Importantly, both glutamines of the Q loop of the D1 domain of DLAR were seen to cluster with the R loop when the D1 domain was present in isolation. This interaction was uncoupled in the presence of the D2 domain of DLAR where one of the glutamines now clustered separately. This could perhaps account for the decrease in the activity of the D1 domain of DLAR in the presence of its D2 domain as it disrupts the glutamine network with the active site residues. Interestingly, in the case of PTP99A, the residues of the WPD loop formed a separate cluster from the active site when the D1 domain was present alone. This WPD loop cluster was seen to be merged with the active site residues in the presence of the D2 domain. It thus appears likely that the D2 domain of PTP99A enhances the activity of its D1 domain by strengthening the interaction networks between the active site residues and the WPD loop. Differences in the functional roles of RPTPs have often been explained by sequence-structure variations as well as spatiotemporal effects in developmental processes. The role of extracellular domains of these RPTPs is clear from unambiguous genetic data – deletions in the Immunoglobulin�Clike domains of DLAR are lethal, while deletions in the Fibronectin type III repeats are not. The Fibronectin type III repeats are essential for Drosophila oogenesis suggesting that these domains are used in distinct signaling pathways and cell fate decisions in Drosophila development . While the extracellular domains of these RPTPs are required for their proper localization in the nerve cell membrane, the signaling pathways at the growing axon cone are coordinated by the concerted activity of their cytosolic PTP domains. The tandem PTP domains of double domain RPTPs form an interesting model system. In particular, the role of the catalytic D2 domain in the function of these proteins is unclear from genetic data. For example, the D1 domains of DLAR and DPTP69D have been examined for their ability to rescue the homozygous deletion mutations of these genes. In the case of DLAR, D1 was found to be redundant as D2 could itself partially rescue the DLAR 2/2 phenotype . In the case of DPTP69D however, the active D1 domain was essential to rescue the DPTP69D 2/2 lethality . These contradictory findings suggest a complex PD-0325901 biological activity interplay between the PTP domains when attached in tandem. A combination of biochemical studies using activity measurements, protein-substrate interactions and MD simulations were performed to understand the molecular basis of modulation of phosphatase activity in the two tandem PTP domains of DLAR and PTP99A.