Structure of a presenilin family intramembrane aspartate protease

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γ-Secretase is an intramembrane protease responsible for the generation of amyloid-β (Aβ) peptides. Aberrant accumulation of Aβ leads to the formation of amyloid plaques in the brain of patients with Alzheimer's disease. Nicastrin is the putative substrate-recruiting component of the γ-secretase complex. No atomicresolution structure had been identified on γ-secretase or any of its four components, hindering mechanistic understanding of γ-secretase function. Here we report the crystal structure of nicastrin from Dictyostelium purpureum at 1.95-Å resolution. The extracellular domain of nicastrin contains a large lobe and a small lobe. The large lobe of nicastrin, thought to be responsible for substrate recognition, associates with the small lobe through a hydrophobic pivot at the center. The putative substrate-binding pocket is shielded from the small lobe by a lid, which blocks substrate entry. These structural features suggest a working model of nicastrin function. Analysis of nicastrin structure provides insights into the assembly and architecture of the γ-secretase complex.

Section: Discussionmentioning

confidence: 99%

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confidence: 99%

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Crystal structure of the γ-secretase component nicastrin

Xie

Yan

Zhou

et al. 2014

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“…Despite a number of structures solved recently (14)(15)(16)(17), these mechanisms Significance Sterol regulatory element-binding protein (SREBP) signaling is responsible for transcriptional regulation of cellular lipid homeostasis. Aberrant regulation of the feedback loop that switches on transcription of related genes upon depletion of fatty acids and cholesterol abrogates cellular integrity and is a hallmark of many cancers and other diseases.…”

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confidence: 99%

The membrane anchor of the transcriptional activator SREBP is characterized by intrinsic conformational flexibility

Linser

Salvi

Briones

et al. 2015

Regulated intramembrane proteolysis (RIP) is a conserved mechanism crucial for numerous cellular processes, including signaling, transcriptional regulation, axon guidance, cell adhesion, cellular stress responses, and transmembrane protein fragment degradation. Importantly, it is relevant in various diseases including Alzheimer's disease, cardiovascular diseases, and cancers. Even though a number of structures of different intramembrane proteases have been solved recently, fundamental questions concerning mechanistic underpinnings of RIP and therapeutic interventions remain. In particular, this includes substrate recognition, what properties render a given substrate amenable for RIP, and how the lipid environment affects the substrate cleavage. Members of the sterol regulatory element-binding protein (SREBP) family of transcription factors are critical regulators of genes involved in cholesterol/lipid homeostasis. After site-1 protease cleavage of the inactive SREBP transmembrane precursor protein, RIP of the anchor intermediate by site-2 protease generates the mature transcription factor. In this work, we have investigated the labile anchor intermediate of SREBP-1 using NMR spectroscopy. Surprisingly, NMR chemical shifts, site-resolved solvent exposure, and relaxation studies show that the cleavage site of the lipid-signaling protein intermediate bears rigid α-helical topology. An evolutionary conserved motif, by contrast, interrupts the secondary structure ∼9-10 residues C-terminal of the scissile bond and acts as an inducer of conformational flexibility within the carboxyl-terminal transmembrane region. These results are consistent with molecular dynamics simulations. Topology, stability, and site-resolved dynamics data suggest that the cleavage of the α-helical substrate in the case of RIP may be associated with a hinge motion triggered by the molecular environment.SREBP | regulated intramembrane proteolysis | membrane proteins | cellular lipid homeostasis | cancer

“…With this knowledge in hand, the position of presenilin could be assigned to the structure with more certainty using a model of presenilin obtained from the crystal structure of an archaeal presenilin homolog (14). Based on this new model, it is likely that nicastrin, Aph-1, and presenilin CTF (C-terminal fragment, TMDs 7-9) are located to the thick end of the horseshoe shape, whereas Pen2 and presenilin NTF (N-terminal fragment, TMDs 1-6) are located toward the thin end (Fig.…”

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confidence: 99%

Structure of nicastrin unveils secrets of γ-secretase

Bolduc

Wolfe

2014

Despite afflicting tens of millions worldwide, Alzheimer's disease (AD) remains a devastating brain-destroying malady with no effective treatment or cure. A central hallmark of AD is the deposition of amyloid plaques in the brain. These plaques are primarily composed of the amyloid β-peptide (Aβ), a byproduct of proteolytic processing of the amyloid precursor protein (APP) within its transmembrane domain by γ-secretase. Mutations in both APP and presenilin, the catalytic component of γ-secretase, are associated with dominant early-onset AD, highlighting their central importance in pathogenesis (1). Gaining a detailed mechanistic understanding of how γ-secretase processes APP-and its other substrates, such as Notch receptorsis critically important for biology and medicine (2). Despite a wealth of biochemical studies, key details of how γ-secretase functions have remained elusive because of a lack of high-resolution structural data. In PNAS, Xie et al. present a crystal structure of nicastrin, the first atomic-resolution structure of a component of a γ-secretase complex (3).The membrane-embedded γ-secretase complex is comprised of four proteins that are necessary and sufficient for its activity: Presenilin, Pen-2, Aph-1, and nicastrin (4). Presenilin, an aspartyl protease, contains catalytic aspartates on transmembrane domains (TMDs) 6 and 7 of its nine TMD helices. Upon assembly of the four components within the endoplasmic reticulum, presenilin undergoes autoproteolysis between TMDs 6 and 7 to form catalytically active γ-secretase. Pen2 has two TMDs and is thought to be important for triggering presenilin self-cleavage (5, 6). Little is known about the biochemical function of the seven-TMD Aph-1 other than that it is required for complex formation and full maturation of γ-secretase, although a recent study suggests a role in determining the length of Aβ peptide proteolytic products (7). The fourth component of the complex, nicastrin, is a single-TMD protein with a large ectodomain.γ-Secretase is a member of a broader family of intramembrane-cleaving proteases, which include the site 2 protease (S2P) family of metalloproteases and the rhomboid family of serine proteases (8). Unlike S2P and rhomboid, whose high-resolution structures were solved some years ago, detailed structural information of γ-secretase has been slow to develop. Until recently, the only structural information known about γ-secretase has been gleaned from low-resolution (∼12 Å at best) electron microscopy (EM) studies. With the advent of advanced cryo-EM techniques and equipment, a much more detailed structure of the complex was recently obtained (9). Although the resolution of this structure is still too poor to see atomic details, the overall architecture of the complex was visualized for the first time. Individual TMDs could be seen, although not assigned with certainty to each component of the complex. The most well-resolved portion of the complex was the ectodomain of nicastrin, although all of the glycosylation sites and several long segme...