High-resolution structure of exo-arabinanase from Penicillium chrysogenum

Acta Crystallogr D Biol Crystallogr. 2011 May;67(Pt 5):415-22. doi: 10.1107/S0907444911006299. Epub 2011 Apr 13.

Abstract

Arabinanase Abnx from Penicillium chrysogenum 31B, which belongs to the GH93 family, releases arabinobiose from the nonreducing terminus of α-1,5-L-arabinan, which is distributed in the primary cell walls of higher plants. Crystal structures of Abnx and of its complex with arabinobiose were determined at the high resolutions of 1.14 Å to an R(work) of 10.7% (R(free) = 12.8%) and 1.04 Å to an R(work) of 10.4% (R(free) = 12.5%). Abnx has a six-bladed β-propeller fold with a typical ring-closure mode called `Velcro', in which the last four-stranded β-sheet is completed by the incorporation of a strand from the N-terminus. Catalytic residues which act as a nucleophile and an acid/base were proposed from the structures and confirmed by site-directed mutagenesis. The substrate-binding groove is enclosed at one end by two residues, Glu64 and Tyr66, which contribute to the recognition of the nonreducing chain end of the polysaccharide. A comparison with the related enzyme Arb93A which has a quite similar overall structure suggested that Abnx has different mechanisms to funnel substrates to the active site and/or to stabilize the transition state.

MeSH terms

  • Binding Sites
  • Crystallography, X-Ray
  • Disaccharides / metabolism
  • Glycoside Hydrolases / chemistry*
  • Glycoside Hydrolases / metabolism
  • Models, Molecular
  • Penicillium chrysogenum / chemistry
  • Penicillium chrysogenum / enzymology*
  • Protein Conformation
  • Substrate Specificity

Substances

  • Disaccharides
  • arabinobiose
  • Glycoside Hydrolases
  • exo-alpha-L-arabinanase

Associated data

  • PDB/3A71
  • PDB/3A72