Our previous studies demonstrated that JWA, a novel retinoic acids responsive and cytoskeleton related gene, is associated with cell differentiation and apoptosis. In the present study, to elucidate if the JWA is a novel kind of microtubule-associated proteins (MAPs) and functionally link to microtubule, we first successfully identified JWA from the physically purified MAPs complex of rat brain tissues. The results of co-immunoprecipitation, gene transfection and immunofluorescence microscopy assays from HBE and NIH3T3 cells provide strong evidence for a linkage between JWA and β-tubulin. In general, JWA is stably binding to β-tubulin whenever microtubule is polymerized or not, and it may be critical to the mitosis process. In addition, by use of the antisense oligonucleotides technique, we also showed that JWA is a negative modulator on intracellular amino acids in PC12 cells. Further analysis indicated that JWA selectively regulates both taurine, an inhibitory amino acid, and glutamate, an excitatory amino acid. In conclusion, JWA is not only structurally associated, but also a novel functional MAP.