Alpha-N-arabinofuranosidase

 

Involved in the degradation of arabinan and is a key enzyme in the complete degradation of the plant cell wall. Catalyses the cleavage of terminal alpha-(1->5)-arabinofuranosyl bonds in different hemicellulosic homopolysaccharides (branched and debranched arabinans). It acts preferentially on aryl-alpha-L-arabinofuranosides, and is much less effective on aryl-beta-D-xylopyranosides. It is a member of the glycosyl hydrolase 51 family.

 

Reference Protein and Structure

Sequence
Q9XBQ3 UniProt (3.2.1.55) IPR017853 (Sequence Homologues) (PDB Homologues)
Biological species
Geobacillus stearothermophilus (Bacteria) Uniprot
PDB
1pz3 - Crystal structure of a family 51 (GH51) alpha-L-arabinofuranosidase from Geobacillus stearothermophilus T6 (1.75 Å) PDBe PDBsum 1pz3
Catalytic CATH Domains
3.20.20.80 CATHdb (see all for 1pz3)
Click To Show Structure

Enzyme Reaction (EC:3.2.1.55)

water
CHEBI:15377ChEBI
+
beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranose
CHEBI:73180ChEBI
→
beta-L-arabinofuranose
CHEBI:28272ChEBI
+
beta-L-arabinofuranose
CHEBI:28272ChEBI
Alternative enzyme names: Alpha-L-arabinanase, Alpha-L-arabinofuranoside hydrolase, Alpha-L-arabinosidase, Alpha-arabinofuranosidase, Alpha-arabinosidase, L-arabinosidase, Arabinosidase, Polysaccharide alpha-L-arabinofuranosidase, Arabinofuranosidase, Alpha-L-arabinofuranosidase,

Enzyme Mechanism

Introduction

Glu294 forms a covalent bond with the sugar substrate, eliminating the furanose substrate with concomitant deprotonation of Glu175. Glu175 then activates a catalytic water, which adds back to the bound sugar and cleaves it from the enzyme.

Catalytic Residues Roles

UniProt PDB* (1pz3)
Glu294 Glu294A Acts as a nucleophile. Forms a covalent bond between the sugar substrate and enzyme during the course of the reaction. covalently attached, nucleofuge, nucleophile
Glu175 Glu175A Donates a proton to leaving group when GLU294 makes a nucleophilic attack to form the intermediate. Later, abstracts a proton from a water molecule; the resulting hydroxide ion makes a nucleophilic attack to break up the covalent intermediate. proton acceptor, proton donor, activator, increase nucleophilicity, promote heterolysis
*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

overall product formed, overall reactant used, intermediate formation, proton transfer, bimolecular nucleophilic substitution, hydrolysis, native state of enzyme regenerated, intermediate terminated

References

  1. Hövel K et al. (2003), EMBO J, 22, 4922-4932. Crystal structure and snapshots along the reaction pathway of a family 51  -L-arabinofuranosidase. DOI:10.1093/emboj/cdg494. PMID:14517232.
  2. Carapito R et al. (2009), J Biol Chem, 284, 12285-12296. Molecular basis of arabinobio-hydrolase activity in phytopathogenic fungi: crystal structure and catalytic mechanism of Fusarium graminearum GH93 exo-alpha-L-arabinanase. DOI:10.1074/jbc.M900439200. PMID:19269961.

Step 1. Glu294 performs a nucleophilic attack on C1. This leads to the cleavage of the glycosidic bond with the concomitant protonation of the leaving group by Glu175.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Glu175A promote heterolysis
Glu294A covalently attached, nucleophile
Glu175A proton donor

Chemical Components

overall product formed, overall reactant used, intermediate formation, proton transfer, ingold: bimolecular nucleophilic substitution

Step 2. Glu175 activates a water for nucleophilic attack on the intermediate, which leads to its hydrolysis.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Glu175A activator, increase nucleophilicity
Glu294A nucleofuge
Glu175A proton acceptor

Chemical Components

overall product formed, hydrolysis, ingold: bimolecular nucleophilic substitution, proton transfer, native state of enzyme regenerated, intermediate terminated
Download: Image, Marvin File

Step 1. Glu294 performs a nucleophilic attack on C1. This leads to the cleavage of the glycosidic bond with the concomitant protonation of the leaving group by Glu175.

Step 2. Glu175 activates a water for nucleophilic attack on the intermediate, which leads to its hydrolysis.

Products.

Contributors

Mei Leung, Gemma L. Holliday, James Willey