{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T19:37:03Z","timestamp":1768505823501,"version":"3.49.0"},"posted":{"date-parts":[[2023,3,9]]},"group-title":"Biochemistry","reference-count":71,"publisher":"openRxiv","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2023,4,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  An increasing number of mutations associated with devastating human diseases are diagnosed by whole-genome\/exon sequencing. Recurrent\n                  <jats:italic>de novo<\/jats:italic>\n                  missense mutations have been discovered in B56\u03b4 (encoded by\n                  <jats:italic>PPP2R5D<\/jats:italic>\n                  ), a regulatory subunit of protein phosphatase 2A (PP2A), that cause intellectual disabilities (ID), macrocephaly, Parkinsonism, and a broad range of neurological symptoms. Single-particle cryo-EM structures show that the PP2A-B56\u03b4 holoenzyme possesses closed latent and open active forms. In the closed form, the long, disordered arms of B56\u03b4 termini fold against each other and the holoenzyme core, establishing dual autoinhibition of the phosphatase active site and the substrate-binding protein groove. The resulting interface spans over 190 \u00c5 and harbors unfavorable contacts, activation phosphorylation sites, and nearly all residues with ID-associated mutations. Our studies suggest that this dynamic interface is close to an allosteric network responsive to activation phosphorylation and altered globally by mutations. Furthermore, we found that ID mutations perturb the activation phosphorylation rates, and the severe variants significantly increase the mitotic duration and error rates compared to the wild variant.\n                <\/jats:p>","DOI":"10.1101\/2023.03.09.530109","type":"posted-content","created":{"date-parts":[[2023,3,13]],"date-time":"2023-03-13T09:36:05Z","timestamp":1678700165000},"source":"Crossref","is-referenced-by-count":0,"title":["Extended regulation interface coupled to the allosteric network and disease mutations in the PP2A-B56\u03b4 holoenzyme"],"prefix":"10.64898","author":[{"given":"Cheng-Guo","family":"Wu","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vijaya K.","family":"Balakrishnan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pankaj S.","family":"Parihar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kirill","family":"Konovolov","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yu-Chia","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ronald A","family":"Merrill","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hui","family":"Wei","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bridget","family":"Carragher","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ramya","family":"Sundaresan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qiang","family":"Cui","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Brian E.","family":"Wadzinski","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mark R.","family":"Swingle","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alla","family":"Musiyenko","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Richard","family":"Honkanen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wendy K.","family":"Chung","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aussie","family":"Suzuki","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stefan","family":"Strack","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xuhui","family":"Huang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yongna","family":"Xing","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","reference":[{"key":"2023040808250565000_2023.03.09.530109v2.1","doi-asserted-by":"publisher","DOI":"10.1007\/s10555-008-9128-9"},{"key":"2023040808250565000_2023.03.09.530109v2.2","doi-asserted-by":"publisher","DOI":"10.3109\/10409238.2016.1143913"},{"key":"2023040808250565000_2023.03.09.530109v2.3","doi-asserted-by":"publisher","DOI":"10.1016\/S0955-0674(99)00074-5"},{"key":"2023040808250565000_2023.03.09.530109v2.4","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M202992200"},{"key":"2023040808250565000_2023.03.09.530109v2.5","doi-asserted-by":"publisher","DOI":"10.1021\/bi902160t"},{"key":"2023040808250565000_2023.03.09.530109v2.6","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2009.10.006"},{"key":"2023040808250565000_2023.03.09.530109v2.7","doi-asserted-by":"publisher","DOI":"10.1038\/nature21062"},{"key":"2023040808250565000_2023.03.09.530109v2.8","doi-asserted-by":"publisher","DOI":"10.1007\/s10048-015-0466-9"},{"key":"2023040808250565000_2023.03.09.530109v2.9","doi-asserted-by":"publisher","DOI":"10.1172\/JCI79860"},{"key":"2023040808250565000_2023.03.09.530109v2.10","doi-asserted-by":"publisher","DOI":"10.1158\/2159-8290.CD-12-0095"},{"key":"2023040808250565000_2023.03.09.530109v2.11","doi-asserted-by":"crossref","unstructured":"Gao, J. et al. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal 6, pl1 (2013).","DOI":"10.1126\/scisignal.2004088"},{"key":"2023040808250565000_2023.03.09.530109v2.12","doi-asserted-by":"crossref","unstructured":"Biswas, D. , Cary, W. & Nolta, J.A . PPP2R5D-Related Intellectual Disability and Neurodevelopmental Delay: A Review of the Current Understanding of the Genetics and Biochemical Basis of the Disorder. Int J Mol Sci 21(2020).","DOI":"10.3390\/ijms21041286"},{"key":"2023040808250565000_2023.03.09.530109v2.13","doi-asserted-by":"crossref","unstructured":"Oyama, N. et al. Clinical, neuroimaging and molecular characteristics of PPP2R5D-related neurodevelopmental disorders: an expanded series with functional characterisation and genotype-phenotype analysis. J Med Genet (2022).","DOI":"10.1136\/jmg-2022-108713"},{"key":"2023040808250565000_2023.03.09.530109v2.14","doi-asserted-by":"publisher","DOI":"10.1002\/ana.25943"},{"key":"2023040808250565000_2023.03.09.530109v2.15","doi-asserted-by":"crossref","unstructured":"Hetzelt, K. et al. Early-onset parkinsonism in PPP2R5D-related neurodevelopmental disorder. Eur J Med Genet 64, 104123 (2021).","DOI":"10.1016\/j.ejmg.2020.104123"},{"key":"2023040808250565000_2023.03.09.530109v2.16","doi-asserted-by":"publisher","DOI":"10.1002\/ana.25863"},{"key":"2023040808250565000_2023.03.09.530109v2.17","doi-asserted-by":"crossref","unstructured":"Wu, C.G. et al. PP2A-B\u2019 holoenzyme substrate recognition, regulation and role in cytokinesis. Cell Discov 3, 17027 (2017).","DOI":"10.1038\/celldisc.2017.27"},{"key":"2023040808250565000_2023.03.09.530109v2.18","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2016.06.024"},{"key":"2023040808250565000_2023.03.09.530109v2.19","doi-asserted-by":"publisher","DOI":"10.1007\/s13238-016-0283-4"},{"key":"2023040808250565000_2023.03.09.530109v2.20","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2016.09.006"},{"key":"2023040808250565000_2023.03.09.530109v2.21","doi-asserted-by":"crossref","unstructured":"Davey, N.E. , Cyert, M.S. & Moses, A.M . Short linear motifs\u2013ex nihilo evolution of protein regulation. Cell Communication and Signaling 13, 43 (2015).","DOI":"10.1186\/s12964-015-0120-z"},{"key":"2023040808250565000_2023.03.09.530109v2.22","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2020.06.029"},{"key":"2023040808250565000_2023.03.09.530109v2.23","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2019.08.029"},{"key":"2023040808250565000_2023.03.09.530109v2.24","doi-asserted-by":"publisher","DOI":"10.1111\/j.1742-4658.2012.08547.x"},{"key":"2023040808250565000_2023.03.09.530109v2.25","doi-asserted-by":"crossref","unstructured":"Nasa, I. , Rusin, S.F. , Kettenbach, A.N. & Moorhead, G.B . Aurora B opposes PP1 function in mitosis by phosphorylating the conserved PP1-binding RVxF motif in PP1 regulatory proteins. Science signaling 11(2018).","DOI":"10.1126\/scisignal.aai8669"},{"key":"2023040808250565000_2023.03.09.530109v2.26","doi-asserted-by":"publisher","DOI":"10.1016\/j.str.2016.09.010"},{"key":"2023040808250565000_2023.03.09.530109v2.27","doi-asserted-by":"publisher","DOI":"10.1242\/jcs.122481"},{"key":"2023040808250565000_2023.03.09.530109v2.28","doi-asserted-by":"publisher","DOI":"10.1083\/jcb.201409129"},{"key":"2023040808250565000_2023.03.09.530109v2.29","doi-asserted-by":"crossref","unstructured":"Ueki, Y. et al. A highly conserved pocket on PP2A-B56 is required for hSgo1 binding and cohesion protection during mitosis. EMBO Rep 22, e52295 (2021).","DOI":"10.15252\/embr.202052295"},{"key":"2023040808250565000_2023.03.09.530109v2.30","doi-asserted-by":"publisher","DOI":"10.1093\/emboj\/19.4.562"},{"key":"2023040808250565000_2023.03.09.530109v2.31","doi-asserted-by":"crossref","unstructured":"Li, Y. et al. Coupling to short linear motifs creates versatile PME-1 activities in PP2A holoenzyme demethylation and inhibition. Elife 11(2022).","DOI":"10.7554\/eLife.79736"},{"key":"2023040808250565000_2023.03.09.530109v2.32","doi-asserted-by":"crossref","first-page":"5748","DOI":"10.1038\/s41467-021-26079-0","article-title":"A complex of BRCA2 and PP2A-B56 is required for DNA repair by homologous recombination","volume":"12","year":"2021","journal-title":"Nat Commun"},{"key":"2023040808250565000_2023.03.09.530109v2.33","doi-asserted-by":"crossref","unstructured":"Kim, S.H. , Wu, C.G. , Jia, W. , Xing, Y. & Tibbetts, R.S . Roles of constitutive and signal- dependent protein phosphatase 2A docking motifs in burst attenuation of the cyclic AMP response element-binding protein. J Biol Chem 297, 100908 (2021).","DOI":"10.1016\/j.jbc.2021.100908"},{"key":"2023040808250565000_2023.03.09.530109v2.34","doi-asserted-by":"publisher","DOI":"10.1038\/onc.2017.350"},{"key":"2023040808250565000_2023.03.09.530109v2.35","doi-asserted-by":"publisher","DOI":"10.1177\/1947601912448067"},{"key":"2023040808250565000_2023.03.09.530109v2.36","doi-asserted-by":"publisher","DOI":"10.1038\/emboj.2008.279"},{"key":"2023040808250565000_2023.03.09.530109v2.37","doi-asserted-by":"publisher","DOI":"10.1007\/s10555-008-9128-9"},{"key":"2023040808250565000_2023.03.09.530109v2.38","doi-asserted-by":"publisher","DOI":"10.1128\/MCB.26.7.2832-2844.2006"},{"key":"2023040808250565000_2023.03.09.530109v2.39","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M109.034868"},{"key":"2023040808250565000_2023.03.09.530109v2.40","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0611532104"},{"key":"2023040808250565000_2023.03.09.530109v2.41","doi-asserted-by":"publisher","DOI":"10.1210\/me.2007-0457"},{"key":"2023040808250565000_2023.03.09.530109v2.42","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2006.10.035"},{"key":"2023040808250565000_2023.03.09.530109v2.43","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0709879104"},{"key":"2023040808250565000_2023.03.09.530109v2.44","doi-asserted-by":"publisher","DOI":"10.1038\/onc.2011.95"},{"key":"2023040808250565000_2023.03.09.530109v2.45","doi-asserted-by":"crossref","unstructured":"Levitz, T.S. , Brignole, E.J. , Fong, I. , Darrow, M.C. & Drennan, C.L . Effects of chameleon dispense-to-plunge speed on particle concentration, complex formation, and final resolution: A case study using the Neisseria gonorrhoeae ribonucleotide reductase inactive complex. J Struct Biol 214, 107825 (2022).","DOI":"10.1016\/j.jsb.2021.107825"},{"key":"2023040808250565000_2023.03.09.530109v2.46","doi-asserted-by":"publisher","DOI":"10.1016\/j.jsb.2012.04.020"},{"key":"2023040808250565000_2023.03.09.530109v2.47","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2006.11.033"},{"key":"2023040808250565000_2023.03.09.530109v2.48","doi-asserted-by":"publisher","DOI":"10.1038\/nature05351"},{"key":"2023040808250565000_2023.03.09.530109v2.49","doi-asserted-by":"publisher","DOI":"10.1021\/jp204407d"},{"key":"2023040808250565000_2023.03.09.530109v2.50","doi-asserted-by":"crossref","unstructured":"Papke, C.M. et al. A disorder-related variant (E420K) of a PP2A-regulatory subunit (PPP2R5D) causes constitutively active AKT-mTOR signaling and uncoordinated cell growth. J Biol Chem 296, 100313 (2021).","DOI":"10.1016\/j.jbc.2021.100313"},{"key":"2023040808250565000_2023.03.09.530109v2.51","doi-asserted-by":"crossref","unstructured":"Liu, R. et al. A novel nonsense mutation in PPP2R5D is associated with neurodevelopmental disorders and shows incomplete penetrance in a Chinese pedigree. Clin Neurol Neurosurg 223, 107524 (2022).","DOI":"10.1016\/j.clineuro.2022.107524"},{"key":"2023040808250565000_2023.03.09.530109v2.52","unstructured":"Disease Mutations and Phosphorylation Alter the Allosteric Pathways Involved in Autoinhibition of Protein Phosphatase 2A. (2023)."},{"key":"2023040808250565000_2023.03.09.530109v2.53","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2010.12.030"},{"key":"2023040808250565000_2023.03.09.530109v2.54","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-03327-4"},{"key":"2023040808250565000_2023.03.09.530109v2.55","doi-asserted-by":"publisher","DOI":"10.1038\/s41596-018-0068-8"},{"key":"2023040808250565000_2023.03.09.530109v2.56","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1016\/j.jsb.2018.01.001","article-title":"Optimizing \u201cself-wicking\u201d nanowire grids","volume":"202","year":"2018","journal-title":"J Struct Biol"},{"key":"2023040808250565000_2023.03.09.530109v2.57","doi-asserted-by":"publisher","DOI":"10.1016\/j.jsb.2005.03.010"},{"key":"2023040808250565000_2023.03.09.530109v2.58","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4169"},{"key":"2023040808250565000_2023.03.09.530109v2.59","doi-asserted-by":"crossref","unstructured":"Punjani, A. & Fleet, D.J . 3D variability analysis: Resolving continuous flexibility and discrete heterogeneity from single particle cryo-EM. J Struct Biol 213, 107702 (2021).","DOI":"10.1016\/j.jsb.2021.107702"},{"key":"2023040808250565000_2023.03.09.530109v2.60","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.20084"},{"key":"2023040808250565000_2023.03.09.530109v2.61","doi-asserted-by":"publisher","DOI":"10.1107\/S0907444910007493"},{"key":"2023040808250565000_2023.03.09.530109v2.62","doi-asserted-by":"publisher","DOI":"10.1107\/S0907444909052925"},{"key":"2023040808250565000_2023.03.09.530109v2.63","doi-asserted-by":"publisher","DOI":"10.1107\/S0907444909042073"},{"key":"2023040808250565000_2023.03.09.530109v2.64","doi-asserted-by":"publisher","DOI":"10.1021\/ct700301q"},{"key":"2023040808250565000_2023.03.09.530109v2.65"},{"key":"2023040808250565000_2023.03.09.530109v2.66","doi-asserted-by":"crossref","unstructured":"Melo, M.C.R. , Bernardi, R.C. , de la Fuente-Nunez, C. & Luthey-Schulten, Z . Generalized correlation-based dynamical network analysis: a new high-performance approach for identifying allosteric communications in molecular dynamics trajectories. J Chem Phys 153, 134104 (2020).","DOI":"10.1063\/5.0018980"},{"key":"2023040808250565000_2023.03.09.530109v2.67","doi-asserted-by":"publisher","DOI":"10.1021\/acscatal.7b02954"},{"key":"2023040808250565000_2023.03.09.530109v2.68","doi-asserted-by":"publisher","DOI":"10.1002\/prot.20784"},{"key":"2023040808250565000_2023.03.09.530109v2.69","doi-asserted-by":"crossref","first-page":"2116","DOI":"10.1021\/acs.jctc.8b01197","article-title":"Robust Determination of Protein Allosteric Signaling Pathways","volume":"15","year":"2019","journal-title":"J Chem Theory Comput"},{"key":"2023040808250565000_2023.03.09.530109v2.70","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-019-1711-4"},{"key":"2023040808250565000_2023.03.09.530109v2.71","doi-asserted-by":"crossref","unstructured":"K. A. Smolen , C.M.P., M. R. Swingle , A. Musiyenko , C. Li , A. D. Camp , R. E. Honkanen , A. N Kettenbach . Quantitative proteomics and phosphoproteomics of PPP2R5D variants reveal deregulation of RPS6 phosphorylation through converging signaling cascades. Vol. https:\/\/www.biorxiv.org\/content\/10.1101\/2023.03.27.534397v1 (bioRxiv, 2023).","DOI":"10.1101\/2023.03.27.534397"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2023.03.09.530109","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T04:22:18Z","timestamp":1768450938000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2023.03.09.530109"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,3,9]]},"references-count":71,"URL":"https:\/\/doi.org\/10.1101\/2023.03.09.530109","relation":{},"subject":[],"published":{"date-parts":[[2023,3,9]]},"subtype":"preprint"}}