Protein glycosylation has been widely reported in diverse bacteria in recent years. Studies have shown that bacterial glycosylation has important roles in host:pathogen interactions, receptor recognition and immunoevasion. Gram-negative bacteria, such as Neisseria meningitidis, Neisseria gonorrhoeae, and Bacteroides fragilis, possess general O-linked glycosylation systems, in which a single O-oligosaccharyltransferase is capable of modifying various proteins using a pyrophosphate-polyprenyl carrier-linked glycan as the substrate donor. In pathogenic Neisseria, the O-oligosaccharyltransferase PglL is able to transfer glycan to serine or threonine of various substrate proteins including pilin and AniA. However, PglL does not appear to modify a defined consensus sequence in the protein substrate. Instead, our earlier study showed that in N. meningitidis, efficient glycosylation of additional protein substrates requires local structural similarity to the pilin acceptor site. In the present study, we propose that the C-terminal region of PglL has a tetratrico peptide repeat (TPR) region that is involved in protein substrate target recognition, or subcellular localisation of PglL. The deletion of the PglL TPR domain results in loss of glycosylation of pili and AniA. To further characterise the role of the TPR domain in PglL function, a bacterial two-hybrid system was used to identify and examine the key interactions between the TPR domain and the substrate protein. Overexpression of the PglL TPR domain, to compete with full-length PglL for substrate binding, was used to test the role of TPR domain in O-oligosaccharyltransferase activity. Understanding bacterial glycosylation systems and glycotransferase function will give insight into the evolution of general glycosylation systems in bacteria and lead to new opportunities to engineer glycoproteins with potential value as novel vaccines or drug delivery systems.