γ-Secretase is an intramembrane-cleaving protease that processes many type-I integral membrane proteins within the lipid bilayer, an event preceded by shedding of most of the substrate’s ectodomain by α- or β-secretases. The mechanism by which γ-secretase selectively recognizes and recruits ectodomain-shed substrates for catalysis remains unclear. In contrast to previous reports that substrate is actively recruited for catalysis when its remaining short ectodomain interacts with the nicastrin component of γ-secretase, we find that substrate ectodomain is entirely dispensable for cleavage. Instead, γ-secretase–substrate binding is driven by an apparent tight-binding interaction derived from substrate transmembrane domain, a mechanism in stark contrast to rhomboid—another family of intramembrane-cleaving proteases. Disruption of the nicastrin fold allows for more efficient cleavage of substrates retaining longer ectodomains, indicating that nicastrin actively excludes larger substrates through steric hindrance, thus serving as a molecular gatekeeper for substrate binding and catalysis.Regulated intramembrane proteolysis (RIP) involves the cleavage of a wide variety of integral membrane proteins within their transmembrane domains (TMDs) by a highly diverse family of intramembrane-cleaving proteases (I-CLiPs) (
1). I-CLiPs are found in all forms of life and govern many important biological functions, including but not limited to organism development (
2), lipid homeostasis (
3), the unfolded protein response (
4), and bacterial quorum sensing (
5). As the name implies, RIP must be tightly regulated to ensure that the resultant signaling events occur only when prompted by the cell and to prevent cleavage of the many nonsubstrate “bystander” proteins present within cellular membranes. Despite this, very little is known about the molecular mechanisms by which I-CLiPs achieve their exquisite specificity. Although traditional soluble proteases maintain substrate specificity by recognizing distinct amino acid sequences flanking the scissile bond, substrates for intramembrane proteases have little to no sequence similarity.Recent work on rhomboid proteases has demonstrated that this family of I-CLiPs achieves substrate specificity via a mechanism that is dependent on the transmembrane dynamics of the substrate rather than its sequence of amino acids (
6,
7). Here, rhomboid possesses a very weak binding affinity for substrate and, in a rate-driven reaction, only cleaves those substrates that have unstable TMD helices that have had time to unfold into the catalytic active site, where they are cleaved before they can dissociate from the enzyme–substrate complex. Although it may be tempting to speculate that this is a conserved mechanism for all I-CLiPs, rhomboid is the only family of I-CLiPs that does not require prior activation of substrate through an initial cleavage by another protease (
8). Specifically, site-2 protease substrates must be first cleaved by site-1 protease (
9), signal peptide peptidase substrates are first cleaved by signal peptidase (
10), and ectodomain shedding by α- or β-secretase is required before γ-secretase cleavage of its substrates (
11,
12). These facts suggest that the diverse families of I-CLiPs likely have evolved fundamentally different mechanisms by which they recognize and cleave their substrates.Presenilin/γ-secretase is the founding member of the aspartyl family of I-CLiPs. The importance of γ-secretase function in biology and medicine is highlighted by its cleavage of the notch family of receptors, which is required for cell fate determination in all metazoans (
2,
13–
16), and of the amyloid precursor protein (APP), which is centrally implicated in Alzheimer’s disease (AD) (
14,
17). In addition to APP and notch, γ-secretase has over 90 other reported substrates, many of which are involved in important signaling events (
12,
18). Despite this, little is known about the mechanism by which γ-secretase binds and cleaves its substrates. Currently, the only known prerequisite for a substrate to be bound and hydrolyzed by γ-secretase is that it be a type-I integral membrane protein that first has most of its ectodomain removed by a sheddase, either α- or β-secretases (
11,
12,
19). How γ-secretase selectively recognizes ectodomain-shed substrates and recruits them for catalysis while at the same time preventing cleavage of nonsubstrates remains unsettled.γ-Secretase is a multimeric complex composed of four integral membrane proteins both necessary and sufficient for full activity: presenilin, nicastrin, Aph-1, and Pen-2 (
20–
24). Presenilin is the proteolytic component, housing catalytic aspartates on TMDs 6 and 7 of its nine TMDs (
17,
25,
26). After initial complex formation, the mature proteolytically active complex is formed when presenilin undergoes auto-proteolysis, resulting in
N- and C-terminal fragments (NTF and CTF, respectively) (
17,
27,
28), a process thought to be stimulated by the three-TMD component Pen-2 (
29). The seven-TMD protein Aph-1 is believed to play a scaffolding role in complex formation (
30,
31). Nicastrin is a type-I integral membrane protein with a large, heavily glycosylated ectodomain (
32–
34) that contains multiple stabilizing disulfide bridges (
24,
34).The ectodomain of nicastrin is structurally homologous to a bacterial amino peptidase (
34). Although nicastrin lacks the specific amino acids required for peptidase activity, it has been proposed to bind the N terminus of ectodomain-shed substrate, thereby directing substrate TMD to the γ-secretase active site for cleavage (
35,
36). This mechanism has been suggested to depend on a key binding interaction between the free amine at the N terminus of the shortened substrate ectodomain and E333 of the vestigial amino peptidase domain of nicastrin (
35,
36). However, the importance of nicastrin in substrate recognition has been questioned (
37,
38), and although an initial high-resolution structure of γ-secretase suggested a role for nicastrin in substrate recognition (
24), the most recent structures of the γ-secretase complex and the nicastrin ectodomain reveal that E333 is actually buried within the interior of nicastrin and resides on the opposite side of the complex relative to the active site (
39,
40). Although this makes it unlikely that nicastrin is involved in direct substrate binding barring a large, energy-intensive conformational change, the basic mechanism of substrate recognition by γ-secretase remains controversial and requires resolution.Here, we demonstrate that nicastrin functions to sterically exclude substrates based on ectodomain size rather than actively recruit them for catalysis. This blocking mechanism allows γ-secretase to distinguish substrate from nonsubstrate and explains why substrate ectodomain shedding by α- or β-secretases is a prerequisite for γ-secretase catalysis. In contrast to rhomboid, γ-secretase apparently binds substrate TMD tightly, making the nicastrin steric hindrance mechanism necessary to prevent cleavage of nonectodomain-shed substrates and nonsubstrates alike.
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