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Recently we have identified the novel mitochondrial peptidase responsible for degrading presequences and other short unstructured peptides in mitochondria, the presequence peptidase, which we named PreP peptidasome. In the present study we have identified and characterized the human PreP homologue, hPreP, in brain mitochondria, and we show its capacity to degrade the amyloid ␤-protein (A␤). PreP belongs to the pitrilysin oligopeptidase family M16C containing an inverted zincbinding motif. We show that hPreP is localized to the mitochondrial matrix. In situ immuno-inactivation studies in human brain mitochondria using anti-hPreP antibodies showed complete inhibition of proteolytic activity against A␤. We have cloned, overexpressed, and purified recombinant hPreP and its mutant with catalytic base Glu 78 in the inverted zinc-binding motif replaced by Gln. In vitro studies using recombinant hPreP and liquid chromatography nanospray tandem mass spectrometry revealed novel cleavage specificities against A␤-(1-42), A␤-(1-40), and A␤ Arctic, a protein that causes increased protofibril formation an early onset familial variant of Alzheimer disease. In contrast to insulin degrading enzyme, which is a functional analogue of hPreP, hPreP does not degrade insulin but does degrade insulin B-chain. Molecular modeling of hPreP based on the crystal structure at 2.1 Å resolution of AtPreP allowed us to identify Cys 90 and Cys 527 that form disulfide bridges under oxidized conditions and might be involved in redox regulation of the enzyme. Degradation of the mitochondrial A␤ by hPreP may potentially be of importance in the pathology of Alzheimer disease.Several human disorders are associated with the deposition of aggregated peptides. One of them is Alzheimer disease (AD) 4 in which the polymerization of amyloid ␤-protein (A␤) into insoluble fibrils in brain seems to be a pathological event. An extracellular accumulation of A␤ has been the main focus of molecular studies associated with AD (1). However, increasing attention is directed toward intracellular events including the mitochondrial role in AD (2). There are many links between mitochondrial dysfunctions and AD (3, 4). Impairment of mitochondrial energy metabolism and altered cytochrome c oxidase activity are among the earliest detectable defects in AD (5, 6). It has been shown that Alzheimer amyloid precursor protein (APP) 695 is not only targeted to the plasma membrane but also to mitochondria (5). Accumulation of APP in the outer mitochondrial membrane caused dysfunctions and impaired energy metabolism. The active ␥-secretase complex including presenilin, nicastrin, APH-1, and PEN-2, which cleave APP to generate A␤, has been shown to be present in the mitochondrial outer membrane (7). Furthermore, the occurrence of A␤ in mitochondria of AD patients and its direct binding to ABAD (A␤-binding alcohol dehydrogenase, also called ERAB) induces apoptosis and free radical generation in neurons (8). A recent study demonstrated that A␤ is present in the mitochondrial matrix in A...

Presequence protease PreP is a novel protease that degrades targeting peptides as well as other unstructured peptides in both mitochondria and chloroplasts. The first structure of PreP from Arabidopsis thaliana refined at 2.1 Å resolution shows how the 995‐residue polypeptide forms a unique proteolytic chamber of more than 10 000 Å3 in which the active site resides. Although there is no visible opening to the chamber, a peptide is bound to the active site. The closed conformation places previously unidentified residues from the C‐terminal domain at the active site, separated by almost 800 residues in sequence to active site residues located in the N‐terminal domain. Based on the structure, a novel mechanism for proteolysis is proposed involving hinge‐bending motions that cause the protease to open and close in response to substrate binding. In support of this model, cysteine double mutants designed to keep the chamber covalently locked show no activity under oxidizing conditions. The manner in which substrates are processed inside the chamber is reminiscent of the proteasome; therefore, we refer to this protein as a peptidasome.

A number of proteins related to the homotetrameric transport protein transthyretin (TTR) forms a highly conserved protein family, which we present in an integrated analysis of data from different sources combined with an initial biochemical characterization. Homologues of the transthyretinrelated protein (TRP) can be found in a wide range of species including bacteria, plants and animals, whereas transthyretins have so far only been identified in vertebrates. A multiple sequence alignment of 49 TRP sequences from 47 species to TTR suggests that the tertiary and quaternary features of the three-dimensional structure are most likely preserved. Interestingly, while some of the TRP orthologues show as little as 30% identity, the residues at the putative ligandbinding site are almost entirely conserved. RT/PCR analysis in Caenorhabditis elegans confirms that one TRP gene is transcribed, spliced and predominantly expressed in the worm, which suggests that at least one of the two C. elegans TRP genes encodes a functional protein. We used doublestranded RNA-mediated interference techniques in order to determine the loss-of-function phenotype for the two TRP genes in C. elegans but detected no apparent phenotype. The cloning and initial characterization of purified TRP from Escherichia coli reveals that, while still forming a homotetramer, this protein does not recognize thyroid hormones that are the natural ligands of TTR. The ligand for TRP is not known; however, genomic data support a functional role involving purine catabolism especially linked to urate oxidase (uricase) activity.