Coupling to short linear motifs creates versatile PME-1 activities in PP2A holoenzyme demethylation and inhibition
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin at Madison, School of Medicine and Public Health, United States
- Biophysics program, University of Wisconsin at Madison, United States
- Department of Chemistry – BMC, Uppsala University, Sweden
- Department of Neuroscience and Pharmacology, University of Iowa, United States
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, United States
Figures
Figure 1 with 1 supplement
PP2A methylesterase 1 (PME-1) directly interacts with and demethylates protein phosphatase 2A (PP2A) holoenzymes.
(a) Structural overlay of the PP2A-B56γ1 holoenzyme (PDB code: 2NPP) to the PP2A core enzyme–PME-1 complex (PDB code: 3C5W) aligned via PP2Ac (c) and the C-terminal five …
-
Figure 1—source data 1
Source data for Figure 1b.
- https://cdn.elifesciences.org/articles/79736/elife-79736-fig1-data1-v2.zip
-
Figure 1—source data 2
Source data for Figure 1c.
- https://cdn.elifesciences.org/articles/79736/elife-79736-fig1-data2-v2.zip
-
Figure 1—source data 3
Source data for Figure 1d.
- https://cdn.elifesciences.org/articles/79736/elife-79736-fig1-data3-v2.zip
-
Figure 1—source data 4
Source data for Figure 1e.
- https://cdn.elifesciences.org/articles/79736/elife-79736-fig1-data4-v2.zip
Figure 1—figure supplement 1
PP2A methylesterase 1 (PME-1) interactions with different B56 family members, likely via the conserved B56 common core.
(a) Domain structures of regulatory subunits in the B56 family. The conserved common core in B56 subunits is colored yellow. Other family members have distinct N- and C-terminal extensions. B56δ has …
-
Figure 1—figure supplement 1—source data 1
Source data for Figure 2—figure supplement 1b.
- https://cdn.elifesciences.org/articles/79736/elife-79736-fig1-figsupp1-data1-v2.zip
-
Figure 1—figure supplement 1—source data 2
Source data for Figure 2—figure supplement 1c.
- https://cdn.elifesciences.org/articles/79736/elife-79736-fig1-figsupp1-data2-v2.zip
-
Figure 1—figure supplement 1—source data 3
Source data for Figure 2—figure supplement 1d.
- https://cdn.elifesciences.org/articles/79736/elife-79736-fig1-figsupp1-data3-v2.zip
Figure 2 with 3 supplements
Mapping of PP2A methylesterase 1 (PME-1) interactions with protein phosphatase 2A (PP2A) regulatory subunits and holoenzymes.
(a) Summary of mapping results (Figure 2—figure supplement 1) on the roles of PME-1 disordered regions in interactions with different PP2A regulatory subunits (left) and illustration of disordered …
-
Figure 2—source data 1
Source data for Figure 2b.
- https://cdn.elifesciences.org/articles/79736/elife-79736-fig2-data1-v2.zip
-
Figure 2—source data 2
Source data for Figure 2c.
- https://cdn.elifesciences.org/articles/79736/elife-79736-fig2-data2-v2.zip
-
Figure 2—source data 3
Source data for Figure 2d.
- https://cdn.elifesciences.org/articles/79736/elife-79736-fig2-data3-v2.zip
-
Figure 2—source data 4
Source data for Figure 2e.
- https://cdn.elifesciences.org/articles/79736/elife-79736-fig2-data4-v2.zip
Figure 2—figure supplement 1
PP2A methylesterase 1 (PME-1) interactions with Bα and PR70 regulatory subunits and holoenzymes.
(a) Isothermal titration calorimetry (ITC) measured the binding affinities of B56γ1 to PME-1 FL, ΔIL, or ΔN18. (b) ITC measured the binding affinities of PR70 to PME-1 FL, ΔIL, or ΔN18. (c) Pulldown …
-
Figure 2—figure supplement 1—source data 1
Source data for Figure 2—figure supplement 1c.
- https://cdn.elifesciences.org/articles/79736/elife-79736-fig2-figsupp1-data1-v2.zip
Figure 2—figure supplement 2
Mapping and characterization of CRTC3 peptide motif that interacts with Bα regulatory subunit.
(a) Amino acid sequence of CRTC3 290–401 and illustration of truncated fragments. (b) Pulldown of Bα by GST-tagged CRTC3 fragments. GST was used as control. The shortest fragment, GST-CRTC3 380–401, …
-
Figure 2—figure supplement 2—source data 1
Source data for Figure 2—figure supplement 2b.
- https://cdn.elifesciences.org/articles/79736/elife-79736-fig2-figsupp2-data1-v2.zip
-
Figure 2—figure supplement 2—source data 2
Source data for Figure 2—figure supplement 2c.
- https://cdn.elifesciences.org/articles/79736/elife-79736-fig2-figsupp2-data2-v2.zip
Figure 2—figure supplement 3
PP2A methylesterase 1 (PME-1) inhibits substrate binding to protein phosphatase 2A (PP2A) holoenzymes.
(a) Pulldown of PP2A-B6γ1 (top), PP2A-Bα (middle), and PP2A-PR70 (bottom) holoenzymes via GST-tagged substrate peptides (GST-SYT16, GST-CRTC3, and GST-Cdc6) in the present and absence of increasing …
-
Figure 2—figure supplement 3—source data 1
Source data for Figure 2—figure supplement 3a.
- https://cdn.elifesciences.org/articles/79736/elife-79736-fig2-figsupp3-data1-v2.zip
Figure 3 with 4 supplements
Cryoelectron microscopy (cryo-EM) structure of the protein phosphatase 2A (PP2A)-B56γ1–PP2A methylesterase 1 (PME-1) complex.
(a) Overall structure of the PP2A-B56γ1–PME-1 complex. Two perpendicular views are shown. The A-subunit, PP2Ac, B56γ1, and PME-1 are shown in cartoon and colored green, blue, yellow, and magenta, …
Figure 3—figure supplement 1
Cryoelectron microscopy (cryo-EM) data processing and model building.
(a) Representative micrograph. (b) 2D classes selected for model building. (c) Gold-standard Fourier shell correlation (FSC) curves of the final 3D reconstruction from CryoSPARC. (d) Final …
Figure 3—figure supplement 2
Representative cryoelectron microscopy (cryo-EM) density maps for the structural fragments in the A-subunit, B56γ1, PP2Ac, and PP2A methylesterase 1 (PME-1) of the protein phosphatase 2A (PP2A)-B56γ1–PME complex.
Figure 3—figure supplement 3
A minor 3D class gives a low-resolution model for the protein phosphatase 2A (PP2A)-B56γ1 holoenzyme.
(a) Model fit of the PP2A-B56γ1 holoenzyme (PDB code: 2NPP) to the map. The scaffold A-subunit, PP2Ac, and B56γ1 are colored red, cyan, and orange, respectively. (b) Poor model fit of the …
Figure 3—figure supplement 4
Illustration of the role of B56 internal loop in facilitating substrate entry to the holoenzyme active site.
The structural model of protein phosphatase 2A (PP2A)-B56 holoenzyme bound to B56 short linear motif (SLiM) (left) highlighted the negatively charged residues in the internal loop of B56γ1 near the …
Figure 4
B56–PP2A methylesterase 1 (PME-1) interfaces.
(a) An overview of interactions between B56γ1 (yellow) and PME-1 (magenta). The short linear motif (SLiM) in the PME-1 internal loop was perfectly overlaid with the BubR1 substrate peptide (669LDPIIE…
-
Figure 4—source data 1
Source data for Figure 4e.
- https://cdn.elifesciences.org/articles/79736/elife-79736-fig4-data1-v2.zip
-
Figure 4—source data 2
Source data for Figure 4f.
- https://cdn.elifesciences.org/articles/79736/elife-79736-fig4-data2-v2.zip
-
Figure 4—source data 3
Source data for Figure 4g.
- https://cdn.elifesciences.org/articles/79736/elife-79736-fig4-data3-v2.zip
Figure 5 with 2 supplements
Different effects of PP2A methylesterase 1 (PME-1) inhibitor and B56–PME-1 interface mutations.
(a) The time-dependent demethylation curves of protein phosphatase 2A (PP2A)-B56γ1 holoenzyme (upper left), the AC dimeric core enzyme (upper right), PP2A-Bα holoenzyme (lower left), and PP2A-PR70 …
-
Figure 5—source data 1
Source data for Figure 5a.
- https://cdn.elifesciences.org/articles/79736/elife-79736-fig5-data1-v2.zip
-
Figure 5—source data 2
Source data for Figure 5b.
- https://cdn.elifesciences.org/articles/79736/elife-79736-fig5-data2-v2.zip
Figure 5—figure supplement 1
Time course of protein phosphatase 2A (PP2A) holoenzyme demethylation.
The time-dependent demethylation of PP2A-B56γ1 (a), AC dimeric core enzyme (b), PP2A-Bα holoenzyme (c), and PP2A-PR70 (d) by PP2A methylesterase 1 (PME-1) WT and 3MU mutant. The intensity of …
-
Figure 5—figure supplement 1—source data 1
Source data for Figure 5—figure supplement 1a.
- https://cdn.elifesciences.org/articles/79736/elife-79736-fig5-figsupp1-data1-v2.zip
-
Figure 5—figure supplement 1—source data 2
Source data for Figure 5—figure supplement 1b.
- https://cdn.elifesciences.org/articles/79736/elife-79736-fig5-figsupp1-data2-v2.zip
-
Figure 5—figure supplement 1—source data 3
Source data for Figure 5—figure supplement 1c.
- https://cdn.elifesciences.org/articles/79736/elife-79736-fig5-figsupp1-data3-v2.zip
-
Figure 5—figure supplement 1—source data 4
Source data for Figure 5—figure supplement 1d.
- https://cdn.elifesciences.org/articles/79736/elife-79736-fig5-figsupp1-data4-v2.zip
Figure 5—figure supplement 2
Structural model illustrating B factors of the cryoelectron microscopy (cryo-EM) structure of the protein phosphatase 2A (PP2A)-B56γ1–PP2A methylesterase 1 (PME-1) complex.
The overall view of the entire structure (left) and the closeup view of the PME-1 active site pocket (right) are shown.
Figure 6 with 1 supplement
PP2A methylesterase 1 (PME-1) function in p53 signaling.
(a) Effects of PME-1 inhibitor versus B56 interface mutations in PME-1 (3MU) on p53 phosphorylation at Thr55 and cellular PP2Ac methylation. The mock vector, wild-type, or mutant PME-1 were …
-
Figure 6—source data 1
Source data for Figure 6a.
- https://cdn.elifesciences.org/articles/79736/elife-79736-fig6-data1-v2.zip
-
Figure 6—source data 2
Source data for Figure 6b.
- https://cdn.elifesciences.org/articles/79736/elife-79736-fig6-data2-v2.zip
-
Figure 6—source data 3
Source data for Figure 6c.
- https://cdn.elifesciences.org/articles/79736/elife-79736-fig6-data3-v2.zip
-
Figure 6—source data 4
Source data for Figure 6d.
- https://cdn.elifesciences.org/articles/79736/elife-79736-fig6-data4-v2.zip
-
Figure 6—source data 5
Source data for Figure 6e.
- https://cdn.elifesciences.org/articles/79736/elife-79736-fig6-data5-v2.zip
-
Figure 6—source data 6
Source data for Figure 6f.
- https://cdn.elifesciences.org/articles/79736/elife-79736-fig6-data6-v2.zip
-
Figure 6—source data 7
Source data for Figure 6g.
- https://cdn.elifesciences.org/articles/79736/elife-79736-fig6-data7-v2.zip
Figure 6—figure supplement 1
Amplification and mutation of the PPME-1 gene that encodes PP2A methylesterase 1 (PME-1) in cancer are associated with poorer survival outcome.
(a) The PPME-1 gene is frequently altered and amplified in multiple types of cancers (cbioportal.org). (b) The survival data from 10,953 cancer patients from the The Cancer Genome Atlas (TCGA) …
Figure 7
Illustration of the signaling loop of protein phosphatase 2A (PP2A) holoenzyme biogenesis and recycling and the multifaceted roles of PP2A methylesterase 1 (PME-1), including demethylation of the PP2A core enzyme to suppress holoenzyme assembly, inhibition of holoenzyme substrate recognitions, and demethylation of PP2A holoenzymes.
The latter provides a mechanism for priming PP2A holoenzymes for demethylation-dependent decommissioning.
Tables
Table 1
Cryoelectron and 36 are marked as headers microscopy (cryo-EM) data collection, model building, and structure refinements for the protein phosphatase 2A (PP2A)-B56γ1–PP2A methylesterase 1 (PME-1) complex.
| Summary of data collection and model statistics | |
|---|---|
| Data collection and processing | |
| Number of grids used | 1 |
| Grid type | Quantifoil 300 mesh R 1.2/1/3 with ultrathin carbon |
| Microscope | Titan Krios |
| Detector | Gatan K3 Summit |
| Voltage (kV) | 300 |
| Electron dose (e−/Å2) | 50.8 |
| Defocus range (μm) | 1.5–2.3 |
| Pixel size (A) | 1.059 |
| Number of movies | 7529 |
| Number of particles | 276,737 |
| PDB | 7SOY |
| EMD | EMD-25363 |
| Symmetry | C1 |
| Map resolution (Å) | 3.4 |
| FSC threshold | 0.143 |
| Refinement (Phenix) | |
| Initial model used (PDB code) | 3C5W, 2NPP |
| Resolution (Å) | 3.4 |
| Map CC | 0.84 |
| Map sharpening B factor (Å2) | −10 |
| Model composition | |
| Number of chains | 4 |
| Nonhydrogen atoms | 12180 |
| Protein residues/waters | 1529/0 |
| Ligands/metals | 0/0 |
| R.m.s. deviations | |
| Bonds length (Å) | 0.003 |
| Bonds angle (°) | 0.572 |
| Validation | |
| MolProbity score | 1.66 |
| Clashscore | 13.36 |
| Rotamer outerliers (%) | 0 |
| C-Beta outerliers (%) | 0 |
| Ramachandran plot statistics (%) | |
| Favored | 98.42 |
| Allowed | 1.58 |
| Outlier | 0 |
