Mutations in PTEN-induced putative kinase 1 (PINK1) are a cause of autosomal recessive familial Parkinson's disease (PD). Efforts in deducing the PINK1 signaling pathway have been hindered by controversy around its subcellular and submitochondrial localization and the authenticity of its reported substrates. We show here that this mitochondrial protein exhibits a topology in which the kinase domain faces the cytoplasm and the N-terminal tail is inside the mitochondria. Although deletion of the transmembrane domain disrupts this topology, common PD-linked PINK1 mutations do not. These results are critical in rectifying the location and orientation of PINK1 in mitochondria, and they should help decipher its normal physiological function and potential pathogenic role in PD.parkin ͉ Parkinson's disease ͉ mitochondria ͉ topology P arkinson's disease (PD), the second most common neurodegenerative disorder, is a sporadic condition that can occasionally be inherited (1). The rationale for studying the rare genetic forms of PD is based on the phenotypic similarity between the familial and sporadic forms of the disease, implying that the two share important pathogenic mechanisms. Among the different gene products associated with familial PD (2), PTEN-induced putative kinase-1 (PINK1) is localized to the mitochondria (3-10), an organelle strongly linked to PD pathogenesis. Although recessively inherited PD mutations in PINK1 are found throughout the protein, they are most commonly found in the only recognized functional domain of PINK1 (3,11,12), which is a serine/threonine kinase domain similar to that in the Ca 2ϩ /calmodulin kinase family (13,14). Overexpression of wild-type PINK1 can rescue the phenotype caused by PINK1 mutations in Drosophila (15, 16), supporting the notion that the mutated allele gives rise to a loss-of-function phenotype.Human PINK1 is a 581-aa polypeptide with a predicted N-terminal mitochondrial targeting signal (MTS), consistent with the observation that PINK1 localizes to mitochondria (Fig. 1A) (3-10). Loss-of-function mutations in the gene encoding parkin (an E3 ubiquitin ligase) cause the most frequent forms of recessive familial PD (17). In Drosophila, parkin is thought to operate within the same molecular pathway as PINK1 to modulate mitochondrial morphology (15,16,18), an intriguing observation given the fact that parkin has been reported to essentially be cytosolic (19).Both the subcellular and submitochondrial locations of PINK1 and the authenticity of its reported substrates have been controversial. Although it is agreed that PINK1 is a mitochondrialtargeted protein, PINK1 has been reported to reside in the inner mitochondrial membrane (IMM) (6,7,9,20), the mitochondrial intermembrane space (IMS) (6,8,9), the outer mitochondrial membrane (OMM) (7), and even the cytoplasm (21-24). Furthermore, the tumor necrosis factor type 1 receptor-associated protein (TRAP1) and the serine protease HtrA2/Omi have been identified as putative PINK1 substrates (8, 9). Although TRAP1 is localized mainly i...