In this study, we analyzed the srtE gene from Corynebacterium glutamicum ATCC 13032, which codes for class E sortase, a transpeptidase involved in attaching surface proteins to the cell wall peptidoglycan. The surface proteins contain an N-terminal leader sequence and a C-terminal sorting signal which consist of a LAXTG motif, a transmembrane region, and a few positively charged amino acids. Sortase E deletion or its overexpression alters the attachment of the surface proteins to the cell wall peptidoglycan; however, the effects on morphology and bacterial physiology have not been studied. Thus, we constructed three C. glutamicum derivatives such as srtE deletion mutant, complemented and overexpressed strains to monitor the possible impact of the gene on cell growth, morphology, and physiological changes. Interestingly, deletion of the gene did not show any change in growth or morphology in C. glutamicum but showed a decrease in cell surface hydrophobicity and heat stress. However, the cells overexpressing the protein not only showed elongated cell morphology and a reduction in hydrophobicity when compared to wild-type and complemented strain, but also showed an increased sensitivity to heat. These results suggest that C. glutamicum sortase E deletion or overexpression causes sorting intermediates to accumulate, altering cellular morphology and physiology and adversely impacting the membrane integrity.