Acetylxylan esterase from Caldanaerobacter subterraneus subsp. tengcongensis

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.186 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Crystal structure of acetylxylan esterase from Caldanaerobacter subterraneus subsp. tengcongensis.

Sasamoto, K.Himiyama, T.Moriyoshi, K.Ohmoto, T.Uegaki, K.Nishiya, Y.Nakamura, T.

(2021) Acta Crystallogr F Struct Biol Commun 77: 399-406

  • DOI: https://doi.org/10.1107/S2053230X21009675
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The acetylxylan esterases (AXEs) classified into carbohydrate esterase family 4 (CE4) are metalloenzymes that catalyze the deacetylation of acetylated carbohydrates. AXE from Caldanaerobacter subterraneus subsp. tengcongensis (TTE0866), which belongs to CE4, is composed of three parts: a signal sequence (residues 1-22), an N-terminal region (NTR; residues 23-135) and a catalytic domain (residues 136-324). TTE0866 catalyzes the deacetylation of highly substituted cellulose acetate and is expected to be useful for industrial applications in the reuse of resources. In this study, the crystal structure of TTE0866 (residues 23-324) was successfully determined. The crystal diffracted to 1.9 Å resolution and belonged to space group I2 1 2 1 2 1 . The catalytic domain (residues 136-321) exhibited a (β/α) 7 -barrel topology. However, electron density was not observed for the NTR (residues 23-135). The crystal packing revealed the presence of an intermolecular space without observable electron density, indicating that the NTR occupies this space without a defined conformation or was truncated during the crystallization process. Although the active-site conformation of TTE0866 was found to be highly similar to those of other CE4 enzymes, the orientation of its Trp264 side chain near the active site was clearly distinct. The unique orientation of the Trp264 side chain formed a different-shaped cavity within TTE0866, which may contribute to its reactivity towards highly substituted cellulose acetate.

  • Organizational Affiliation

    Division of Life Science, Graduate School of Science and Engineering, Setsunan University, 17-8 Ikeda-Nakamachi, Neyagawa, Osaka 572-8508, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Predicted xylanase/chitin deacetylase304Caldanaerobacter subterraneus subsp. tengcongensis MB4Mutation(s): 0 
Gene Names: Cda1TTE0866
Find proteins for Q8RBF4 (Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4))
Explore Q8RBF4 
Go to UniProtKB:  Q8RBF4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8RBF4
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NI

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Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.186 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.211α = 90
b = 105.992β = 90
c = 118.077γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan18K06616
Japan Society for the Promotion of Science (JSPS)Japan20K15403
Japan Society for the Promotion of Science (JSPS)Japan20K05740

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-27
    Type: Initial release
  • Version 1.1: 2021-11-17
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Derived calculations, Refinement description