PP2A/B55α substrate recruitment as defined by the retinoblastoma-related protein p107
- Temple University Lewis Katz School of Medicine, United States
- Fox Chase Cancer Center, United States
- University of Arizona, United States
- Hitchcock Medical Center at Dartmouth, United States
- UConn Health, United States
Abstract
Protein phosphorylation is a reversible post-translation modification essential in cell signaling. This study addresses a long-standing question as to how the most abundant serine/threonine Protein Phosphatase 2 (PP2A) holoenzyme, PP2A/B55α, specifically recognizes substrates and presents them to the enzyme active site. Here, we show how the PP2A regulatory subunit B55α recruits p107, a pRB-related tumor suppressor and B55α substrate. Using molecular and cellular approaches, we identified a conserved region 1 (R1, residues 615-626) encompassing the strongest p107 binding site. This enabled us to identify an 'HxRVxxV619-625' short linear motif (SLiM) in p107 as necessary for B55α binding and dephosphorylation of the proximal pSer-615 in vitro and in cells. Numerous B55α/PP2A substrates, including TAU, contain a related SLiM C-terminal from a proximal phosphosite, 'p[ST]-P-x(4,10)-[RK]-V-x-x-[VI]-R'. Mutation of conserved SLiM residues in TAU dramatically inhibits dephosphorylation by PP2A/B55α, validating its generality. A data-guided computational model details the interaction of residues from the conserved p107 SLiM, the B55α groove, and phosphosite presentation. Altogether these data provide key insights into PP2A/B55α mechanisms of substrate recruitment and active site engagement, and also facilitate identification and validation of new substrates, a key step towards understanding PP2A/B55α role in multiple cellular processes.
Data availability
Raw MS data for the the data depicted in Figure 6B are available at MassIVEhttps://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=9c21e08f6a524d7097e8bd45f0d2f375PXD028612.All NMR chemical shifts (Figure 1E-F) have been deposited in the BioMagResBank (BMRB: 28091).Source code folder (PeptideDock_sourceCode) for Figure 7 is a C# project, including retrieval of peptide structures from PDB and other sources such as PISCES, and calculation of distances and data analyses. https://github.com/DunbrackLab/PP2A_PeptideDock.All other data generated or analysed during this study are included in the manuscript and supporting files. Source Data files have been provided.
Article and author information
Author details
Arminja N Kettenbach
Funding
National Institute of General Medical Sciences (R01 GM117437)
- Xavier Graña
National Cancer Institute (R03 CA216134-01)
- Xavier Graña
WW Smith charitable Trust Award (no reference number)
- Xavier Graña
National Cancer Institute (P30 CA006927)
- Roland L Dunbrack Jr.
- Xavier Graña
National Cancer Institute (U54 CA221704)
- Holly Fowle
- Ziran Zhao
National Institute of General Medical Sciences (R01GM134683)
- Wolfgang Peti
National Institute of Neurological Disorders and Stroke (R01NS091336)
- Wolfgang Peti
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2021, Fowle et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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PP2A/B55α substrate recruitment as defined by the retinoblastoma-related protein p107
eLife 10:e63181.
https://doi.org/10.7554/eLife.63181
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Glutamine synthetases (GS) are central enzymes essential for the nitrogen metabolism across all domains of life. Consequently, they have been extensively studied for more than half a century. Based on the ATP-dependent ammonium assimilation generating glutamine, GS expression and activity are strictly regulated in all organisms. In the methanogenic archaeon Methanosarcina mazei, it has been shown that the metabolite 2-oxoglutarate (2-OG) directly induces the GS activity. Besides, modulation of the activity by interaction with small proteins (GlnK1 and sP26) has been reported. Here, we show that the strong activation of M. mazei GS (GlnA1) by 2-OG is based on the 2-OG dependent dodecamer assembly of GlnA1 by using mass photometry (MP) and single particle cryo-electron microscopy (cryo-EM) analysis of purified strep-tagged GlnA1. The dodecamer assembly from dimers occurred without any detectable intermediate oligomeric state and was not affected in the presence of GlnK1. The 2.39 Å cryo-EM structure of the dodecameric complex in the presence of 12.5 mM 2-OG demonstrated that 2-OG is binding between two monomers. Thereby, 2-OG appears to induce the dodecameric assembly in a cooperative way. Furthermore, the active site is primed by an allosteric interaction cascade caused by 2-OG-binding towards an adaption of an open active state conformation. In the presence of additional glutamine, strong feedback inhibition of GS activity was observed. Since glutamine dependent disassembly of the dodecamer was excluded by MP, feedback inhibition most likely relies on the binding of glutamine to the catalytic site. Based on our findings, we propose that under nitrogen limitation the induction of M. mazei GS into a catalytically active dodecamer is not affected by GlnK1 and crucially depends on the presence of 2-OG.
