8HCJ image
Deposition Date 2022-11-01
Release Date 2023-11-15
Last Version Date 2025-01-15
Entry Detail
PDB ID:
8HCJ
Keywords:
Title:
Structure of GH43 family enzyme, Xylan 1, 4 Beta- xylosidase from pseudopedobacter saltans
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.57 Å
R-Value Free:
0.20
R-Value Work:
0.16
Space Group:
P 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Xylan 1,4-beta-xylosidase
Gene (Uniprot):Pedsa_2569
Chain IDs:A (auth: D), B (auth: E), C (auth: H), D (auth: A), E (auth: B), F (auth: G), G (auth: C), H (auth: F)
Chain Length:453
Number of Molecules:8
Biological Source:Pseudopedobacter saltans DSM 12145
Ligand Molecules
Primary Citation
Deciphering the structural and biochemical aspects of xylosidase from Pseudopedobacter saltans.
Int.J.Biol.Macromol. 291 139042 139042 (2024)
PMID: 39708861 DOI: 10.1016/j.ijbiomac.2024.139042

Abstact

Xylose, a key constituent of the heterogeneous hemicellulose polymer, occurs in lignocellulosic biomass and forms xylan polymers through β-1,4 glycosidic linkages. The β-1,4-xylosidase enzyme was isolated from Pseudopedobacter saltans (PsGH43) to find an effective enzyme with enhanced activity to depolymerize xylo-oligosaccharides. β-1,4-xylosidase belongs to the GH431 family as classified in the Carbohydrate-Active Enzyme Database (CAZy). PsGH432 was found to be active only on xylose-based substrate, 4NPX3, with maximum activity occurring at a pH 7 and 30 °C (Km 1.96 ± 0.2 mM and Vmax 0.43 mM/min). The study also confirms the influence of Ca2+ ions on enzymatic activity and thermal stability. Subsequently, native PsGH43 was crystallized at optimum conditions and the structure was determined at 2.5 Å resolution. Crystallographic analysis revealed an asymmetric unit containing eight monomers and 16 calcium ions wherein a tetramer constituted the functional unit. Each monomer exhibits a characteristic GH43 N-terminal β-propeller fold that serves as a catalytic domain accommodating one calcium ion in the centre, while the C-terminal β-sandwich fold associated with the CBM64 family preserves another calcium ion. Our study reveals a novel tetrameric arrangement of β-1,4-xylosidase which unravels its functional indispensability. This study opens newer avenues to engineer a potential enzyme for biofuel and bioethanol industry.

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Primary Citation of related structures