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Background  The aromatic residues of xylanase enzyme, W187, Y124, W144, Y128 and W63 of substrate binding pocket from  Bacillus amyloliquefaciens  were investigated for their role in substrate binding by homology modelling and sequence analysis. These residues are highly conserved and play an important role in substrate binding through steric hindrance. The substitution of these residues with alanine allows the enzyme to accommodate nonspecific substrates.    Results  Wild type and mutated genes were cloned and overexpressed in BL21. Optimum pH and temperature of rBAxn exhibited pH 9.0 and 50 °C respectively and it was stable up to 215 h. Along with the physical properties of rBAxn, kinetic parameters ( K  m  19.34 ± 0.72 mg/ml;  k  cat  6449.12 ± 155.37 min − 1  and  k  cat  /K  m  333.83 ± 6.78 ml min − 1  mg − 1 ) were also compared with engineered enzymes. Out of five mutations, W63A, Y128A and W144A lost almost 90% activity and Y124A and W187A retained almost 40–45% xylanase activity.    Conclusions  The site-specific single mutation, led to alteration in substrate specificity from xylan to CMC while in case of double mutant the substrate specificity was altered from xylan to CMC, FP and avicel, indicating the role of aromatic residues on substrate binding, catalytic process and overall catalytic efficiency.    Electronic supplementary material  The online version of this article (10.1186/s12896-018-0420-7) contains supplementary material, which is available to authorized users.

Effects of substrate binding site residue substitutions of xynA from Bacillus amyloliquefaciens on substrate specificity