Polysialic acid is an anti-adhesive protein modification that promotes cell migration and the plasticity of cell interactions. Because so few proteins carry polysialic acid, we hypothesized that polysialylation is a protein-specific event and that a specific polysialyltransferase-substrate interaction is the basis of this specificity. The major substrate for the polysialyltransferases is the neural cell adhesion molecule, NCAM. Previous work demonstrates that the first fibronectin type III repeat of NCAM (FN1) was necessary for the polysialylation of the N-glycans on the adjacent immunoglobulin domain (Ig5) (Close, B. E., Mendiratta, S. S., Geiger, K. M., Broom, L. J., Ho, L. L., and Colley, K. J. (2003) J. Biol. Chem. 278, 30796-30805). This suggested that FN1 may be a recognition site for the polysialyltransferases. In this study, we showed that the second fibronectin type III repeat (FN2) of NCAM cannot replace FN1. Arg substitution of three unique acidic amino acids on the surface of FN1 eliminated polysialylation not only of a minimal Ig5-FN1 substrate but also of full-length NCAM. Ala substitution of these residues eliminated Ig5-FN1 polysialylation but not that of full-length NCAM, suggesting that the two proteins are interacting differently with the enzymes and that multiple residues are involved in the enzyme-NCAM interaction. By using another truncated protein, Ig5-FN1-FN2, we confirmed the importance of enzyme-substrate positioning for optimal recognition and polysialylation. In sum, we have found that acidic residues on the surface of FN1 are part of a larger protein interaction region that is critical for NCAM recognition and polysialylation by the polysialyltransferases.