9J07

Acetyl xylan esterase B from Aspergillus oryzae (AoAXEB), apo form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.199 (Depositor), 0.209 (DCC) 
  • R-Value Work: 
    0.164 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 
    0.166 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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Literature

Identification and structural characterization of a novel acetyl xylan esterase from Aspergillus oryzae.

Yamada, C.Kato, T.Shiono, Y.Koseki, T.Fushinobu, S.

(2025) FEBS J 

  • DOI: https://doi.org/10.1111/febs.17420
  • Primary Citation of Related Structures:  
    9J07, 9J08

  • PubMed Abstract: 

    Acetyl xylan esterase plays a crucial role in the degradation of xylan, the major plant hemicellulose, by liberating acetic acid from the backbone polysaccharides. Acetyl xylan esterase B from Aspergillus oryzae, designated AoAxeB, was biochemically and structurally investigated. The AoAxeB-encoding gene with a native signal peptide was successfully expressed in Pichia pastoris as an active extracellular protein. The purified recombinant protein had pH and temperature optima of 8.0 and 30 °C, respectively, and was stable up to 35 °C. The optimal substrate for hydrolysis by purified recombinant AoAxeB among a panel of α-naphthyl esters was α-naphthyl acetate. Recombinant AoAxeB catalyzed the release of acetic acid from wheat arabinoxylan. The release of acetic acid from wheat arabinoxylan increased synergistically with xylanase addition. No activity was detected for the methyl esters of ferulic, p-coumaric, caffeic, or sinapic acids. The crystal structures of AoAxeB in the apo and succinate complexes were determined at resolutions of 1.75 and 1.90 Å, respectively. Although AoAxeB has been classified in the Esterase_phb family in the ESTerases and alpha/beta-Hydrolase Enzymes and Relatives (ESTHER) database, its structural features partly resemble those of ferulic acid esterase in the FaeC family. Phylogenetic analysis also indicated that AoAxeB is located between the clades of the two families. Docking analysis provided a plausible binding mode for xylotriose substrates acetylated at the 2- or 3-hydroxy position. This study expands the current knowledge of the structures of acetyl xylan esterases and ferulic acid esterases that are required for complete plant biomass degradation.


  • Organizational Affiliation

    School of Agriculture, Meiji University, Kawasaki, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
feruloyl esterase326Aspergillus oryzae RIB40Mutation(s): 0 
Gene Names: AO090005000945
EC: 3.1.1.73
UniProt
Find proteins for Q2UR69 (Aspergillus oryzae (strain ATCC 42149 / RIB 40))
Explore Q2UR69 
Go to UniProtKB:  Q2UR69
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2UR69
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.199 (Depositor), 0.209 (DCC) 
  • R-Value Work:  0.164 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 0.166 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.614α = 90
b = 63.529β = 90
c = 83.417γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MoRDaphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-05
    Type: Initial release