M yotubular myopathy is an X-linked severe congenital disorder characterized by hypotonia and respiratory insufficiency. Mutations in myotubularin 1 (MTM1) cause the disorder as identified by positional cloning (1). At least 13 MTM1-like proteins have been found in the human genome, and they are termed MTM-related proteins (MTMRs) (2-4). MTMR2 is mutated in a recessive form of Charcot-Marie-Tooth disease type 4B, a demyelinating neurological disorder (5). Because mutations in different MTM proteins cause distinct disorders, it seems that MTM proteins are not redundant (6).MTM proteins contain a dual-specificity protein tyrosine phosphatase (PTP) motif, and MTM1, MTMR1, MTMR2, MTMR3, MTMR4, and MTMR6 have been shown to dephosphorylate the D-3 position of phosphatidylinositol (PtdIns) 3-phosphate [PtdIns(3)P] as the preferred substrate (7-11). Some MTM proteins are thought to be enzymatically inactive because they lack a conserved cysteine residue in the PTP motif that is required for activity. These include MTMR5 [SETbinding factor 1 (Sbf-1)], MTMR9 (LIP-STYX), MTMR10, MTMR11, MTMR12 [3-phosphatase adaptor protein (3-PAP)], and MTMR13 (Sbf-2).PtdIns(3)P phosphatases were isolated before the discovery of MTM proteins. Types I and II PtdIns(3)P phosphatase were shown to be composed of a homo-and a heterodimer, respectively (12). Recently, MTM1 and MTMR12 were shown to be the subunits of type II 3-phosphatase (13,14). MTMR2 has also been found to bind MTMR5 and MTMR12 (14,15). Therefore, inactive MTM proteins may bind to and regulate the localization and͞or activity of the enzymatic molecules as adapter proteins. MTMR5-deficient mice have impaired spermatogenesis and germ-cell differentiation (16), indicating that the adapter proteins are functionally important.Other conserved structures of MTM proteins are a SET interaction domain (SID) and predicted coiled-coil domain. The SET domain is named from the Drosophila proteins Su(var)3-9, Enhancer-of-zeste, and Trithorax, which contain the motif of unknown function (17). MTMR5 was isolated as a SET domainbinding protein of the protooncogene product Hrx by using yeast two-hybrid screening (18). The region that was essential for the binding of MTMR5 to the SET domain was identified and termed the SID (18). A splicing isoform of MTMR12 that lacks the SID failed to interact with MTM1 (14). A deletion of the coiled-coil domain abolished the interaction between MTMR2 and MTMR5 (15).The major substrate of MTM proteins, PtdIns(3)P, is formed by the phosphorylation of PtdIns by PtdIns 3-kinase, and this enzyme is found on the surface of early endosomes (19). In Saccharomyces cerevisiae, disruption of yeast PtdIns 3-kinase (Vps34p) results in decreased cellular PtdIns(3)P levels and defects in vacuolar protein sorting (20)(21)(22)(23)(24). Vps34p is the sole PtdIns 3-kinase in yeast, and it phosphorylates only PtdIns (23). A temperature-sensitive yeast vps34 mutant decreased PtdIns(3)P levels within 1 min after Vps34p was inactivated (22). A defect of yeast MTM (Ymr1P) increased ...