7FBW | pdb_00007fbw

Acetylxylan esterase from Caldanaerobacter subterraneus subsp. tengcongensis

• PDB DOI: https://doi.org/10.2210/pdb7FBW/pdb

• Classification: HYDROLASE
• Organism(s): Caldanaerobacter subterraneus subsp. tengcongensis MB4
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-07-13 Released: 2021-10-27 
• Deposition Author(s): Sasamoto, K., Himiyama, T., Moriyoshi, K., Ohmoto, T., Uegaki, K., Nishiya, Y., Nakamura, T.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.210 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.195 (DCC) 

Starting Model: experimental

Literature

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

• PubMed: 34726178 
• DOI: https://doi.org/10.1107/S2053230X21009675
• Primary Citation Related Structures: 
  7FBW


• 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.

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Organizational Affiliation: 
• Division of Life Science, Graduate School of Science and Engineering, Setsunan University, 17-8 Ikeda-Nakamachi, Neyagawa, Osaka 572-8508, Japan.
Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577, Japan.
Osaka Research Institute of Industrial Science and Technology, 1-6-50 Morinomiya, Joto-ku, Osaka 536-8553, Japan.
Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, 3327-204 Nakamachi, Nara 631-8505, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 34.62 kDa 
• Atom Count: 1,565 
• Modeled Residue Count: 186 
• Deposited Residue Count: 304 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Predicted xylanase/chitin deacetylase	A	304	Caldanaerobacter subterraneus subsp. tengcongensis MB4	Mutation(s): 0  Gene Names: Cda1, TTE0866
UniProt
Find proteins for Q8RBF4 (Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4)) Explore Q8RBF4  Go to UniProtKB:  Q8RBF4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	B [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.210 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.195 (DCC) 

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.211	α = 90
b = 105.992	β = 90
c = 118.077	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-10-27 
Deposition Author(s): Sasamoto, K., Himiyama, T., Moriyoshi, K., Ohmoto, T., Uegaki, K., Nishiya, Y., Nakamura, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	18K06616
Japan Society for the Promotion of Science (JSPS)	Japan	20K15403
Japan Society for the Promotion of Science (JSPS)	Japan	20K05740

Revision History  

• 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