7Y51

Acetylxylan esterase from Caldanaerobacter subterraneus subsp. tengcongensis TTE0866 delta100 mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Functional analysis of the N-terminal region of acetylxylan esterase from Caldanaerobacter subterraneus subsp. tengcongensis.

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

(2022) FEBS Open Bio 12: 1875-1885

  • DOI: https://doi.org/10.1002/2211-5463.13476
  • Primary Citation of Related Structures:  
    7Y51

  • PubMed Abstract: 

    Acetylxylan esterase from Caldanaerobacter subterraneus subsp. tengcongensis (TTE0866) has an N-terminal region (NTR; residues 23-135) between the signal sequence (residues 1-22) and the catalytic domain (residues 136-324), which is of unknown function. Our previous study revealed the crystal structure of the wild-type (WT) enzyme containing the NTR and the catalytic domain. Although the structure of the catalytic domain was successfully determined, that of the NTR was undetermined, as its electron density was unclear. In this study, we investigated the role of the NTR through functional and structural analyses of NTR truncation mutants. Based on sequence and secondary structure analyses, NTR was confirmed to be an intrinsically disordered region. The truncation of NTR significantly decreased the solubility of the proteins at low salt concentrations compared with that of the WT. The NTR-truncated mutant easily crystallized in a conventional buffer solution. The crystal exhibited crystallographic properties comparable with those of the WT crystals suitable for structural determination. These results suggest that NTR plays a role in maintaining the solubility and inhibiting the crystallization of the catalytic domain.


  • Organizational Affiliation

    Division of Life Science, Graduate School of Science and Engineering, Setsunan University, Osaka, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Predicted xylanase/chitin deacetylase204Caldanaerobacter subterraneus subsp. tengcongensis MB4Mutation(s): 0 
Gene Names: Cda1TTE0866
UniProt
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
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.191 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.09α = 90
b = 106.4β = 90
c = 117.78γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



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: 2022-08-31
    Type: Initial release
  • Version 1.1: 2022-09-21
    Changes: Database references
  • Version 1.2: 2022-10-19
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Refinement description