Structural insights of a putative β-1,4-xylosidase (PsGH43F) of glycoside hydrolase family 43 from Pseudopedobacter saltans

Structural and conformational insights of a putative β-1,4-xylosidase (PsGH43F) of glycoside hydrolase family 43 from Pseudopedobacter saltans were investigated by computational and Circular Dichroism (CD) analyses. PsGH43F was cloned and expressed in E. coli BL21 (DE3) cells and the purified enzyme...

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Veröffentlicht in:International journal of biological macromolecules 2022-11, Vol.221, p.751-762
Hauptverfasser: Yadav, Vishwanath, Ahmed, Jebin, Thakur, Abhijeet, Vishwakarma, Poorvi, Singh, Shubha, Kaur, Punit, Goyal, Arun
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container_title International journal of biological macromolecules
container_volume 221
creator Yadav, Vishwanath
Ahmed, Jebin
Thakur, Abhijeet
Vishwakarma, Poorvi
Singh, Shubha
Kaur, Punit
Goyal, Arun
description Structural and conformational insights of a putative β-1,4-xylosidase (PsGH43F) of glycoside hydrolase family 43 from Pseudopedobacter saltans were investigated by computational and Circular Dichroism (CD) analyses. PsGH43F was cloned and expressed in E. coli BL21 (DE3) cells and the purified enzyme gave the size ~50 kDa on SDS-PAGE analysis. Multiple Sequence Alignment of PsGH43F sequence followed by superposition of modeled structure with homologous structures displayed the presence of three conserved catalytic amino acid residues, Asp33, Asp149 and Glu212. The secondary structure analysis by CD showed 2.72 % α-helix and 36.06 % β-strands. The homology modeled structure of PsGH43F displayed a 5-bladed β-propeller fold for catalytic module at N-terminal and a β-sandwich structure for CBM6 at the C-terminal. Ramachandran plot displayed 99.5 % of residues in the allowed regions. MD simulation of PsGH43F revealed the compactness and stability of the structure. Molecular docking studies of PsGH43F with xylo-oligosaccharides revealed its maximum binding affinity for xylobiose. MD simulation of PsGH43F-xylobiose complex confirmed the increased structural and conformational stability in presence of substrate. The Hydrodynamic diameter analysis of PsGH43F by DLS was in the range, 0.25–0.28 μm. [Display omitted] •PsGH43F has 5-bladed β-propeller for catalytic module and β-sandwich fold for CBM6.•Active site is composed of Asp33, Asp149 and Glu210 catalytic amino acid residues.•Secondary structure of PsGH43F has 2.72 % α-helix, 36.06 % β-strands and 62.22 coils.•Molecular docking of PsGH43F revealed maximum affinity with xylobiose.•MD simulation of PsGH43F with xylobiose showed increased conformational stability.
doi_str_mv 10.1016/j.ijbiomac.2022.09.072
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MD simulation of PsGH43F-xylobiose complex confirmed the increased structural and conformational stability in presence of substrate. The Hydrodynamic diameter analysis of PsGH43F by DLS was in the range, 0.25–0.28 μm. 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MD simulation of PsGH43F-xylobiose complex confirmed the increased structural and conformational stability in presence of substrate. The Hydrodynamic diameter analysis of PsGH43F by DLS was in the range, 0.25–0.28 μm. 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PsGH43F was cloned and expressed in E. coli BL21 (DE3) cells and the purified enzyme gave the size ~50 kDa on SDS-PAGE analysis. Multiple Sequence Alignment of PsGH43F sequence followed by superposition of modeled structure with homologous structures displayed the presence of three conserved catalytic amino acid residues, Asp33, Asp149 and Glu212. The secondary structure analysis by CD showed 2.72 % α-helix and 36.06 % β-strands. The homology modeled structure of PsGH43F displayed a 5-bladed β-propeller fold for catalytic module at N-terminal and a β-sandwich structure for CBM6 at the C-terminal. Ramachandran plot displayed 99.5 % of residues in the allowed regions. MD simulation of PsGH43F revealed the compactness and stability of the structure. Molecular docking studies of PsGH43F with xylo-oligosaccharides revealed its maximum binding affinity for xylobiose. MD simulation of PsGH43F-xylobiose complex confirmed the increased structural and conformational stability in presence of substrate. The Hydrodynamic diameter analysis of PsGH43F by DLS was in the range, 0.25–0.28 μm. [Display omitted] •PsGH43F has 5-bladed β-propeller for catalytic module and β-sandwich fold for CBM6.•Active site is composed of Asp33, Asp149 and Glu210 catalytic amino acid residues.•Secondary structure of PsGH43F has 2.72 % α-helix, 36.06 % β-strands and 62.22 coils.•Molecular docking of PsGH43F revealed maximum affinity with xylobiose.•MD simulation of PsGH43F with xylobiose showed increased conformational stability.</abstract><pub>Elsevier B.V</pub><doi>10.1016/j.ijbiomac.2022.09.072</doi><tpages>12</tpages></addata></record>
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PsGH43F
β-1,4-Xylosidase
title Structural insights of a putative β-1,4-xylosidase (PsGH43F) of glycoside hydrolase family 43 from Pseudopedobacter saltans
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