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PDBsum entry 1tml
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* Residue conservation analysis
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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
32:9906-9916
(1993)
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PubMed id:
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Crystal structure of the catalytic domain of a thermophilic endocellulase.
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M.Spezio,
D.B.Wilson,
P.A.Karplus.
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ABSTRACT
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One way to improve the economic feasibility of biomass conversion is to enhance
the catalytic efficiency of cellulases through protein engineering. This
requires that high-resolution structures of cellulases be available. Here we
present the structure of E2cd, the catalytic domain of the thermophilic
endocellulase E2 from Thermomonospora fusca, as determined by X-ray
crystallography. The structure was solved by multiple isomorphous replacement at
2.6-A resolution and has been refined at 1.8-A resolution to an R-value of 18.4%
for all reflections between 10- and 1.8-A resolution. The fold of E2cd is based
on an unusual parallel beta-barrel and is equivalent to the fold determined for
the catalytic domain of cellobiohydrolase II, an exocellulase from Trichoderma
reesei [Rouvinen et al. (1990) Science 249, 380-385]. The active site cleft of
the enzyme, approximately 11 A deep and running the entire length of the
molecule, is seen to be completely free for ligand binding in the crystal. A
2.2-A resolution analysis of crystals of E2cd complexed with cellobiose, an
inhibitor, shows how cellobiose binds in the active site and interacts with
several residues which line the cleft. Catalytic roles are suggested for three
aspartic acid residues at the active site. A comparison of the E2cd and CBHIIcd
structures reveals a large difference in their active site accessibilities and
supports the hypothesis that the main difference between endo- and exocellulases
is the degree to which their active sites are accessible to substrate.
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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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D.W.Cockburn,
and
A.J.Clarke
(2011).
Modulating the pH-activity profile of cellulase A from Cellulomonas fimi by replacement of surface residues.
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Protein Eng Des Sel,
24,
429-437.
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T.V.Vuong,
and
D.B.Wilson
(2009).
The absence of an identifiable single catalytic base residue in Thermobifida fusca exocellulase Cel6B.
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FEBS J,
276,
3837-3845.
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T.V.Vuong,
and
D.B.Wilson
(2009).
Processivity, synergism, and substrate specificity of Thermobifida fusca Cel6B.
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Appl Environ Microbiol,
75,
6655-6661.
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Y.Kurakata,
T.Tonozuka,
Y.Liu,
S.Kaneko,
A.Nishikawa,
K.Fukuda,
and
M.Yoshida
(2009).
Heterologous expression, crystallization and preliminary X-ray characterization of CcCel6C, a glycoside hydrolase family 6 enzyme from the basidiomycete Coprinopsis cinerea.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
65,
140-143.
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F.Moser,
D.Irwin,
S.Chen,
and
D.B.Wilson
(2008).
Regulation and characterization of Thermobifida fusca carbohydrate-binding module proteins E7 and E8.
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Biotechnol Bioeng,
100,
1066-1077.
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L.G.Ljungdahl
(2008).
The cellulase/hemicellulase system of the anaerobic fungus Orpinomyces PC-2 and aspects of its applied use.
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Ann N Y Acad Sci,
1125,
308-321.
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Y.Li,
and
D.B.Wilson
(2008).
Chitin binding by Thermobifida fusca cellulase catalytic domains.
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Biotechnol Bioeng,
100,
644-652.
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B.Mertz,
A.D.Hill,
C.Mulakala,
and
P.J.Reilly
(2007).
Automated docking to explore subsite binding by glycoside hydrolase family 6 cellobiohydrolases and endoglucanases.
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Biopolymers,
87,
249-260.
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T.Nakamura,
S.Mine,
Y.Hagihara,
K.Ishikawa,
and
K.Uegaki
(2007).
Structure of the catalytic domain of the hyperthermophilic chitinase from Pyrococcus furiosus.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
63,
7.
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PDB code:
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A.Dickmanns,
M.Ballschmiter,
W.Liebl,
and
R.Ficner
(2006).
Structure of the novel alpha-amylase AmyC from Thermotoga maritima.
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Acta Crystallogr D Biol Crystallogr,
62,
262-270.
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PDB code:
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S.R.Hughes,
S.B.Riedmuller,
J.A.Mertens,
X.L.Li,
K.M.Bischoff,
N.Qureshi,
M.A.Cotta,
and
P.J.Farrelly
(2006).
High-throughput screening of cellulase F mutants from multiplexed plasmid sets using an automated plate assay on a functional proteomic robotic workcell.
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Proteome Sci,
4,
10.
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A.Varrot,
S.Leydier,
G.Pell,
J.M.Macdonald,
R.V.Stick,
B.Henrissat,
H.J.Gilbert,
and
G.J.Davies
(2005).
Mycobacterium tuberculosis strains possess functional cellulases.
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J Biol Chem,
280,
20181-20184.
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PDB codes:
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B.Mertz,
R.S.Kuczenski,
R.T.Larsen,
A.D.Hill,
and
P.J.Reilly
(2005).
Phylogenetic analysis of family 6 glycoside hydrolases.
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Biopolymers,
79,
197-206.
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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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A.Teplyakov,
G.Obmolova,
P.P.Khil,
A.J.Howard,
R.D.Camerini-Otero,
and
G.L.Gilliland
(2003).
Crystal structure of the Escherichia coli YcdX protein reveals a trinuclear zinc active site.
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Proteins,
51,
315-318.
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PDB codes:
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H.Imamura,
S.Fushinobu,
M.Yamamoto,
T.Kumasaka,
B.S.Jeon,
T.Wakagi,
and
H.Matsuzawa
(2003).
Crystal structures of 4-alpha-glucanotransferase from Thermococcus litoralis and its complex with an inhibitor.
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J Biol Chem,
278,
19378-19386.
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PDB codes:
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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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A.Varrot,
T.P.Frandsen,
H.Driguez,
and
G.J.Davies
(2002).
Structure of the Humicola insolens cellobiohydrolase Cel6A D416A mutant in complex with a non-hydrolysable substrate analogue, methyl cellobiosyl-4-thio-beta-cellobioside, at 1.9 A.
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Acta Crystallogr D Biol Crystallogr,
58,
2201-2204.
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PDB code:
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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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C.C.Lee,
D.W.Wong,
and
G.H.Robertson
(2001).
Cloning and characterization of two cellulase genes from Lentinula edodes.
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FEMS Microbiol Lett,
205,
355-360.
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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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D.M.van Aalten,
B.Synstad,
M.B.Brurberg,
E.Hough,
B.W.Riise,
V.G.Eijsink,
and
R.K.Wierenga
(2000).
Structure of a two-domain chitotriosidase from Serratia marcescens at 1.9-A resolution.
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Proc Natl Acad Sci U S A,
97,
5842-5847.
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PDB code:
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S.Zhang,
B.K.Barr,
and
D.B.Wilson
(2000).
Effects of noncatalytic residue mutations on substrate specificity and ligand binding of Thermobifida fusca endocellulase cel6A.
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Eur J Biochem,
267,
244-252.
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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.
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Eur J Biochem,
267,
3101-3115.
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T.Y.Wong,
L.A.Preston,
and
N.L.Schiller
(2000).
ALGINATE LYASE: review of major sources and enzyme characteristics, structure-function analysis, biological roles, and applications.
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Annu Rev Microbiol,
54,
289-340.
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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.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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B.M.Beadle,
W.A.Baase,
D.B.Wilson,
N.R.Gilkes,
and
B.K.Shoichet
(1999).
Comparing the thermodynamic stabilities of a related thermophilic and mesophilic enzyme.
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Biochemistry,
38,
2570-2576.
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H.D.Ly,
and
S.G.Withers
(1999).
Mutagenesis of glycosidases.
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Annu Rev Biochem,
68,
487-522.
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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.
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Structure,
7,
1035-1045.
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PDB codes:
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L.Lo Leggio,
S.Kalogiannis,
M.K.Bhat,
and
R.W.Pickersgill
(1999).
High resolution structure and sequence of T. aurantiacus xylanase I: implications for the evolution of thermostability in family 10 xylanases and enzymes with (beta)alpha-barrel architecture.
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Proteins,
36,
295-306.
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PDB codes:
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S.Kawaminami,
H.Takahashi,
S.Ito,
Y.Arata,
and
I.Shimada
(1999).
A multinuclear NMR study of the active site of an endoglucanase from a strain of Bacillus. Use of Trp residues as structural probes.
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J Biol Chem,
274,
19823-19828.
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S.Zhang,
D.E.Wolfgang,
and
D.B.Wilson
(1999).
Substrate heterogeneity causes the nonlinear kinetics of insoluble cellulose hydrolysis.
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Biotechnol Bioeng,
66,
35-41.
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B.K.Barr,
D.E.Wolfgang,
K.Piens,
M.Claeyssens,
and
D.B.Wilson
(1998).
Active-site binding of glycosides by Thermomonospora fusca endocellulase E2.
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Biochemistry,
37,
9220-9229.
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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.
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EMBO J,
17,
5551-5562.
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PDB code:
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N.A.Spiridonov,
and
D.B.Wilson
(1998).
Regulation of biosynthesis of individual cellulases in Thermomonospora fusca.
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J Bacteriol,
180,
3529-3532.
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S.E.Brenner,
C.Chothia,
and
T.J.Hubbard
(1998).
Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships.
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Proc Natl Acad Sci U S A,
95,
6073-6078.
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J.Sakon,
D.Irwin,
D.B.Wilson,
and
P.A.Karplus
(1997).
Structure and mechanism of endo/exocellulase E4 from Thermomonospora fusca.
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Nat Struct Biol,
4,
810-818.
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PDB codes:
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M.E.Himmel,
P.A.Karplus,
J.Sakon,
W.S.Adney,
J.O.Baker,
and
S.R.Thomas
(1997).
Polysaccharide hydrolase folds diversity of structure and convergence of function.
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Appl Biochem Biotechnol,
63,
315-325.
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M.K.Bhat,
and
S.Bhat
(1997).
Cellulose degrading enzymes and their potential industrial applications.
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Biotechnol Adv,
15,
583-620.
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X.L.Li,
H.Chen,
and
L.G.Ljungdahl
(1997).
Two cellulases, CelA and CelC, from the polycentric anaerobic fungus Orpinomyces strain PC-2 contain N-terminal docking domains for a cellulase-hemicellulase complex.
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Appl Environ Microbiol,
63,
4721-4728.
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B.K.Barr,
Y.L.Hsieh,
B.Ganem,
and
D.B.Wilson
(1996).
Identification of two functionally different classes of exocellulases.
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Biochemistry,
35,
586-592.
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J.Sakon,
W.S.Adney,
M.E.Himmel,
S.R.Thomas,
and
P.A.Karplus
(1996).
Crystal structure of thermostable family 5 endocellulase E1 from Acidothermus cellulolyticus in complex with cellotetraose.
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Biochemistry,
35,
10648-10660.
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PDB code:
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K.M.Kleman-Leyer,
M.Siika-Aho,
T.T.Teeri,
and
T.K.Kirk
(1996).
The Cellulases Endoglucanase I and Cellobiohydrolase II of Trichoderma reesei Act Synergistically To Solubilize Native Cotton Cellulose but Not To Decrease Its Molecular Size.
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Appl Environ Microbiol,
62,
2883-2887.
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P.M.Alzari,
H.Souchon,
and
R.Dominguez
(1996).
The crystal structure of endoglucanase CelA, a family 8 glycosyl hydrolase from Clostridium thermocellum.
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Structure,
4,
265-275.
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PDB code:
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P.Tomme,
E.Kwan,
N.R.Gilkes,
D.G.Kilburn,
and
R.A.Warren
(1996).
Characterization of CenC, an enzyme from Cellulomonas fimi with both endo- and exoglucanase activities.
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J Bacteriol,
178,
4216-4223.
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S.Janecek
(1996).
Invariant glycines and prolines flanking in loops the strand beta 2 of various (alpha/beta)8-barrel enzymes: a hidden homology?
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Protein Sci,
5,
1136-1143.
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A.H.West,
S.Djordjevic,
E.Martinez-Hackert,
and
A.M.Stock
(1995).
Purification, crystallization, and preliminary X-ray diffraction analyses of the bacterial chemotaxis receptor modifying enzymes.
|
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Proteins,
21,
345-350.
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A.Meinke,
H.G.Damude,
P.Tomme,
E.Kwan,
D.G.Kilburn,
R.C.Miller,
R.A.Warren,
and
N.R.Gilkes
(1995).
Enhancement of the endo-beta-1,4-glucanase activity of an exocellobiohydrolase by deletion of a surface loop.
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J Biol Chem,
270,
4383-4386.
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D.W.Heinz,
M.Ryan,
T.L.Bullock,
and
O.H.Griffith
(1995).
Crystal structure of the phosphatidylinositol-specific phospholipase C from Bacillus cereus in complex with myo-inositol.
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EMBO J,
14,
3855-3863.
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PDB codes:
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G.Davies,
and
B.Henrissat
(1995).
Structures and mechanisms of glycosyl hydrolases.
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Structure,
3,
853-859.
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M.Hahn,
O.Olsen,
O.Politz,
R.Borriss,
and
U.Heinemann
(1995).
Crystal structure and site-directed mutagenesis of Bacillus macerans endo-1,3-1,4-beta-glucanase.
|
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J Biol Chem,
270,
3081-3088.
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PDB code:
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V.Ducros,
M.Czjzek,
A.Belaich,
C.Gaudin,
H.P.Fierobe,
J.P.Belaich,
G.J.Davies,
and
R.Haser
(1995).
Crystal structure of the catalytic domain of a bacterial cellulase belonging to family 5.
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Structure,
3,
939-949.
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PDB code:
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A.Meinke,
N.R.Gilkes,
E.Kwan,
D.G.Kilburn,
R.A.Warren,
and
R.C.Miller
(1994).
Cellobiohydrolase A (CbhA) from the cellulolytic bacterium Cellulomonas fimi is a beta-1,4-exocellobiohydrolase analogous to Trichoderma reesei CBH II.
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Mol Microbiol,
12,
413-422.
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J.D.McCarter,
and
S.G.Withers
(1994).
Mechanisms of enzymatic glycoside hydrolysis.
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Curr Opin Struct Biol,
4,
885-892.
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R.Dominguez,
H.Souchon,
and
P.M.Alzari
(1994).
Characterization of two crystal forms of Clostridium thermocellum endoglucanase CelC.
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Proteins,
19,
158-160.
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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
