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PDBsum entry 1eqc
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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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Exo-b-(1,3)-glucanase from candida albicans in complex with castanospermine at 1.85 a
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Structure:
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Exo-(b)-(1,3)-glucanase. Chain: a. Engineered: yes
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Source:
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Candida albicans. Organism_taxid: 5476. Strain: atcc 10261. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932.
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Resolution:
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1.85Å
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R-factor:
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0.157
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R-free:
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0.186
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Authors:
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S.M.Cutfield,G.J.Davies,G.Murshudov,B.F.Anderson,P.C.E.Moody, P.A.Sullivan,J.F.Cutfield
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Key ref:
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S.M.Cutfield
et al.
(1999).
The structure of the exo-beta-(1,3)-glucanase from Candida albicans in native and bound forms: relationship between a pocket and groove in family 5 glycosyl hydrolases.
J Mol Biol,
294,
771-783.
PubMed id:
DOI:
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Date:
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03-Apr-00
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Release date:
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03-Oct-00
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PROCHECK
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Headers
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References
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P29717
(EXG1_CANAL) -
Glucan 1,3-beta-glucosidase from Candida albicans (strain SC5314 / ATCC MYA-2876)
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Seq:
Struc:
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438 a.a.
394 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 2 residue positions (black
crosses)
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Enzyme class 1:
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E.C.2.4.1.-
- ?????
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Enzyme class 2:
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E.C.3.2.1.58
- glucan 1,3-beta-glucosidase.
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Reaction:
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Successive hydrolysis of beta-D-glucose units from the non-reducing ends of 1,3-beta-D-glucans, releasing alpha-glucose.
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Note, where more than one E.C. class is given (as above), each may
correspond to a different protein domain or, in the case of polyprotein
precursors, to a different mature protein.
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DOI no:
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J Mol Biol
294:771-783
(1999)
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PubMed id:
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The structure of the exo-beta-(1,3)-glucanase from Candida albicans in native and bound forms: relationship between a pocket and groove in family 5 glycosyl hydrolases.
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S.M.Cutfield,
G.J.Davies,
G.Murshudov,
B.F.Anderson,
P.C.Moody,
P.A.Sullivan,
J.F.Cutfield.
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ABSTRACT
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A group of fungal exo-beta-(1,3)-glucanases, including that from the human
pathogen Candida albicans (Exg), belong to glycosyl hydrolase family 5 that also
includes many bacterial cellulases (endo-beta-1, 4-glucanases). Family members,
despite wide sequence variations, share a common mechanism and are characterised
by possessing eight invariant residues making up the active site. These include
two glutamate residues acting as nucleophile and acid/base, respectively. Exg is
an abundant secreted enzyme possessing both hydrolase and transferase activity
consistent with a role in cell wall glucan metabolism and possibly
morphogenesis. The structures of Exg in both free and inhibited forms have been
determined to 1.9 A resolution. A distorted (beta/alpha)8 barrel structure
accommodates an active site which is located within a deep pocket, formed when
extended loop regions close off a cellulase-like groove. Structural analysis of
a covalently bound mechanism-based inhibitor (2-fluoroglucosylpyranoside) and of
a transition-state analogue (castanospermine) has identified the binding
interactions at the -1 glucose binding site. In particular the carboxylate of
Glu27 serves a dominant hydrogen-bonding role. Access by a 1,3-glucan chain to
the pocket in Exg can be understood in terms of a change in conformation of the
terminal glucose residue from chair to twisted boat. The geometry of the pocket
is not, however, well suited for cleavage of 1,4-glycosidic linkages. A second
glucose site was identified at the entrance to the pocket, sandwiched between
two antiparallel phenylalanine side-chains. This aromatic entrance-way must not
only direct substrate into the pocket but also may act as a clamp for an
acceptor molecule participating in the transfer reaction.
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Selected figure(s)
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Figure 1.
Figure 1. Enzyme glycosylation mechanism and two inhibitors of exo-b-(1,3)-glucanase. (a) Formation of the
covalent glycosyl-enzyme intermediate is presumed to proceed through an oxo-carbenium ion-like transition state
and involve nucleophile Glu292 and proton donor Glu192, which act on the glycosidic bond at the non-reducing end
of a b-1,3-glucan chain. The chemical structures of the glucosidase inhibitor, castanospermine, and of the mechanism-
based inactivator 2 ,4 -dinitrophenyl-2-deoxy-2-fluoro-b-D-glucopyranoside are labelled (b) and (c) respectively.
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Figure 6.
Figure 6. GRASP electrostatic surface representation of the binding site of Exg with the two bound saccharides,
following reaction of Exg crystals with the mechanism-based inhibitor DNP-DFG (see Figure 1(c)). Covalently bound
DFG (green spheres) is at the bottom of the pocket (shown left) while a second DFG (yellow spheres) is held between
two phenylalanyl side-chains at the pocket entrance (shown right).
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1999,
294,
771-783)
copyright 1999.
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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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Y.Peng,
G.L.Liu,
X.J.Yu,
X.H.Wang,
L.Jing,
and
Z.M.Chi
(2011).
Cloning of Exo-β-1,3-glucanase Gene from a Marine Yeast Williopsis saturnus and Its Overexpression in Yarrowia lipolytica.
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Mar Biotechnol (NY),
13,
193-204.
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C.Nagao,
N.Nagano,
and
K.Mizuguchi
(2010).
Relationships between functional subclasses and information contained in active-site and ligand-binding residues in diverse superfamilies.
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Proteins,
78,
2369-2384.
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M.S.Macauley,
Y.He,
T.M.Gloster,
K.A.Stubbs,
G.J.Davies,
and
D.J.Vocadlo
(2010).
Inhibition of O-GlcNAcase using a potent and cell-permeable inhibitor does not induce insulin resistance in 3T3-L1 adipocytes.
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Chem Biol,
17,
937-948.
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PDB code:
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W.M.Patrick,
Y.Nakatani,
S.M.Cutfield,
M.L.Sharpe,
R.J.Ramsay,
and
J.F.Cutfield
(2010).
Carbohydrate binding sites in Candida albicans exo-β-1,3-glucanase and the role of the Phe-Phe 'clamp' at the active site entrance.
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FEBS J,
277,
4549-4561.
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PDB codes:
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H.Ichinose,
T.Kotake,
Y.Tsumuraya,
and
S.Kaneko
(2008).
Characterization of an endo-beta-1,6-Galactanase from Streptomyces avermitilis NBRC14893.
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Appl Environ Microbiol,
74,
2379-2383.
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K.Goyal,
and
S.C.Mande
(2008).
Exploiting 3D structural templates for detection of metal-binding sites in protein structures.
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Proteins,
70,
1206-1218.
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N.F.Brás,
S.A.Moura-Tamames,
P.A.Fernandes,
and
M.J.Ramos
(2008).
Mechanistic studies on the formation of glycosidase-substrate and glycosidase-inhibitor covalent intermediates.
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J Comput Chem,
29,
2565-2574.
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R.Puccia,
J.G.McEwen,
and
P.S.Cisalpino
(2008).
Diversity in Paracoccidioides brasiliensis. The PbGP43 gene as a genetic marker.
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Mycopathologia,
165,
275-287.
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W.L.Chaffin
(2008).
Candida albicans cell wall proteins.
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Microbiol Mol Biol Rev,
72,
495-544.
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J.L.Pereira,
E.F.Noronha,
R.N.Miller,
and
O.L.Franco
(2007).
Novel insights in the use of hydrolytic enzymes secreted by fungi with biotechnological potential.
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Lett Appl Microbiol,
44,
573-581.
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K.Martin,
B.M.McDougall,
S.McIlroy,
J.Chen,
and
R.J.Seviour
(2007).
Biochemistry and molecular biology of exocellular fungal beta-(1,3)- and beta-(1,6)-glucanases.
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FEMS Microbiol Rev,
31,
168-192.
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S.Ravaud,
X.Robert,
H.Watzlawick,
R.Haser,
R.Mattes,
and
N.Aghajari
(2007).
Trehalulose synthase native and carbohydrate complexed structures provide insights into sucrose isomerization.
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J Biol Chem,
282,
28126-28136.
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PDB codes:
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T.Sakamoto,
Y.Taniguchi,
S.Suzuki,
H.Ihara,
and
H.Kawasaki
(2007).
Characterization of Fusarium oxysporum beta-1,6-galactanase, an enzyme that hydrolyzes larch wood arabinogalactan.
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Appl Environ Microbiol,
73,
3109-3112.
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T.M.Gloster,
R.Madsen,
and
G.J.Davies
(2006).
Dissection of conformationally restricted inhibitors binding to a beta-glucosidase.
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Chembiochem,
7,
738-742.
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PDB codes:
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Y.Sakamoto,
T.Irie,
and
T.Sato
(2005).
Isolation and characterization of a fruiting body-specific exo-beta-1,3-glucanase-encoding gene, exg1, from Lentinula edodes.
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Curr Genet,
47,
244-252.
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F.M.Dias,
F.Vincent,
G.Pell,
J.A.Prates,
M.S.Centeno,
L.E.Tailford,
L.M.Ferreira,
C.M.Fontes,
G.J.Davies,
and
H.J.Gilbert
(2004).
Insights into the molecular determinants of substrate specificity in glycoside hydrolase family 5 revealed by the crystal structure and kinetics of Cellvibrio mixtus mannosidase 5A.
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J Biol Chem,
279,
25517-25526.
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PDB code:
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M.Hrmova,
R.De Gori,
B.J.Smith,
A.Vasella,
J.N.Varghese,
and
G.B.Fincher
(2004).
Three-dimensional structure of the barley beta-D-glucan glucohydrolase in complex with a transition state mimic.
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J Biol Chem,
279,
4970-4980.
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PDB code:
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R.Conde,
R.Cueva,
G.Pablo,
J.Polaina,
and
G.Larriba
(2004).
A search for hyperglycosylation signals in yeast glycoproteins.
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J Biol Chem,
279,
43789-43798.
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S.C.Taylor,
A.D.Ferguson,
J.J.Bergeron,
and
D.Y.Thomas
(2004).
The ER protein folding sensor UDP-glucose glycoprotein-glucosyltransferase modifies substrates distant to local changes in glycoprotein conformation.
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Nat Struct Mol Biol,
11,
128-134.
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PDB code:
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J.C.Hurlbert,
and
J.F.Preston
(2001).
Functional characterization of a novel xylanase from a corn strain of Erwinia chrysanthemi.
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J Bacteriol,
183,
2093-2100.
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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.
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Structure,
9,
1005-1016.
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PDB codes:
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V.Notenboom,
S.J.Williams,
R.Hoos,
S.G.Withers,
and
D.R.Rose
(2000).
Detailed structural analysis of glycosidase/inhibitor interactions: complexes of Cex from Cellulomonas fimi with xylobiose-derived aza-sugars.
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Biochemistry,
39,
11553-11563.
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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
