5UBJ

Structure of an alpha-L-arabinofuranosidase (GH62) from Aspergillus nidulans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.144 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and functional characterization of a highly secreted alpha-l-arabinofuranosidase (GH62) from Aspergillus nidulans grown on sugarcane bagasse.

Contesini, F.J.Liberato, M.V.Rubio, M.V.Calzado, F.Zubieta, M.P.Riano-Pachon, D.M.Squina, F.M.Bracht, F.Skaf, M.S.Damasio, A.R.

(2017) Biochim. Biophys. Acta 1865: 1758-1769

  • DOI: 10.1016/j.bbapap.2017.09.001

  • PubMed Abstract: 
  • Carbohydrate-Active Enzymes are key enzymes for biomass-to-bioproducts conversion. α-l-Arabinofuranosidases that belong to the Glycoside Hydrolase family 62 (GH62) have important applications in biofuel production from plant biomass by hydrolyzing ar ...

    Carbohydrate-Active Enzymes are key enzymes for biomass-to-bioproducts conversion. α-l-Arabinofuranosidases that belong to the Glycoside Hydrolase family 62 (GH62) have important applications in biofuel production from plant biomass by hydrolyzing arabinoxylans, found in both the primary and secondary cell walls of plants. In this work, we identified a GH62 α-l-arabinofuranosidase (AnAbf62Awt) that was highly secreted when Aspergillus nidulans was cultivated on sugarcane bagasse. The gene AN7908 was cloned and transformed in A. nidulans for homologous production of AnAbf62Awt, and we confirmed that the enzyme is N-glycosylated at asparagine 83 by mass spectrometry analysis. The enzyme was also expressed in Escherichia coli and the studies of circular dichroism showed that the melting temperature and structural profile of AnAbf62Awt and the non-glycosylated enzyme from E. coli (AnAbf62Adeglyc) were highly similar. In addition, the designed glycomutant AnAbf62AN83Q presented similar patterns of secretion and activity to the AnAbf62Awt, indicating that the N-glycan does not influence the properties of this enzyme. The crystallographic structure of AnAbf62Adeglyc was obtained and the 1.7Å resolution model showed a five-bladed β-propeller fold, which is conserved in family GH62. Mutants AnAbf62AY312F and AnAbf62AY312S showed that Y312 was an important substrate-binding residue. Molecular dynamics simulations indicated that the loop containing Y312 could access different conformations separated by moderately low energy barriers. One of these conformations, comprising a local minimum, is responsible for placing Y312 in the vicinity of the arabinose glycosidic bond, and thus, may be important for catalytic efficiency.


    Organizational Affiliation

    Institute of Biology, University of Campinas - UNICAMP, Campinas, SP CEP 13083-862, Brazil; Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Caixa Postal 6192, 13083-970, Brazil.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-L-arabinofuranosidase axhA-2
A
328Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139)Mutation(s): 0 
Gene Names: axhA-2
EC: 3.2.1.55
Find proteins for Q5AUX2 (Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139))
Go to UniProtKB:  Q5AUX2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.144 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.562α = 90.00
b = 57.529β = 104.98
c = 49.371γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
FAPESPBrazil2014/04105-4
FAPESPBrazil2014/50371-8

Revision History 

  • Version 1.0: 2017-09-27
    Type: Initial release
  • Version 1.1: 2017-11-01
    Type: Database references