Affinage

LYPLA2

Acyl-protein thioesterase 2 · UniProt O95372

Length
231 aa
Mass
24.7 kDa
Annotated
2026-06-10
12 papers in source corpus 8 papers cited in narrative 8 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 6/7 claims corpus-supported (86%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

LYPLA2 (APT2) is an acyl protein thioesterase that controls the membrane localization and signaling output of diverse substrate proteins by removing their S-palmitoyl modifications (PMID:28065656, PMID:39255795). Its catalytic machinery comprises a serine-hydrolase triad and oxyanion hole adjacent to an acyl-binding pocket, with isoform-specific gatekeeper residues surrounding the active site that determine accessibility and substrate dynamics, as defined by the crystal structure with the selective inhibitor ML349 (PMID:27748579). APT2 is itself S-acylated by the palmitoyltransferases ZDHHC3 or ZDHHC7 through a stepwise mechanism of electrostatic attraction, hydrophobic-loop insertion, and S-acylation; this membrane anchoring both protects APT2 from proteasomal degradation and positions it to deform the lipid bilayer and extract substrate acyl chains into its hydrophobic pocket for hydrolysis (PMID:33707782). Through depalmitoylation, APT2 displaces the scaffold Scribble from the plasma membrane downstream of the EMT factor Snail and modulates MEK activation (PMID:28065656), suppresses MAVS aggregation to dampen TBK1-IRF3-interferon antiviral signaling (PMID:39255795), and drives STAT3 nuclear translocation to sustain transcription of the ferroptosis inhibitors GPX4 and SLC7A11 (PMID:41604764). APT2 also opposes ZDHHC14-mediated palmitoylation of HSV-2 glycoprotein B, reducing viral entry (PMID:40582294). APT2 activity is chemically tunable: ML349 provides isoform-selective inhibition (PMID:27748579, PMID:28065656), sulforaphane binds Cys56 to attenuate APT2's own palmitoylation and membrane localization (PMID:38905785), and solasonine directly blocks its enzymatic activity (PMID:41604764). In NRAS-mutant melanoma, selective APT2 inhibition had no effect on NRAS signaling or viability (PMID:26771141).

Mechanistic history

Synthesis pass · year-by-year structured walk · 8 steps
  1. 2016 High

    Defined the structural and catalytic basis for isoform-selective inhibition and acyl substrate hydrolysis by APT2, distinguishing it from its paralog at the active site.

    Evidence 1.64 Å crystal structure of APT2 with ML349, reciprocal active-site mutagenesis, and biochemical activity profiling

    PMID:27748579

    Open questions at the time
    • Structure with a bound natural acyl substrate not resolved
    • Conformational dynamics of bilayer engagement not captured in crystal form
  2. 2016 Medium

    Established that APT2 is dispensable for NRAS signaling, narrowing its functional scope away from a presumed RAS-depalmitoylation role.

    Evidence siRNA knockdown and ML349 inhibition with viability and signaling readouts in NRAS-mutant melanoma (negative result)

    PMID:26771141

    Open questions at the time
    • Negative result limited to one cell context; does not exclude NRAS regulation elsewhere
    • Possible redundancy with APT1 not fully resolved
  3. 2017 High

    Identified Scribble as a physiological APT2 substrate and placed APT2 within a palmitoylation cycle controlling scaffold localization and MEK signaling under EMT.

    Evidence siRNA knockdown, ML349 inhibition, palmitoylation assays, immunofluorescence, and MEK activity measurement

    PMID:28065656

    Open questions at the time
    • Direct enzyme-substrate contact with Scribble not structurally defined
    • How Snail-driven APT2 upregulation integrates with broader EMT not detailed
  4. 2021 High

    Resolved how APT2 reaches and engages membranes—being palmitoylated by ZDHHC3/7 to gain stability and bilayer-deforming substrate access—answering how a soluble hydrolase acts on membrane-anchored acyl chains.

    Evidence Computational modeling validated by membrane fractionation, mutagenesis, proteasome-inhibitor rescue, and palmitoylation assays

    PMID:33707782

    Open questions at the time
    • Direct structural visualization of the bilayer-deformed state lacking
    • Regulation of APT2's own depalmitoylation not addressed
  5. 2024 Medium

    Extended APT2 substrate repertoire to MAVS, linking its depalmitoylase activity to suppression of innate antiviral interferon signaling.

    Evidence Palmitoylation assays, genetic and ML349 inhibition, TBK1/IRF3/IFN readouts, and high-fat-diet mouse model

    PMID:39255795

    Open questions at the time
    • Single-lab study; reciprocal validation of MAVS as direct substrate limited
    • Site of MAVS depalmitoylation not pinpointed
  6. 2024 Medium

    Showed APT2 activity is pharmacologically dampened through covalent engagement of Cys56 by sulforaphane, reducing its own palmitoylation and membrane localization.

    Evidence SFaN-bead affinity pulldown, C56 mutagenesis, palmitoylation assay, and subcellular fractionation

    PMID:38905785

    Open questions at the time
    • Whether C56 modification alters catalytic activity directly not separated from localization effect
    • Single-lab study
  7. 2025 Medium

    Demonstrated APT2 acts on a viral substrate, opposing ZDHHC14 to depalmitoylate HSV-2 glycoprotein B and limit viral entry.

    Evidence Acyl-biotin exchange, ML349 inhibition, ZDHHC14-gB co-IP, C8S mutagenesis, and viral entry assay

    PMID:40582294

    Open questions at the time
    • Single study; direct APT2-gB physical interaction not shown
    • Generality across other viral glycoproteins untested
  8. 2026 Medium

    Connected APT2-mediated STAT3 depalmitoylation to nuclear translocation and ferroptosis-inhibitor transcription, defining a cancer-relevant signaling axis druggable by solasonine.

    Evidence Docking, CETSA, SPR direct binding, Western blot, ChIP-qPCR, luciferase reporter, ferroptosis markers, and xenograft

    PMID:41604764

    Open questions at the time
    • Single-lab study; STAT3 palmitoylation site engaged by APT2 not defined
    • Selectivity of solasonine for APT2 over related hydrolases not established

Open questions

Synthesis pass · forward-looking unresolved questions
  • How APT2 substrate selectivity is encoded in cells and what determines which palmitoylated proteins it engages across contexts remains unresolved.
  • No unifying recognition motif or structural rule for substrate choice
  • Spatial/temporal regulation of APT2 substrate access across organelles unknown

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140096 catalytic activity, acting on a protein 5 GO:0016787 hydrolase activity 2
Localization
GO:0005886 plasma membrane 3
Pathway
R-HSA-162582 Signal Transduction 2 R-HSA-392499 Metabolism of proteins 2 R-HSA-168256 Immune System 1
Partners
MAVSSCRIBSTAT3ZDHHC14ZDHHC3ZDHHC7

Evidence

Reading pass · 8 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2016 High-resolution crystal structure of human APT2 (LYPLA2) in complex with isoform-selective inhibitor ML349 (1.64 Å) revealed that the sulfonyl group of ML349 forms hydrogen bonds with active-site-resident waters to indirectly engage the catalytic triad and oxyanion hole. Reciprocal mutagenesis identified several differing residues surrounding the active site that serve as critical gatekeepers for isoform accessibility and dynamics. The inhibitors occupy a putative acyl-binding region, establishing the mechanism for isoform-specific inhibition and hydrolysis of acyl substrates. X-ray crystallography (1.64 Å), active-site mutagenesis, and biochemical activity profiling ACS chemical biology High 27748579
2021 APT2 (LYPLA2) is itself S-acylated (palmitoylated) by palmitoyltransferases ZDHHC3 or ZDHHC7, which is required for stable membrane binding; membrane binding in turn protects APT2 from proteasomal degradation. Membrane interaction proceeds through three consecutive steps: electrostatic attraction, insertion of a hydrophobic loop, and then S-acylation. Once membrane-bound, APT2 is predicted (by computational modeling validated experimentally) to deform the lipid bilayer to extract the acyl chain from its substrate into a hydrophobic pocket for hydrolysis. Computational modeling combined with experimental validation (membrane fractionation, mutagenesis, proteasome inhibitor treatment, palmitoylation assays, structural analysis) Nature chemical biology High 33707782
2017 APT2 (LYPLA2) depalmitoylates the scaffolding protein Scribble (Scrib), and elevated APT2 expression/activity (driven by the EMT transcription factor Snail) causes Scrib displacement from the plasma membrane. Isoform-selective APT2 inhibition (ML349) or APT2 knockdown rescued Scrib membrane localization and palmitoylation while attenuating MEK activation, placing APT2 upstream of Scrib palmitoylation and MEK signaling in the palmitoylation cycle. siRNA knockdown, isoform-selective pharmacological inhibition (ML349), palmitoylation assays, immunofluorescence localization, MEK activity measurement Cell chemical biology High 28065656
2024 APT2 (LYPLA2) depalmitoylates MAVS (mitochondrial antiviral signaling protein), thereby inhibiting MAVS aggregation and suppressing the TBK1-IRF3-interferon antiviral signaling pathway. APT2 inhibition with ML349 reverses this effect and enhances antiviral innate immune responses. Palmitoylation assays, genetic and pharmacological inhibition (ML349), signaling pathway readouts (TBK1, IRF3, IFN levels), in vitro and in vivo (high-fat-diet mouse) models Molecular cell Medium 39255795
2024 Sulforaphane (SFaN) directly binds APT2 (LYPLA2) via cysteine residue C56, attenuating APT2's own S-palmitoylation and thereby reducing APT2 plasma membrane localization. Chemical pulldown (SFaN-bead affinity), mutagenesis of C56, palmitoylation assay, subcellular fractionation/localization Biochemical and biophysical research communications Medium 38905785
2025 APT2 (LYPLA2) acts as a negative regulator of HSV-2 glycoprotein B (gB) palmitoylation at cysteine C8, opposing the palmitoyltransferase ZDHHC14. APT2 inhibition impairs HSV-2 pseudotyped particle entry efficiency, demonstrating that APT2-mediated depalmitoylation of gB reduces its plasma membrane localization and viral infectivity. Acyl-biotin exchange assay, pharmacological APT2 inhibition, co-immunoprecipitation (ZDHHC14-gB interaction), site-directed mutagenesis (C8S), viral entry assay Virology Medium 40582294
2026 APT2 (LYPLA2) depalmitoylates STAT3, and direct inhibition of APT2 enzymatic activity by solasonine blocks STAT3 depalmitoylation, preventing phospho-STAT3 nuclear translocation and suppressing transcription of ferroptosis inhibitors GPX4 and SLC7A11 in gallbladder cancer cells. Molecular docking, CETSA (cellular thermal shift assay), surface plasmon resonance (direct binding), Western blot for STAT3 nuclear translocation, ChIP-qPCR, dual-luciferase reporter assay, ferroptosis markers (MDA, ROS, GSH, Fe2+), in vivo xenograft Phytotherapy research Medium 41604764
2016 siRNA-mediated knockdown of APT2 (LYPLA2), as well as the selective APT2 inhibitor ML349, had no biologically significant effects on NRAS downstream signaling or cell viability in NRAS mutant melanoma cells (negative result). The dual APT1/APT2 inhibitor palmostatin B, but not isoform-selective inhibition of APT2 alone, affected NRAS signaling. siRNA knockdown, isoform-selective pharmacological inhibition (ML349), cell viability assay, downstream signaling readout Oncotarget Medium 26771141

Source papers

Stage 0 corpus · 12 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2016 Molecular Mechanism for Isoform-Selective Inhibition of Acyl Protein Thioesterases 1 and 2 (APT1 and APT2). ACS chemical biology 92 27748579
2017 APT2 Inhibition Restores Scribble Localization and S-Palmitoylation in Snail-Transformed Cells. Cell chemical biology 68 28065656
2021 Palmitoylated acyl protein thioesterase APT2 deforms membranes to extract substrate acyl chains. Nature chemical biology 58 33707782
2016 Acyl protein thioesterase 1 and 2 (APT-1, APT-2) inhibitors palmostatin B, ML348 and ML349 have different effects on NRAS mutant melanoma cells. Oncotarget 40 26771141
2024 Targeting APT2 improves MAVS palmitoylation and antiviral innate immunity. Molecular cell 30 39255795
1999 APT1, but not APT2, codes for a functional adenine phosphoribosyltransferase in Saccharomyces cerevisiae. Journal of bacteriology 17 9864350
2023 Functional Analysis of the P-Type ATPases Apt2-4 from Cryptococcus neoformans by Heterologous Expression in Saccharomyces cerevisiae. Journal of fungi (Basel, Switzerland) 4 36836316
2025 The flippases Apt1 and Apt2 differentially influence extracellular vesicle cargo and polysaccharide secretion in Cryptococcus neoformans. Journal of proteomics 3 40543703
2024 Identification of a novel target of sulforaphane: Sulforaphane binds to acyl-protein thioesterase 2 (APT2) and attenuates its palmitoylation. Biochemical and biophysical research communications 3 38905785
2025 ZDHHC14 and APT2 regulate the palmitoylation of HSV-2 gB. Virology 1 40582294
2026 Pharmacological Inhibition of APT2 by Solasonine Promotes Ferroptosis Through Palmitoylation Modulation in Gallbladder Cancer. Phytotherapy research : PTR 0 41604764
2026 ZIC2 affects oral squamous cell carcinoma stemness by regulating glycerophosphocholine metabolism via LYPLA2. Cell death & disease 0 41856987

Missed literature

Know a paper Affinage missed for LYPLA2? Flag it for the maintainers and the community.

No submissions yet.