellulosomal cellulases from Clostridium cellulovorans.
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J Bacteriol,
184,
5088-5095.
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L.R.Lynd,
P.J.Weimer,
W.H.van Zyl,
and
I.S.Pretorius
(2002).
Microbial cellulose utilization: fundamentals and biotechnology.
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Microbiol Mol Biol Rev,
66,
506.
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M.Hrmova,
T.Imai,
S.J.Rutten,
J.K.Fairweather,
L.Pelosi,
V.Bulone,
H.Driguez,
and
G.B.Fincher
(2002).
Mutated barley (1,3)-beta-D-glucan endohydrolases synthesize crystalline (1,3)-beta-D-glucans.
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J Biol Chem,
277,
30102-30111.
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W.A.Breyer,
and
B.W.Matthews
(2001).
A structural basis for processivity.
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Protein Sci,
10,
1699-1711.
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W.Huang,
L.Boju,
L.Tkalec,
H.Su,
H.O.Yang,
N.S.Gunay,
R.J.Linhardt,
Y.S.Kim,
A.Matte,
and
M.Cygler
(2001).
Active site of chondroitin AC lyase revealed by the structure of enzyme-oligosaccharide complexes and mutagenesis.
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Biochemistry,
40,
2359-2372.
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PDB codes:
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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
