spacer
spacer

PDBsum entry 1cz1

Go to PDB code: 
protein links
Hydrolase PDB id
1cz1
Jmol
Contents
Protein chain
394 a.a. *
Waters ×309
* Residue conservation analysis
PDB id:
1cz1
Name: Hydrolase
Title: Exo-b-(1,3)-glucanase from candida albicans at 1.85 a resolution
Structure: Protein (exo-b-(1,3)-glucanase). Chain: a. Engineered: yes
Source: Candida albicans. Organism_taxid: 5476. Strain: atcc 10261. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932.
Resolution:
1.85Å     R-factor:   0.166     R-free:   0.196
Authors: S.M.Cutfield,G.J.Davies,G.Murshudov,B.F.Anderson, P.C.E.Moody,P.A.Sullivan,J.F.Cutfield
Key ref:
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: 10610795 DOI: 10.1006/jmbi.1999.3287
Date:
01-Sep-99     Release date:   03-Jan-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P29717  (EXG_CANAL) -  Glucan 1,3-beta-glucosidase
Seq:
Struc:
438 a.a.
394 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.58  - Glucan 1,3-beta-glucosidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Successive hydrolysis of beta-D-glucose units from the non-reducing ends of 1,3-beta-D-glucans, releasing alpha-glucose.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   4 terms 
  Biological process     metabolic process   10 terms 
  Biochemical function     transferase activity     6 terms  

 

 
DOI no: 10.1006/jmbi.1999.3287 J Mol Biol 294:771-783 (1999)
PubMed id: 10610795  
 
 
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.
S.M.Cutfield, G.J.Davies, G.Murshudov, B.F.Anderson, P.C.Moody, P.A.Sullivan, J.F.Cutfield.
 
  ABSTRACT  
 
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.
 
  Selected figure(s)  
 
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.
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).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 294, 771-783) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20336338 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.
  Mar Biotechnol (NY), 13, 193-204.  
20544971 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.
  Proteins, 78, 2369-2384.  
20851343 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.
  Chem Biol, 17, 937-948.
PDB code: 2xj7
20875088 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.
  FEBS J, 277, 4549-4561.
PDB codes: 2pc8 2pf0 3n9k 3o6a
18310439 H.Ichinose, T.Kotake, Y.Tsumuraya, and S.Kaneko (2008).
Characterization of an endo-beta-1,6-Galactanase from Streptomyces avermitilis NBRC14893.
  Appl Environ Microbiol, 74, 2379-2383.  
17847089 K.Goyal, and S.C.Mande (2008).
Exploiting 3D structural templates for detection of metal-binding sites in protein structures.
  Proteins, 70, 1206-1218.  
18470964 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.
  J Comput Chem, 29, 2565-2574.  
18777634 R.Puccia, J.G.McEwen, and P.S.Cisalpino (2008).
Diversity in Paracoccidioides brasiliensis. The PbGP43 gene as a genetic marker.
  Mycopathologia, 165, 275-287.  
18772287 W.L.Chaffin (2008).
Candida albicans cell wall proteins.
  Microbiol Mol Biol Rev, 72, 495-544.  
17576216 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.
  Lett Appl Microbiol, 44, 573-581.  
17313520 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.
  FEMS Microbiol Rev, 31, 168-192.  
17597061 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.
  J Biol Chem, 282, 28126-28136.
PDB codes: 1zja 2pwd 2pwe 2pwf 2pwg 2pwh
17351093 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.
  Appl Environ Microbiol, 73, 3109-3112.  
16628756 T.M.Gloster, R.Madsen, and G.J.Davies (2006).
Dissection of conformationally restricted inhibitors binding to a beta-glucosidase.
  Chembiochem, 7, 738-742.
PDB codes: 2cbu 2cbv
15724214 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.
  Curr Genet, 47, 244-252.  
15014076 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.
  J Biol Chem, 279, 25517-25526.
PDB code: 1uuq
14597633 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.
  J Biol Chem, 279, 4970-4980.
PDB code: 1lq2
15280361 R.Conde, R.Cueva, G.Pablo, J.Polaina, and G.Larriba (2004).
A search for hyperglycosylation signals in yeast glycoproteins.
  J Biol Chem, 279, 43789-43798.  
14730348 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.
  Nat Struct Mol Biol, 11, 128-134.
PDB code: 1h4p
11222610 J.C.Hurlbert, and J.F.Preston (2001).
Functional characterization of a novel xylanase from a corn strain of Erwinia chrysanthemi.
  J Bacteriol, 183, 2093-2100.  
11709165 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.
  Structure, 9, 1005-1016.
PDB codes: 1ieq 1iev 1iew 1iex
10995222 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.
  Biochemistry, 39, 11553-11563.
PDB codes: 1fh7 1fh8 1fh9 1fhd
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.