In this study, a novel protein glutaminase derived from Chryseobacterium lactis CGMCC 33780 (CLPG) was successfully purified via a one-step cell surface display approach, yielding its mature form. Subsequently, the enzymatic properties of CLPG were characterized. It exhibited optimal activity at a pH of 5 and a reaction temperature of 50 °C, and retained over 70% of its activity after a 12 h incubation at 50 °C. The study further investigated the impact of CLPG-mediated deamidation on the structural and functional attributes of krill protein isolate (KPI). A comprehensive analysis was conducted on the deamidation extent, conformational alterations, and microstructural morphology of KPI, employing techniques such as FTIR, CD, DSC, and SEM. After deamidation treatment with CLPG, the foaming and emulsifying properties of KPI were moderately shifted. When the CLPG dosage was 1.0 U/g with a corresponding deamidation degree of 15.18%, the emulsifying property of KPI reached the maximum value of 23%. These property enhancements were possibly primarily attributed to the increased electrostatic repulsion and hydrophobicity induced during the deamidation process. This work not only pioneers a novel method for the expression and purification of protein glutaminase but also applies it to the modification of krill protein, offering fresh insights for the development and application of protein glutaminases.