The sequence and structure of the target protein exert a marked effect on its soluble expression in Escherichia coli. The effects of the mutation of an amylase isolated from Bacillus licheniformis (BLA) on its soluble expression in E. coli were investigated. A random mutation library of BLA was constructed to screen for mutations that resulted in enhanced soluble expression in E. coli. Two interesting mutations (A390I and D401V) were identified, which are located at the interaction surface between the A and C domains of BLA. The A390I mutation enhanced soluble BLA expression by 2.0-fold compared to wild type, while D401V decreased soluble expression 160-fold. Structural analysis revealed that A390 and D401 residues could affect the interaction between the A and C domains of BLA. Therefore, soluble expression of the target protein in E. coli could be affected by introduction of a mutation in the protein sequence.