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PDBsum entry 1cbg

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Hydrolase (o-glycosyl) PDB id
1cbg
Jmol
Contents
Protein chain
490 a.a. *
Waters ×436
* Residue conservation analysis
PDB id:
1cbg
Name: Hydrolase (o-glycosyl)
Title: The crystal structure of a cyanogenic beta-glucosidase from clover (trifolium repens l.), A family 1 glycosyl-hydrolase
Structure: Cyanogenic beta-glucosidase. Chain: a. Ec: 3.2.1.21
Source: Trifolium repens. White clover. Organism_taxid: 3899. Variant: l. Organ: leaves. Tissue: leaves
Biol. unit: Dimer (from PQS)
Resolution:
2.15Å     R-factor:   0.195     R-free:   0.247
Authors: T.E.Barrett,C.G.Suresh,S.P.Tolley,M.A.Hughes
Key ref:
T.Barrett et al. (1995). The crystal structure of a cyanogenic beta-glucosidase from white clover, a family 1 glycosyl hydrolase. Structure, 3, 951-960. PubMed id: 8535788 DOI: 10.1016/S0969-2126(01)00229-5
Date:
31-Jul-95     Release date:   15-Oct-95    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P26205  (BGLT_TRIRP) -  Cyanogenic beta-glucosidase (Fragment)
Seq:
Struc:
425 a.a.
490 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 12 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.21  - Beta-glucosidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of terminal, non-reducing beta-D-glucose residues with release of beta-D-glucose.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     hydrolase activity     4 terms  

 

 
DOI no: 10.1016/S0969-2126(01)00229-5 Structure 3:951-960 (1995)
PubMed id: 8535788  
 
 
The crystal structure of a cyanogenic beta-glucosidase from white clover, a family 1 glycosyl hydrolase.
T.Barrett, C.G.Suresh, S.P.Tolley, E.J.Dodson, M.A.Hughes.
 
  ABSTRACT  
 
BACKGROUND: beta-glucosidases occur in a variety of organisms and catalyze the hydrolysis of aryl and alkyl-beta-D-glucosides as well as glucosides with only a carbohydrate moiety (such as cellobiose). The cyanogenic beta-glucosidase from white clover (subsequently referred to as CBG) is responsible for the cleavage of cyanoglucosides. Both CBG and the cyanoglucosides occur within the plant cell wall where they are found in separate compartments and only come into contact when the leaf tissue experiences mechanical damage. This results in the eventual production of hydrogen cyanide which acts as a deterrent to grazing animals. beta-glucosidases have been assigned to particular glycosyl hydrolase families on the basis of sequence similarity; this classification has placed CBG in family 1 (there are a total of over 40 families) for which a three-dimensional structure has so far not been determined. This is the first report of the three-dimensional structure of a glycosyl hydrolase from family 1. RESULTS: The crystal structure of CBG has been determined using multiple isomorphous replacement. The final model has been refined at 2.15 A resolution to an R factor of 18.9%. The overall fold of the molecule is a (beta/alpha)8 [or (alpha/beta)8] barrel (in common with a number of glycosyl hydrolases) with all residues located in a single domain. CONCLUSIONS: Sequence comparisons between beta-glucosidases of the same family show that residues Glu183 and Glu397 are highly conserved. Both residues are positioned at the end of a pocket located at the C terminus of the barrel and have been assigned the respective roles of proton donor and nucleophile on the basis of inhibitor-binding and mutagenesis experiments. These roles are consistent with the environments of the two residues. The pocket itself is typical of a sugar-binding site as it contains a number of charged, aromatic and polar groups. In support of this role, we present crystallographic data on a possible product complex between CBG and glucose, resulting from co-crystallization of the native enzyme with its natural substrate, linamarin.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. The reaction catalyzed by the cyanogenic β-glucosidase from white clover. Figure 1. The reaction catalyzed by the cyanogenic β-glucosidase from white clover.
Figure 5.
Figure 5. The solvent-accessible surface for the entire molecule, showing the active-site pocket (Glu83 magenta and Glu397 yellow). The probe radius used was 1.4 å. (Figure generated using GRASP [43].). Figure 5. The solvent-accessible surface for the entire molecule, showing the active-site pocket (Glu83 magenta and Glu397 yellow). The probe radius used was 1.4 å. (Figure generated using GRASP [[3]43].).
 
  The above figures are reprinted by permission from Cell Press: Structure (1995, 3, 951-960) copyright 1995.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18458107 K.M.Olsen, S.C.Hsu, and L.L.Small (2008).
Evidence on the molecular basis of the Ac/ac adaptive cyanogenesis polymorphism in white clover (Trifolium repens L).
  Genetics, 179, 517-526.  
17683331 I.Matsui, and K.Harata (2007).
Implication for buried polar contacts and ion pairs in hyperthermostable enzymes.
  FEBS J, 274, 4012-4022.  
17784921 K.M.Olsen, B.L.Sutherland, and L.L.Small (2007).
Molecular evolution of the Li/li chemical defence polymorphism in white clover (Trifolium repens L.).
  Mol Ecol, 16, 4180-4193.  
17503162 M.León, P.Isorna, M.Menéndez, J.Sanz-Aparicio, and J.Polaina (2007).
Comparative study and mutational analysis of distinctive structural elements of hyperthermophilic enzymes.
  Protein J, 26, 435-444.
PDB code: 1uwi
17548373 Y.O.Ahn, H.Saino, M.Mizutani, B.Shimizu, and K.Sakata (2007).
Vicianin hydrolase is a novel cyanogenic beta-glycosidase specific to beta-vicianoside (6-O-alpha-L-arabinopyranosyl-beta-D-glucopyranoside) in seeds of Vicia angustifolia.
  Plant Cell Physiol, 48, 938-947.  
16609814 B.Di Lauro, M.Rossi, and M.Moracci (2006).
Characterization of a beta-glycosidase from the thermoacidophilic bacterium Alicyclobacillus acidocaldarius.
  Extremophiles, 10, 301-310.  
16307283 K.A.Nielsen, M.Hrmova, J.N.Nielsen, K.Forslund, S.Ebert, C.E.Olsen, G.B.Fincher, and B.L.Møller (2006).
Reconstitution of cyanogenesis in barley (Hordeum vulgare L.) and its implications for resistance against the barley powdery mildew fungus.
  Planta, 223, 1010-1023.  
  16880561 W.Chuenchor, S.Pengthaisong, J.Yuvaniyama, R.Opassiri, J.Svasti, and J.R.Ketudat Cairns (2006).
Purification, crystallization and preliminary X-ray analysis of rice BGlu1 beta-glucosidase with and without 2-deoxy-2-fluoro-beta-D-glucoside.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 798-801.  
15930622 X.Ma, J.Koepke, A.Bayer, G.Fritzsch, H.Michel, and J.Stöckigt (2005).
Crystallization and preliminary X-ray analysis of native and selenomethionyl vinorine synthase from Rauvolfia serpentina.
  Acta Crystallogr D Biol Crystallogr, 61, 694-696.  
15520879 A.Bektas, S.H.Schurman, A.A.Sharov, M.G.Carter, H.C.Dietz, and C.A.Francomano (2004).
Klotho gene variation and expression in 20 inbred mouse strains.
  Mamm Genome, 15, 759-767.  
15111395 L.Maragliano, G.Cottone, L.Cordone, and G.Ciccotti (2004).
Atomic mean-square displacements in proteins by molecular dynamics: a case for analysis of variance.
  Biophys J, 86, 2765-2772.  
15340929 T.Akiba, M.Nishio, I.Matsui, and K.Harata (2004).
X-ray structure of a membrane-bound beta-glycosidase from the hyperthermophilic archaeon Pyrococcus horikoshii.
  Proteins, 57, 422-431.
PDB code: 1vff
14976214 Y.O.Ahn, M.Mizutani, H.Saino, and K.Sakata (2004).
Furcatin hydrolase from Viburnum furcatum Blume is a novel disaccharide-specific acuminosidase in glycosyl hydrolase family 1.
  J Biol Chem, 279, 23405-23414.  
15604686 Z.Xu, L.Escamilla-Treviño, L.Zeng, M.Lalgondar, D.Bevan, B.Winkel, A.Mohamed, C.L.Cheng, M.C.Shih, J.Poulton, and A.Esen (2004).
Functional genomic analysis of Arabidopsis thaliana glycoside hydrolase family 1.
  Plant Mol Biol, 55, 343-367.  
14653813 S.R.Marana, L.M.Mendonça, E.H.Andrade, W.R.Terra, and C.Ferreira (2003).
The role of residues R97 and Y331 in modulating the pH optimum of an insect beta-glycosidase of family 1.
  Eur J Biochem, 270, 4866-4875.  
12837801 X.Wang, X.He, S.Yang, X.An, W.Chang, and D.Liang (2003).
Structural basis for thermostability of beta-glycosidase from the thermophilic eubacterium Thermus nonproteolyticus HG102.
  J Bacteriol, 185, 4248-4255.
PDB code: 1np2
12012341 B.Cobucci-Ponzano, M.Moracci, B.Di Lauro, M.Ciaramella, R.D'Avino, and M.Rossi (2002).
Ionic network at the C-terminus of the beta-glycosidase from the hyperthermophilic archaeon Sulfolobus solfataricus: Functional role in the quaternary structure thermal stabilization.
  Proteins, 48, 98.  
11784319 J.G.Berrin, W.R.McLauchlan, P.Needs, G.Williamson, A.Puigserver, P.A.Kroon, and N.Juge (2002).
Functional expression of human liver cytosolic beta-glucosidase in Pichia pastoris. Insights into its role in the metabolism of dietary glucosides.
  Eur J Biochem, 269, 249-258.  
11900558 T.Kaper, H.H.van Heusden, B.van Loo, A.Vasella, J.van der Oost, and W.M.de Vos (2002).
Substrate specificity engineering of beta-mannosidase and beta-glucosidase from Pyrococcus by exchange of unique active site residues.
  Biochemistry, 41, 4147-4155.  
11179970 B.Pontoppidan, B.Ekbom, S.Eriksson, and J.Meijer (2001).
Purification and characterization of myrosinase from the cabbage aphid (Brevicoryne brassicae), a brassica herbivore.
  Eur J Biochem, 268, 1041-1048.  
11134937 J.Vévodová, J.Marek, J.Zouhar, B.Brzobohatý, and X.D.Su (2001).
Purification, crystallization and preliminary X-ray analysis of a maize cytokinin glucoside specific beta-glucosidase.
  Acta Crystallogr D Biol Crystallogr, 57, 140-142.  
11352732 M.Vallmitjana, M.Ferrer-Navarro, R.Planell, M.Abel, C.Ausín, E.Querol, A.Planas, and J.A.Pérez-Pons (2001).
Mechanism of the family 1 beta-glucosidase from Streptomyces sp: catalytic residues and kinetic studies.
  Biochemistry, 40, 5975-5982.  
11679733 X.Y.He, X.Q.Wang, S.J.Yang, W.R.Chang, and D.C.Liang (2001).
Overexpression, purification, crystallization and preliminary crystallographic studies on a thermostable beta-glycosidase from Thermus nonproteolyticus HG102.
  Acta Crystallogr D Biol Crystallogr, 57, 1650-1651.  
10966578 A.J.Harvey, M.Hrmova, R.De Gori, J.N.Varghese, and G.B.Fincher (2000).
Comparative modeling of the three-dimensional structures of family 3 glycoside hydrolases.
  Proteins, 41, 257-269.  
11106394 M.Czjzek, M.Cicek, V.Zamboni, D.R.Bevan, B.Henrissat, and A.Esen (2000).
The mechanism of substrate (aglycone) specificity in beta -glucosidases is revealed by crystal structures of mutant maize beta -glucosidase-DIMBOA, -DIMBOAGlc, and -dhurrin complexes.
  Proc Natl Acad Sci U S A, 97, 13555-13560.
PDB codes: 1e4l 1e4n 1e55 1e56
10819960 T.Kaper, J.H.Lebbink, J.Pouwels, J.Kopp, G.E.Schulz, J.van der Oost, and W.M.de Vos (2000).
Comparative structural analysis and substrate specificity engineering of the hyperthermostable beta-glucosidase CelB from Pyrococcus furiosus.
  Biochemistry, 39, 4963-4970.  
10089468 A.Guasch, M.Vallmitjana, R.Pérez, E.Querol, J.A.Pérez-Pons, and M.Coll (1999).
Cloning, overexpression, crystallization and preliminary X-ray analysis of a family 1 beta--glucosidase from Streptomyces.
  Acta Crystallogr D Biol Crystallogr, 55, 679-682.  
10409626 B.Garner, S.Vazquez, R.Griffith, R.A.Lindner, J.A.Carver, and R.J.Truscott (1999).
Identification of glutathionyl-3-hydroxykynurenine glucoside as a novel fluorophore associated with aging of the human lens.
  J Biol Chem, 274, 20847-20854.  
  10210191 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.
  Protein Sci, 8, 122-136.  
10872458 H.D.Ly, and S.G.Withers (1999).
Mutagenesis of glycosidases.
  Annu Rev Biochem, 68, 487-522.  
10368285 J.N.Varghese, M.Hrmova, and G.B.Fincher (1999).
Three-dimensional structure of a barley beta-D-glucan exohydrolase, a family 3 glycosyl hydrolase.
  Structure, 7, 179-190.
PDB code: 1ex1
10391926 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.
  J Biol Chem, 274, 19823-19828.  
10583402 V.Rotrekl, E.Nejedlá, I.Kucera, F.Abdallah, K.Palme, and B.Brzobohatý (1999).
The role of cysteine residues in structure and enzyme activity of a maize beta-glucosidase.
  Eur J Biochem, 266, 1056-1065.  
9485319 G.J.Davies, M.Dauter, A.M.Brzozowski, M.E.Bjørnvad, K.V.Andersen, and M.Schülein (1998).
Structure of the Bacillus agaradherans family 5 endoglucanase at 1.6 A and its cellobiose complex at 2.0 A resolution.
  Biochemistry, 37, 1926-1932.
PDB codes: 1a3h 2a3h
9556600 M.Hrmova, E.A.MacGregor, P.Biely, R.J.Stewart, and G.B.Fincher (1998).
Substrate binding and catalytic mechanism of a barley beta-D-Glucosidase/(1,4)-beta-D-glucan exohydrolase.
  J Biol Chem, 273, 11134-11143.  
9860830 M.W.Bauer, and R.M.Kelly (1998).
The family 1 beta-glucosidases from Pyrococcus furiosus and Agrobacterium faecalis share a common catalytic mechanism.
  Biochemistry, 37, 17170-17178.  
9893955 S.D'Auria, M.Moracci, F.Febbraio, F.Tanfani, R.Nucci, and M.Rossi (1998).
Structure-function studies on beta-glycosidase from Sulfolobus solfataricus. Molecular bases of thermostability.
  Biochimie, 80, 949-957.  
9593194 S.García-Vallvé, A.Rojas, J.Palau, and A.Romeu (1998).
Circular permutants in beta-glucosidases (family 3) within a predicted double-domain topology that includes a (beta/alpha)8-barrel.
  Proteins, 31, 214-223.  
9312086 S.He, and S.G.Withers (1997).
Assignment of sweet almond beta-glucosidase as a family 1 glycosidase and identification of its active site nucleophile.
  J Biol Chem, 272, 24864-24867.  
9195886 W.P.Burmeister, S.Cottaz, H.Driguez, R.Iori, S.Palmieri, and B.Henrissat (1997).
The crystal structures of Sinapis alba myrosinase and a covalent glycosyl-enzyme intermediate provide insights into the substrate recognition and active-site machinery of an S-glycosidase.
  Structure, 5, 663-675.
PDB codes: 1myr 2myr
8718854 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.
  Biochemistry, 35, 10648-10660.
PDB code: 1ece
8905079 R.A.Warren (1996).
Microbial hydrolysis of polysaccharides.
  Annu Rev Microbiol, 50, 183-212.  
  8762144 S.Janecek (1996).
Invariant glycines and prolines flanking in loops the strand beta 2 of various (alpha/beta)8-barrel enzymes: a hidden homology?
  Protein Sci, 5, 1136-1143.  
8535779 G.Davies, and B.Henrissat (1995).
Structures and mechanisms of glycosyl hydrolases.
  Structure, 3, 853-859.  
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.