Acetyl xylan esterase from Paenibacillus sp. R4

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Crystal structure and functional characterization of a cold-active acetyl xylan esterase (PbAcE) from psychrophilic soil microbe Paenibacillus sp.

Park, S.H.Yoo, W.Lee, C.W.Jeong, C.S.Shin, S.C.Kim, H.W.Park, H.Kim, K.K.Kim, T.D.Lee, J.H.

(2018) PLoS One 13: e0206260-e0206260

  • DOI: https://doi.org/10.1371/journal.pone.0206260
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Cold-active acetyl xylan esterases allow for reduced bioreactor heating costs in bioenergy production. Here, we isolated and characterized a cold-active acetyl xylan esterase (PbAcE) from the psychrophilic soil microbe Paenibacillus sp. R4. The enzyme hydrolyzes glucose penta-acetate and xylan acetate, reversibly producing acetyl xylan from xylan, and it shows higher activity at 4°C than at 25°C. We solved the crystal structure of PbAcE at 2.1-Å resolution to investigate its active site and the reason for its low-temperature activity. Structural analysis showed that PbAcE forms a hexamer with a central substrate binding tunnel, and the inter-subunit interactions are relatively weak compared with those of its mesophilic and thermophilic homologs. PbAcE also has a shorter loop and different residue composition in the β4-α3 and β5-α4 regions near the substrate binding site. Flexible subunit movements and different active site loop conformations may enable the strong low-temperature activity and broad substrate specificity of PbAcE. In addition, PbAcE was found to have strong activity against antibiotic compound substrates, such as cefotaxime and 7-amino cephalosporanic acid (7-ACA). In conclusion, the PbAcE structure and our biochemical results provide the first example of a cold-active acetyl xylan esterase and a starting template for structure-based protein engineering.

  • Organizational Affiliation

    Unit of Polar Genomics, Korea Polar Research Institute, Incheon, Republic of Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
acetyl xylan esterase
A, B, C, D, E
A, B, C, D, E, F
321Paenibacillus sp. R4Mutation(s): 0 
Find proteins for A0A452CSP2 (Paenibacillus sp. R4)
Explore A0A452CSP2 
Go to UniProtKB:  A0A452CSP2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A452CSP2
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.797α = 90
b = 141.659β = 104.49
c = 105.369γ = 90
Software Package:
Software NamePurpose
MxDCdata collection
HKL-2000data scaling
Cootmodel building

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-10
    Type: Initial release
  • Version 1.1: 2018-12-26
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references