Beta-glucosidase (GH1)

 

beta-glucosidases are an important group of enzymes that are responsible for cleaving a range of biologically significant compounds. Many show a strict specificity for their substrates although others, like the cyanogenic beta-glucosidase from white clover (CBG) are less stringent, cleaving xylosides and arabinosides as well as glucosides. In general, they hydrolyse terminal, non-reducing beta-D-glucosyl residues with release of beta-D-glucose.

Member of the Glycoside Hydrolase Family 1 (GH1). GH1 comprises enzymes with a number of known activities; beta-glucosidase (EC:3.2.1.21); beta-galactosidase (EC:3.2.1.23); 6-phospho-beta-galactosidase (EC:3.2.1.85); 6-phospho-beta-glucosidase (EC:3.2.1.86); lactase-phlorizin hydrolase (EC:3.2.1.62), (EC:3.2.1.108); beta-mannosidase(EC:3.2.1.25); myrosinase (EC:3.2.1.147). However, we consider myrosinase to be a different entry due to the fact that is lacking in one of the catalytic glutamates (the general acid/base) and cleaves a C-S bond, rather than the C-O bond of this entry (i.e. has a different reactive centre)

 

Reference Protein and Structure

Sequence
P26205 UniProt (3.2.1.21) IPR001360 (Sequence Homologues) (PDB Homologues)
Biological species
Trifolium repens (white clover) Uniprot
PDB
1cbg - THE CRYSTAL STRUCTURE OF A CYANOGENIC BETA-GLUCOSIDASE FROM WHITE CLOVER (TRIFOLIUM REPENS L.), A FAMILY 1 GLYCOSYL-HYDROLASE (2.15 Å) PDBe PDBsum 1cbg
Catalytic CATH Domains
3.20.20.80 CATHdb (see all for 1cbg)
Click To Show Structure

Enzyme Reaction (EC:3.2.1.21)

water
CHEBI:15377ChEBI
+
beta-cellobiose
CHEBI:36217ChEBI
→
beta-D-glucose
CHEBI:15903ChEBI
+
beta-D-glucose
CHEBI:15903ChEBI
Alternative enzyme names: Beta-1,6-glucosidase, Beta-D-glucosidase, Beta-glucoside glucohydrolase, p-nitrophenyl beta-glucosidase, Amygdalase, Amygdalinase, Arbutinase, Aryl-beta-glucosidase, Cellobiase, Elaterase, Emulsin, Gentiobiase, Limarase, Primeverosidase, Salicilinase, Gentobiase,

Enzyme Mechanism

Introduction

In this retaining mechanism, the nucleophile (Glu397) performs a nucleophilic attack at the anomeric carbon, which results in formation of a glucose-enzyme intermediate. In this process, aglucone departure is facilitated by protonation of the glucosidic oxygen by the acid catalyst (Glu183). During the second catalytic step (deglucosylation), a water molecule is activated by the catalytic base (Glu183) to serve as a nucleophile for hydrolysis of the glucosidic bond and release of the glucose.

Catalytic Residues Roles

UniProt PDB* (1cbg)
Asn335 Asn324A Involved in the positioning and ionisation of the general acid/base glutamate residue. modifies pKa, steric role
Glu408 Glu397A Catalytic nucleophile covalent catalysis
Glu194 Glu183A Acts as a general acid/base. proton shuttle (general acid/base)
Arg102, Tyr337 Arg91A, Tyr326A Perturbs the pKa of nucleophilic glutamic acid such that it is negatively charged in the enzyme ground state. modifies pKa
His148 His137A Involved in stabilising the transition states. transition state stabiliser
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

References

  1. Barrett T et al. (1995), Structure, 3, 951-960. The crystal structure of a cyanogenic β-glucosidase from white clover, a family 1 glycosyl hydrolase. DOI:10.1016/s0969-2126(01)00229-5. PMID:8535788.
  2. Mahajan C et al. (2015), J Mol Model, 21, 184-. In silico ligand binding studies of cyanogenic β-glucosidase, dhurrinase-2 from Sorghum bicolor. DOI:10.1007/s00894-015-2730-1. PMID:26139075.
  3. Khairudin NB et al. (2013), Bioinformation, 9, 813-817. Molecular Docking Study of Beta-Glucosidase with Cellobiose, Cellotetraose and Cellotetriose. DOI:10.6026/97320630009813. PMID:24143051.
  4. Shaik NM et al. (2013), Mol Biol Rep, 40, 1351-1363. Functional characterization, homology modeling and docking studies of β-glucosidase responsible for bioactivation of cyanogenic hydroxynitrile glucosides from Leucaena leucocephala (subabul). DOI:10.1007/s11033-012-2179-6. PMID:23079707.
  5. Ketudat Cairns JR et al. (2010), Cell Mol Life Sci, 67, 3389-3405. β-Glucosidases. DOI:10.1007/s00018-010-0399-2. PMID:20490603.
  6. Morant AV et al. (2008), Phytochemistry, 69, 1795-1813. β-Glucosidases as detonators of plant chemical defense. DOI:10.1016/j.phytochem.2008.03.006. PMID:18472115.
  7. Chuenchor W et al. (2008), J Mol Biol, 377, 1200-1215. Structural Insights into Rice BGlu1 β-Glucosidase Oligosaccharide Hydrolysis and Transglycosylation. DOI:10.1016/j.jmb.2008.01.076. PMID:18308333.
  8. Mendonça LM et al. (2008), FEBS J, 275, 2536-2547. The role in the substrate specificity and catalysis of residues forming the substrate aglycone-binding site of a β-glycosidase. DOI:10.1111/j.1742-4658.2008.06402.x. PMID:18422657.
  9. Isorna P et al. (2007), J Mol Biol, 371, 1204-1218. Crystal Structures of Paenibacillus polymyxa β-Glucosidase B Complexes Reveal the Molecular Basis of Substrate Specificity and Give New Insights into the Catalytic Machinery of Family I Glycosidases. DOI:10.1016/j.jmb.2007.05.082. PMID:17585934.
  10. Marana SR et al. (2003), Eur J Biochem, 270, 4866-4875. The role of residues R97 and Y331 in modulating the pH optimum of an insect β-glycosidase of family 1. DOI:10.1046/j.1432-1033.2003.03887.x.
  11. Keresztessy Z et al. (2001), Biochem J, 353, 199-205. Identification of essential active-site residues in the cyanogenic β-glucosidase (linamarase) from cassava (Manihot esculenta Crantz) by site-directed mutagenesis. DOI:10.1042/0264-6021:3530199. PMID:11139381.
  12. Vallmitjana M et al. (2001), Biochemistry, 40, 5975-5982. Mechanism of the family 1 beta-glucosidase from Streptomyces sp: catalytic residues and kinetic studies. PMID:11352732.
  13. Marana SR et al. (2001), Biochim Biophys Acta, 1545, 41-52. Amino acid residues involved in substrate binding and catalysis in an insect digestive beta-glycosidase. PMID:11342030.
  14. Czjzek M et al. (2000), Proc Natl Acad Sci U S A, 97, 13555-13560. The mechanism of substrate (aglycone) specificity in beta -glucosidases is revealed by crystal structures of mutant maize beta -glucosidase-DIMBOA, -DIMBOAGlc, and -dhurrin complexes. DOI:10.1073/pnas.97.25.13555. PMID:11106394.
  15. Sanz-Aparicio J et al. (1998), J Mol Biol, 275, 491-502. Crystal structure of β-glucosidase A from Bacillus polymyxa: insights into the catalytic activity in family 1 glycosyl hydrolases. DOI:10.1006/jmbi.1997.1467. PMID:9466926.
  16. Lawson SL et al. (1998), Biochem J, 330 ( Pt 1), 203-209. Mechanistic consequences of replacing the active-site nucleophile Glu-358 in Agrobacterium sp. beta-glucosidase with a cysteine residue. PMID:9461511.
  17. Bauer MW et al. (1998), Biochemistry, 37, 17170-17178. The Family 1 β-Glucosidases fromPyrococcus furiosusandAgrobacterium faecalisShare a Common Catalytic Mechanism†. DOI:10.1021/bi9814944. PMID:9860830.
  18. Wang Q et al. (1995), Biochemistry, 34, 14554-14562. Identification of the acid/base catalyst in Agrobacterium faecalis beta-glucosidase by kinetic analysis of mutants. PMID:7578061.

Step 1.

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Catalytic Residues Roles

Residue Roles
Glu183A proton shuttle (general acid/base)
Glu397A covalent catalysis
Tyr326A modifies pKa
Arg91A modifies pKa
Asn324A modifies pKa, steric role
His137A transition state stabiliser

Chemical Components

Step 1.

Contributors

Gemma L. Holliday, Nozomi Nagano, Craig Porter