Nucleotide diphosphate kinase A (NDPK-A) acts as a metastasis promoter in neuroblastoma. Overexpression or the S120G mutation of NDPK-A, detected in patients with advanced neuroblastoma, promotes neuroblastoma cell invasiveness and metastasis in vitro and in vivo. Relative to the wild type, NDPK-AS120G appears to be a more potent promoter. Currently it is unclear how NDPK-A mechanistically promotes neuroblastoma metastasis. Using the yeast two-hybrid system, we have identified a novel protein (termed Protein Y) that interacted with NDPK-A, but not with NDPK-AS120G. Immunocytochemistry shows that Protein Y was translocated in human neuroblastoma NB69, IMR32 and, to a lesser degree, SH-SY5Y cell lines, and which is correlated with mutations in the Protein Y mRNA. In NB69 derivatives, ectopic expression of NDPK-A or NDPK-AS120G increased cell migration by two fold, whereas ectopic expression of Protein Y decreased cell migration by 47% in the transwell assay. In the clonogenic assay Protein Y reduced the colony number by 17%, whereas NDPK-A or NDPK-AS120G increased the number by 20-25%. Co-expression of Protein Y almost completely abolished the invasiveness-promoting ability of NDPK-A, but not NDPK-AS120G. Furthermore, deletion of the N-terminus of Protein Y abolished its ability to suppress the invasiveness-promoting ability of NDPK-A and, to a lesser degree, NDPK-AS120G. Knockdown of Protein Y expression restored the ability of NDPK-A to promote cell invasiveness. In xenograft zebrafish, NDPK-A or NDPK-AS120G increased NB69 extravasation by 3.9 and 1.9 folds, respectively. In contrast, Protein Y decreased NB69 extravasation by 14%. Co-expression of Protein Y reduced the extravasation-promoting ability of NDPK-A and NDPK-AS120G by 19.5% and 2.5%, respectively. In conclusion, Protein Y behaved as a suppressor and counteracted the invasiveness-promoting ability of NDPK-A and, to a lesser degree, NDPK-AS120G in NB69 cells. However, this invasiveness-suppressing ability of Protein Y is likely abrogated by mutations, as detected in the human neuroblastoma cell lines examined.