Three cryo-EM structures of CD109 reveal its mechanism of protease inhibition

Ana V. Almeida; Kathrine T. Jensen; Seandean L. Harwood; Martin H. Jørgensen; Nadia S. Nielsen; Ida B. Thøgersen; Jan J. Enghild; Gregers R. Andersen

doi:10.1016/j.celrep.2025.115787

Three cryo-EM structures of CD109 reveal its mechanism of protease inhibition

Ana V. Almeida, Kathrine T. Jensen, Seandean L. Harwood, Martin H. Jørgensen, Nadia S. Nielsen, Ida B. Thøgersen, Jan J. Enghild, Gregers R. Andersen^*

^*Corresponding author af dette arbejde

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avis › Tidsskriftartikel › Forskning › peer review

Abstract

CD109 is a glycosylphosphatidylinositol-anchored protein. In addition to regulating transforming growth factor β (TGF-β) network signaling, CD109 is also a protease inhibitor. Protease cleavage of its bait region triggers a conformational change releasing the major fragment from the cell surface, exposing a reactive thioester that can conjugate proteases. To understand this protease inhibition mechanism, we determined cryoelectron microscopy structures of CD109 in native, protease-activated, and methylamine-activated conformations. Despite CD109’s low sequence similarity with the protease inhibitor A2ML1, CD109 adopts a similar protease-activated conformation, suggesting a shared mechanism of protease inhibition. Deglycosylation of CD109 does not affect chymotrypsin conjugation but enhances substrate access, suggesting that CD109 glycans contribute to protease inhibition. Our data provide a structural basis for understanding CD109’s protease-triggered membrane release, its protease inhibitory mechanism, and additional biological functions.

Originalsprog	Engelsk
Artikelnummer	115787
Tidsskrift	Cell Reports
Vol/bind	44
Nummer	6
ISSN	2639-1856
DOI	https://doi.org/10.1016/j.celrep.2025.115787
Status	Udgivet - 24 jun. 2025

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10.1016/j.celrep.2025.115787Licens: CC BY-NC

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title = "Three cryo-EM structures of CD109 reveal its mechanism of protease inhibition",

abstract = "CD109 is a glycosylphosphatidylinositol-anchored protein. In addition to regulating transforming growth factor β (TGF-β) network signaling, CD109 is also a protease inhibitor. Protease cleavage of its bait region triggers a conformational change releasing the major fragment from the cell surface, exposing a reactive thioester that can conjugate proteases. To understand this protease inhibition mechanism, we determined cryoelectron microscopy structures of CD109 in native, protease-activated, and methylamine-activated conformations. Despite CD109{\textquoteright}s low sequence similarity with the protease inhibitor A2ML1, CD109 adopts a similar protease-activated conformation, suggesting a shared mechanism of protease inhibition. Deglycosylation of CD109 does not affect chymotrypsin conjugation but enhances substrate access, suggesting that CD109 glycans contribute to protease inhibition. Our data provide a structural basis for understanding CD109{\textquoteright}s protease-triggered membrane release, its protease inhibitory mechanism, and additional biological functions.",

keywords = "CD109, conformational rearrangement, CP: Molecular biology, cryoelectron microscopy, glycosylation, protease inhibitor, TGF-β signaling, thioester protein",

author = "Almeida, {Ana V.} and Jensen, {Kathrine T.} and Harwood, {Seandean L.} and J{\o}rgensen, {Martin H.} and Nielsen, {Nadia S.} and Th{\o}gersen, {Ida B.} and Enghild, {Jan J.} and Andersen, {Gregers R.}",

year = "2025",

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T1 - Three cryo-EM structures of CD109 reveal its mechanism of protease inhibition

AU - Almeida, Ana V.

AU - Jensen, Kathrine T.

AU - Harwood, Seandean L.

AU - Jørgensen, Martin H.

AU - Nielsen, Nadia S.

AU - Thøgersen, Ida B.

AU - Enghild, Jan J.

AU - Andersen, Gregers R.

PY - 2025/6/24

Y1 - 2025/6/24

N2 - CD109 is a glycosylphosphatidylinositol-anchored protein. In addition to regulating transforming growth factor β (TGF-β) network signaling, CD109 is also a protease inhibitor. Protease cleavage of its bait region triggers a conformational change releasing the major fragment from the cell surface, exposing a reactive thioester that can conjugate proteases. To understand this protease inhibition mechanism, we determined cryoelectron microscopy structures of CD109 in native, protease-activated, and methylamine-activated conformations. Despite CD109’s low sequence similarity with the protease inhibitor A2ML1, CD109 adopts a similar protease-activated conformation, suggesting a shared mechanism of protease inhibition. Deglycosylation of CD109 does not affect chymotrypsin conjugation but enhances substrate access, suggesting that CD109 glycans contribute to protease inhibition. Our data provide a structural basis for understanding CD109’s protease-triggered membrane release, its protease inhibitory mechanism, and additional biological functions.

AB - CD109 is a glycosylphosphatidylinositol-anchored protein. In addition to regulating transforming growth factor β (TGF-β) network signaling, CD109 is also a protease inhibitor. Protease cleavage of its bait region triggers a conformational change releasing the major fragment from the cell surface, exposing a reactive thioester that can conjugate proteases. To understand this protease inhibition mechanism, we determined cryoelectron microscopy structures of CD109 in native, protease-activated, and methylamine-activated conformations. Despite CD109’s low sequence similarity with the protease inhibitor A2ML1, CD109 adopts a similar protease-activated conformation, suggesting a shared mechanism of protease inhibition. Deglycosylation of CD109 does not affect chymotrypsin conjugation but enhances substrate access, suggesting that CD109 glycans contribute to protease inhibition. Our data provide a structural basis for understanding CD109’s protease-triggered membrane release, its protease inhibitory mechanism, and additional biological functions.

KW - CD109

KW - conformational rearrangement

KW - CP: Molecular biology

KW - cryoelectron microscopy

KW - glycosylation

KW - protease inhibitor

KW - TGF-β signaling

KW - thioester protein

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U2 - 10.1016/j.celrep.2025.115787

DO - 10.1016/j.celrep.2025.115787

M3 - Journal article

C2 - 40482031

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SN - 2639-1856

VL - 44

JO - Cell Reports

JF - Cell Reports

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M1 - 115787

ER -

Three cryo-EM structures of CD109 reveal its mechanism of protease inhibition

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