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PDBsum entry 1ulp
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Cellulose degradation
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PDB id
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1ulp
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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
35:14381-14394
(1996)
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PubMed id:
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Structure of the N-terminal cellulose-binding domain of Cellulomonas fimi CenC determined by nuclear magnetic resonance spectroscopy.
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P.E.Johnson,
M.D.Joshi,
P.Tomme,
D.G.Kilburn,
L.P.McIntosh.
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ABSTRACT
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Multidimensional heteronuclear nuclear magnetic resonance (NMR) spectroscopy was
used to determine the tertiary structure of the 152 amino acid N-terminal
cellulose-binding domain from Cellulomonas fimi 1,4-beta-glucanase CenC (CBDN1).
CBDN1 was studied in the presence of saturating concentrations of cellotetraose,
but due to spectral overlap, the oligosaccharide was not included in the
structure calculations. A total of 1705 interproton nuclear Overhauser effect
(NOE), 56 phi, 88 psi, 42 chi 1, 9 chi 2 dihedral angle, and 88 hydrogen-bond
restraints were used to calculate 25 final structures. These structures have a
rmsd from the average of 0.79 +/- 0.11 A for all backbone atoms excluding
disordered termini and 0.44 +/- 0.05 A for residues with regular secondary
structures. CBDN1 is composed of 10 beta-strands, folded into two antiparallel
beta-sheets with the topology of a jelly-roll beta-sandwich. The strands forming
the face of the protein previously determined by chemical shift perturbations to
be responsible for cellooligosaccharide binding [Johnson, P. E., Tomme, P.,
Joshi, M. D., & McIntosh, L. P. (1996) Biochemistry 35, 13895-13906] are
shorter than those forming the opposite side of the protein. This results in a
5-stranded binding cleft, containing a central strip of hydrophobic residues
that is flanked on both sides by polar hydrogen-bonding groups. The presence of
this cleft provides a structural explanation for the unique selectivity of CBDN1
for amorphous cellulose and other soluble oligosaccharides and the lack of
binding to crystalline cellulose. The tertiary structure of CBDN1 is strikingly
similar to that of the bacterial 1,3-1,4-beta-glucanases, as well as other
sugar-binding proteins with jelly-roll folds.
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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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C.A.Dodson,
N.Ferguson,
T.J.Rutherford,
C.M.Johnson,
and
A.R.Fersht
(2010).
Engineering a two-helix bundle protein for folding studies.
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Protein Eng Des Sel,
23,
357-364.
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PDB code:
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Y.M.Cheng,
T.Y.Hong,
C.C.Liu,
and
M.Meng
(2009).
Cloning and functional characterization of a complex endo-beta-1,3-glucanase from Paenibacillus sp.
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Appl Microbiol Biotechnol,
81,
1051-1061.
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PDB codes:
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C.R.Pigott,
and
D.J.Ellar
(2007).
Role of receptors in Bacillus thuringiensis crystal toxin activity.
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Microbiol Mol Biol Rev,
71,
255-281.
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A.Roberts,
J.G.Pelton,
and
D.E.Wemmer
(2006).
Structural studies of MJ1529, an O6-methylguanine-DNA methyltransferase.
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Magn Reson Chem,
44,
S71-S82.
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PDB code:
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P.Boonserm,
M.Mo,
C.Angsuthanasombat,
and
J.Lescar
(2006).
Structure of the functional form of the mosquito larvicidal Cry4Aa toxin from Bacillus thuringiensis at a 2.8-angstrom resolution.
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J Bacteriol,
188,
3391-3401.
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PDB code:
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H.Ichinose,
M.Yoshida,
T.Kotake,
A.Kuno,
K.Igarashi,
Y.Tsumuraya,
M.Samejima,
J.Hirabayashi,
H.Kobayashi,
and
S.Kaneko
(2005).
An exo-beta-1,3-galactanase having a novel beta-1,3-galactan-binding module from Phanerochaete chrysosporium.
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J Biol Chem,
280,
25820-25829.
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C.J.Liu,
T.Suzuki,
S.Hirata,
and
K.Kawai
(2003).
The processing of high-molecular-weight xylanase (XynE, 110 kDa) from Aeromonas caviae ME-1 to 60-kDa xylanase (XynE60) in Escherichia coli and purification and characterization of XynE60.
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J Biosci Bioeng,
95,
95.
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D.J.Rigden,
and
M.J.Jedrzejas
(2003).
Genome-based identification of a carbohydrate binding module in Streptococcus pneumoniae hyaluronate lyase.
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Proteins,
52,
203-211.
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M.Roberge,
R.N.Lewis,
F.Shareck,
R.Morosoli,
D.Kluepfel,
C.Dupont,
and
R.N.McElhaney
(2003).
Differential scanning calorimetric, circular dichroism, and Fourier transform infrared spectroscopic characterization of the thermal unfolding of xylanase A from Streptomyces lividans.
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Proteins,
50,
341-354.
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T.Arai,
R.Araki,
A.Tanaka,
S.Karita,
T.Kimura,
K.Sakka,
and
K.Ohmiya
(2003).
Characterization of a cellulase containing a family 30 carbohydrate-binding module (CBM) derived from Clostridium thermocellum CelJ: importance of the CBM to cellulose hydrolysis.
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J Bacteriol,
185,
504-512.
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B.W.McLean,
A.B.Boraston,
D.Brouwer,
N.Sanaie,
C.A.Fyfe,
R.A.Warren,
D.G.Kilburn,
and
C.A.Haynes
(2002).
Carbohydrate-binding modules recognize fine substructures of cellulose.
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J Biol Chem,
277,
50245-50254.
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P.J.Simpson,
S.J.Jamieson,
M.Abou-Hachem,
E.N.Karlsson,
H.J.Gilbert,
O.Holst,
and
M.P.Williamson
(2002).
The solution structure of the CBM4-2 carbohydrate binding module from a thermostable Rhodothermus marinus xylanase.
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Biochemistry,
41,
5712-5719.
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PDB codes:
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A.B.Boraston,
A.L.Creagh,
M.M.Alam,
J.M.Kormos,
P.Tomme,
C.A.Haynes,
R.A.Warren,
and
D.G.Kilburn
(2001).
Binding specificity and thermodynamics of a family 9 carbohydrate-binding module from Thermotoga maritima xylanase 10A.
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Biochemistry,
40,
6240-6247.
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D.N.Bolam,
H.Xie,
P.White,
P.J.Simpson,
S.M.Hancock,
M.P.Williamson,
and
H.J.Gilbert
(2001).
Evidence for synergy between family 2b carbohydrate binding modules in Cellulomonas fimi xylanase 11A.
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Biochemistry,
40,
2468-2477.
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PDB codes:
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H.Xie,
H.J.Gilbert,
S.J.Charnock,
G.J.Davies,
M.P.Williamson,
P.J.Simpson,
S.Raghothama,
C.M.Fontes,
F.M.Dias,
L.M.Ferreira,
and
D.N.Bolam
(2001).
Clostridium thermocellum Xyn10B carbohydrate-binding module 22-2: the role of conserved amino acids in ligand binding.
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Biochemistry,
40,
9167-9176.
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PDB codes:
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I.A.Kataeva,
R.D.Seidel,
X.L.Li,
and
L.G.Ljungdahl
(2001).
Properties and mutation analysis of the CelK cellulose-binding domain from the Clostridium thermocellum cellulosome.
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J Bacteriol,
183,
1552-1559.
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M.A.Sung,
K.Fleming,
H.A.Chen,
and
S.Matthews
(2001).
The solution structure of PapGII from uropathogenic Escherichia coli and its recognition of glycolipid receptors.
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EMBO Rep,
2,
621-627.
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M.Czjzek,
D.N.Bolam,
A.Mosbah,
J.Allouch,
C.M.Fontes,
L.M.Ferreira,
O.Bornet,
V.Zamboni,
H.Darbon,
N.L.Smith,
G.W.Black,
B.Henrissat,
and
H.J.Gilbert
(2001).
The location of the ligand-binding site of carbohydrate-binding modules that have evolved from a common sequence is not conserved.
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J Biol Chem,
276,
48580-48587.
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PDB code:
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M.K.Ali,
H.Hayashi,
S.Karita,
M.Goto,
T.Kimura,
K.Sakka,
and
K.Ohmiya
(2001).
Importance of the carbohydrate-binding module of Clostridium stercorarium Xyn10B to xylan hydrolysis.
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Biosci Biotechnol Biochem,
65,
41-47.
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V.Notenboom,
A.B.Boraston,
D.G.Kilburn,
and
D.R.Rose
(2001).
Crystal structures of the family 9 carbohydrate-binding module from Thermotoga maritima xylanase 10A in native and ligand-bound forms.
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Biochemistry,
40,
6248-6256.
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PDB codes:
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C.D.Mackereth,
C.H.Arrowsmith,
A.M.Edwards,
and
L.P.McIntosh
(2000).
Zinc-bundle structure of the essential RNA polymerase subunit RPB10 from Methanobacterium thermoautotrophicum.
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Proc Natl Acad Sci U S A,
97,
6316-6321.
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PDB code:
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E.Brun,
P.E.Johnson,
A.L.Creagh,
P.Tomme,
P.Webster,
C.A.Haynes,
and
L.P.McIntosh
(2000).
Structure and binding specificity of the second N-terminal cellulose-binding domain from Cellulomonas fimi endoglucanase C.
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Biochemistry,
39,
2445-2458.
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PDB code:
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J.F.Espinosa,
J.L.Asensio,
J.L.García,
J.Laynez,
M.Bruix,
C.Wright,
H.C.Siebert,
H.J.Gabius,
F.J.Cañada,
and
J.Jiménez-Barbero
(2000).
NMR investigations of protein-carbohydrate interactions binding studies and refined three-dimensional solution structure of the complex between the B domain of wheat germ agglutinin and N,N', N"-triacetylchitotriose.
|
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Eur J Biochem,
267,
3965-3978.
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J.Kormos,
P.E.Johnson,
E.Brun,
P.Tomme,
L.P.McIntosh,
C.A.Haynes,
and
D.G.Kilburn
(2000).
Binding site analysis of cellulose binding domain CBD(N1) from endoglucanse C of Cellulomonas fimi by site-directed mutagenesis.
|
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Biochemistry,
39,
8844-8852.
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J.L.Asensio,
H.C.Siebert,
C.W.von Der Lieth,
J.Laynez,
M.Bruix,
U.M.Soedjanaamadja,
J.J.Beintema,
F.J.Cañada,
H.J.Gabius,
and
J.Jiménez-Barbero
(2000).
NMR investigations of protein-carbohydrate interactions: studies on the relevance of Trp/Tyr variations in lectin binding sites as deduced from titration microcalorimetry and NMR studies on hevein domains. Determination of the NMR structure of the complex between pseudohevein and N,N',N"-triacetylchitotriose.
|
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Proteins,
40,
218-236.
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L.J.Shimon,
S.Pagès,
A.Belaich,
J.P.Belaich,
E.A.Bayer,
R.Lamed,
Y.Shoham,
and
F.Frolow
(2000).
Structure of a family IIIa scaffoldin CBD from the cellulosome of Clostridium cellulolyticum at 2.2 A resolution.
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Acta Crystallogr D Biol Crystallogr,
56,
1560-1568.
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PDB code:
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M.Hashimoto,
T.Ikegami,
S.Seino,
N.Ohuchi,
H.Fukada,
J.Sugiyama,
M.Shirakawa,
and
T.Watanabe
(2000).
Expression and characterization of the chitin-binding domain of chitinase A1 from Bacillus circulans WL-12.
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J Bacteriol,
182,
3045-3054.
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D.H.Juers,
R.E.Huber,
and
B.W.Matthews
(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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G.Wang,
G.P.Wylie,
P.D.Twigg,
D.L.Caspar,
J.R.Murphy,
and
T.M.Logan
(1999).
Solution structure and peptide binding studies of the C-terminal src homology 3-like domain of the diphtheria toxin repressor protein.
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Proc Natl Acad Sci U S A,
96,
6119-6124.
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PDB code:
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P.J.Simpson,
D.N.Bolam,
A.Cooper,
A.Ciruela,
G.P.Hazlewood,
H.J.Gilbert,
and
M.P.Williamson
(1999).
A family IIb xylan-binding domain has a similar secondary structure to a homologous family IIa cellulose-binding domain but different ligand specificity.
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Structure,
7,
853-864.
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PDB codes:
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T.Tanaka,
S.Fujiwara,
S.Nishikori,
T.Fukui,
M.Takagi,
and
T.Imanaka
(1999).
A unique chitinase with dual active sites and triple substrate binding sites from the hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1.
|
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Appl Environ Microbiol,
65,
5338-5344.
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A.L.Creagh,
J.Koska,
P.E.Johnson,
P.Tomme,
M.D.Joshi,
L.P.McIntosh,
D.G.Kilburn,
and
C.A.Haynes
(1998).
Stability and oligosaccharide binding of the N1 cellulose-binding domain of Cellulomonas fimi endoglucanase CenC.
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Biochemistry,
37,
3529-3537.
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A.Schmidt,
A.Schlacher,
W.Steiner,
H.Schwab,
and
C.Kratky
(1998).
Structure of the xylanase from Penicillium simplicissimum.
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Protein Sci,
7,
2081-2088.
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PDB code:
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E.A.Bayer,
H.Chanzy,
R.Lamed,
and
Y.Shoham
(1998).
Cellulose, cellulases and cellulosomes.
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Curr Opin Struct Biol,
8,
548-557.
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E.N.Karlsson,
E.Bartonek-Roxå,
and
O.Holst
(1998).
Evidence for substrate binding of a recombinant thermostable xylanase originating from Rhodothermus marinus.
|
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FEMS Microbiol Lett,
168,
1-7.
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M.Caffrey,
M.Cai,
J.Kaufman,
S.J.Stahl,
P.T.Wingfield,
D.G.Covell,
A.M.Gronenborn,
and
G.M.Clore
(1998).
Three-dimensional solution structure of the 44 kDa ectodomain of SIV gp41.
|
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EMBO J,
17,
4572-4584.
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PDB codes:
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P.E.Johnson,
A.L.Creagh,
E.Brun,
K.Joe,
P.Tomme,
C.A.Haynes,
and
L.P.McIntosh
(1998).
Calcium binding by the N-terminal cellulose-binding domain from Cellulomonas fimi beta-1,4-glucanase CenC.
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Biochemistry,
37,
12772-12781.
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R.B.Russell,
and
C.P.Ponting
(1998).
Protein fold irregularities that hinder sequence analysis.
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Curr Opin Struct Biol,
8,
364-371.
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S.Walter,
E.Wellmann,
and
H.Schrempf
(1998).
The cell wall-anchored Streptomyces reticuli avicel-binding protein (AbpS) and its gene.
|
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J Bacteriol,
180,
1647-1654.
|
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V.V.Zverlov,
G.V.Velikodvorskaya,
W.H.Schwarz,
K.Bronnenmeier,
J.Kellermann,
and
W.L.Staudenbauer
(1998).
Multidomain structure and cellulosomal localization of the Clostridium thermocellum cellobiohydrolase CbhA.
|
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J Bacteriol,
180,
3091-3099.
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Y.Gao,
K.Kaluarachchi,
and
D.P.Giedroc
(1998).
Solution structure and backbone dynamics of Mason-Pfizer monkey virus (MPMV) nucleocapsid protein.
|
| |
Protein Sci,
7,
2265-2280.
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PDB code:
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A.Marchler-Bauer,
and
S.H.Bryant
(1997).
A measure of success in fold recognition.
|
| |
Trends Biochem Sci,
22,
236-240.
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K.Sorimachi,
M.F.Le Gal-Coëffet,
G.Williamson,
D.B.Archer,
and
M.P.Williamson
(1997).
Solution structure of the granular starch binding domain of Aspergillus niger glucoamylase bound to beta-cyclodextrin.
|
| |
Structure,
5,
647-661.
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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
code is
shown on the right.
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Links
