Low-resolution SAXS and comparative modeling based structure analysis of endo-β-1,4-xylanase a family 10 glycoside hydrolase from Pseudopedobacter saltans comb. nov

Abstract

The structure and biophysical properties of endo β-1,4-xylanase (PsGH10A) of family 10 glycoside hydrolase were characterized. The modeled PsGH10A structure showed classical (β/α)₈-barrel fold. Ramachandran plot displayed 99.1% residues in favored and 0.3% in the generously allowed region and only 0.6% residues in disallowed region. The secondary structure analysis of PsGH10A by CD revealed 31.75% α-helices 20.0% β-strands and 48.25% random coils. Protein melting study of PsGH10A showed complete unfolding at 60°C and did not require any metal ion for its stability. Structural superposition and docking analysis confirmed the involvement of Glu156 and Glu263 residues in catalysis. SAXS analysis displayed that PsGH10A is monomeric in nature showing fully folded state in solution form. Guinier analysis gave the radius of gyration (Rg) 2.23-2.29nm. Kratky plot indicated that the protein is fully folded globular shaped and flexible in solution form. The ab initio derived dummy model of PsGH10A displayed chicken thigh like shape. The ab initio derived dummy model superposed well with its comparative modeled structure except the N-terminal His-tag region.

Keywords: Comparative modeling; Endo-β 1,4-xylanase; Molecular docking and SAXS analysis; PsGH10A; Pseudopedobacter saltans.