The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Functional site class:
PP2A holoenzyme B56-docking site
Functional site description:
Reversible protein phosphorylation is an essential regulatory mechanism in eukaryotes. PP2A-mediated protein dephosphorylation is involved in a broad range of cellular processes including cell-cycle progression, cytoskeletal dynamics, and growth factor signalling. The regulatory subunits of PP2A holoenzyme determine the substrate specificity. In humans there exist five isoforms of the B56 type regulatory subunit and they bind to their interacting proteins through a conserved LxxIxE motif. The motif is conserved in essential proteins throughout the eukaryotic domain of life and also in human viruses, suggesting that the motifs are required for basic cellular function.
ELM Description:
Protein dephosphorylation by the PP2A phosphatase is mainly achieved through the interaction of its regulatory subunit with the associated proteins. The human genome contains at least 15 regulatory subunits of PP2A, falling into four subfamilies (B (B55), B' (B56), B'', and B'''). Moreover, many of them are alternatively spliced, indicating the vastness of distinct PP2A heterotrimeric holoenzymes.The B56 family is the largest of the regulatory subunit families, comprising five human isoforms (α, β, γ, δ, and ε) characterized by conserved pseudo-HEAT repeats. Most of the B56 binding proteins contain a conserved motif LxxIxE which acts as a docking site for B56. The motif binds to a well conserved and surface-exposed binding groove formed between the B56 HEAT repeats 3 and 4. The pocket is essentially linear, with a basic patch interacting with the acidic residues in the C-terminal end of the motif and the hydrophobic patch interacting with the two key hydrophobic residues of the motif. The B56 docking site has a consensus sequence ([LMFYWIC]..I.E)|(L..[IVLWC].E). One of, but not both, the amino acids in position P1 or P4 of the motif can be a variable hydrophobic residue for B56 binding, while P6 has the invariant glutamic acid. A higher degree of flexibility is observed in the intervening and surrounding positions and a stronger binding affinity is observed when the residues at the position P2 or P7-P9 were either phosphorylated or an acidic residue is already present, as the negative charge engages with the basic patch of B56 (Wang,2016). The higher degree of plasticity of the motif and the transient interaction provides a regulatory mechanism that acts to secure a proper balance between phosphatase and kinase activity in a given signaling network. The motif is found throughout eukaryotes and and in some viruses, which emphasises the general mechanism of B56 binding and its pivotal role in many cellular functions.
Pattern: ([LMFYWIC]..I.E)|(L..[IVLWC].E).
Pattern Probability: 0.0014581
Present in taxons: Eukaryota Viruses
Interaction Domain:
Armadillo-type fold (IPR016024) This entry represents a structural domain with an armadillo (ARM)-like fold, consisting of a multi-helical fold comprised of two curved layers of alpha helices arranged in a regular right-handed superhelix, where the repeats that make up this structure are arranged about a common axis [ ]. These superhelical structures present an extensive solvent-accessible surface that is well suited to binding large substrates such as proteins and nucleic acids. Domains and repeats with an ARM-like fold have been found in a number of proteins, including: ARM repeat domain, found in beta-catenins, importins, karyopherin and exportins. HEAT repeat domain, found in protein phosphatase 2a and initiation factor eIF4G. PHAT domain, found in the RNA-binding protein Smaug. Leucine-rich repeat variant, which contain an FeS cluster. Pumilo repeat domain, found in Pumilo protein. Regulatory subunit H of V-type ATPases. PBS lyase HEAT-like repeat. Mo25 protein. MIF4G domain-like, found in eukaryotic initiation factor eIF4G, translation initiation factor eIF-2b epsilon and nuclear cap-binding protein CBP80. The N-terminal domain of eukaryotic translation initiation factor 3 subunit 12. The C-terminal domain of leukotriene A4 hydrolase. The helical domain of phosphoinositide 3-kinase. The N-terminal fragment of adaptin alpha-C and beta subunits. The proximal leg segment and the linker domain of the clathrin heavy chain. The sequence similarity among these different repeats or domains is low, however they exhibit considerable structural similarity. Furthermore, the number of repeats present in the superhelical structure can vary between orthologues, indicating that rapid loss/gain of repeats has occurred frequently in evolution. A common phylogenetic origin has been proposed for the armadillo and HEAT repeats [ ]. (Stochiometry: 1 : 1)
o See 18 Instances for DOC_PP2A_B56_1
o Abstract
Protein phosphatase 2A (PP2A) belongs to the superfamily of phosphoprotein phosphatases (PPPs) and catalyzes protein dephosphorylation by hydrolyzing Ser/Thr-linked phosphate ester bonds (Heroes,2013). A heterotrimeric enzyme, PP2A contains a 36 kDa catalytic C subunit, a 65 kDa structural A subunit, and a variable regulatory B subunit. The largest family of cellular regulatory B subunits is B56 (McCright,1996), which contains five isoforms (B56 alpha to epsilon). Unlike some other protein phosphatases, which make use of their catalytic subunits to obtain substrate specificity, PP2A uses the regulatory B subunits for targeting substrates. The B56 interaction is mediated by a conserved motif present in the substrate proteins and a groove formed between B56 HEAT repeats 3 and 4. It is a general motif for B56 interaction and the key interacting residues in B56 are conserved in different B56 isoforms and are expected to have the same mode of interaction (Hertz,2016).
The composition of the motif modulates the affinity for B56, which can in turn determine the phosphorylation status of associated substrates. Phosphorylation of amino acid residues within the motif may strengthen B56 binding, allowing integration of kinase and phosphatase activity. In Repo-Man, phosphorylation of S591 within the B56 docking site promotes the binding of B56 and subsequently aids the dephosphorylation of another phosphorylated residue, S893, within the same protein (Qian,2013). This motif was first identified in BubR1 as a site essential for kinetochore-microtubule attachment and was known as the KARD (Kinetochore Attachment Regulatory Domain) motif, which also binds to the PP2A-B56 complex (Suijkerbuijk,2012). The KARD motif in human BubR1 contains three phosphorylated residues (S670, S676 and T680) which stimulates the interaction of the B56 subunit and BubR1. The binding of BubR1 promotes the localisation of PP2A-B56 to kinetochores where it acts to dephosphorylate the Aurora B substrates and noteworthy does not appear to dephosphorylate the BubR1 S670/676 sites or any nearby phosphorylated sites, as the dephosphorylation of these sites would prevent PP2A from reaching the kinetochore. So binding of a phosphatase to a protein does not always guarantee that it is a substrate of the phosphatase. Thus the B56 subunit also regulates the localization of the PP2A holoenzyme to specific intracellular compartments where the substrates themselves may not contain LxxIxE motifs (Wang,2016; Suijkerbuijk,2012).
The B56 binding LxxIxE motifs have been identified in many important proteins from virus to human but how they affect the biological process are known for only a few examples. In RACGAP1, the mutation of the motif prevented its dephosphorylation and results in cytokinesis defects. For FOXO3, mutation of the motif affects the binding affinity to B56 and altered its localization (7453045). In a viral example, B56 can bind to the integrase and promote δ-retroviral infection (Maertens,2016). Thus the study of the B56 binding motifs may pave the way to discover new PP2A–B56 substrates, with therapeutic potential.

o 9 selected references:

o 11 GO-Terms:

o 18 Instances for DOC_PP2A_B56_1
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
590 595 IASKKPLLSPIPELPEVPEM TP 5 Homo sapiens (Human)
P47074 MAD3
477 482 SAVKPRQLTPILEMRESNSF TP 2 Saccharomyces cerevisiae (Baker"s yeast)
Q4G163 FBXO43
384 390 LGRSRRLSTLREQSSQSETE TP 1 Homo sapiens (Human)
O43524 FOXO3
448 453 NSLRQSPMQTIQENKPATFS TP 2 Homo sapiens (Human)
P18272 NP
562 567 GSTSPRMLTPINEEADPLDD TP 2 Ebola virus - Mayinga, Zaire, 1976
P14078 gag-pro-pol
1378 1383 QLHHSPRLQPIPETHSLSNK TP 2 Human T-cell lymphotrophic virus type 1 (Caribbean isolate)
Q96L42 KCNH8
706 711 NGNINKRLPSIVEDEEEEEE TP 2 Homo sapiens (Human)
P51587 BRCA2
1114 1119 QKAEITELSTILEESGSQFE TP 2 Homo sapiens (Human)
O15169 AXIN1
238 244 KGISGYLPTLNEDEEWKCDQ TP 3 Homo sapiens (Human)
143 148 SNAGNKRLSTIDESGSILSD TP 3 Homo sapiens (Human)
Q6T4R5-1 NHS
1626 1631 CRLYNTPMQAISEGETENSD TP 2 Homo sapiens (Human)
P51959 CCNG1
287 292 QLKHSYYRITHLPTIPEMVP TP 2 Homo sapiens (Human)
O96017 CHEK2
71 76 ETVSTQELYSIPEDQEPEDQ TP 3 Homo sapiens (Human)
732 737 SPAPHFAMPPIHEDHLEKVF TP 2 Homo sapiens (Human)
Q14674 ESPL1
1485 1490 ARPGPEIMRTIPEEELTDNW TP 3 Homo sapiens (Human)
O60566 BUB1B
669 674 QTLSIKKLSPIIEDSREATH TP 10 Homo sapiens (Human)
Q92974 ARHGEF2
967 972 SPRDFTRMQDIPEETESRDG TP 4 Homo sapiens (Human)
O95239 KIF4A
1224 1229 ALASNTSFFSGCSPIEEEAH TP 4 Homo sapiens (Human)
Please cite: The Eukaryotic Linear Motif resource: 2022 release. (PMID:34718738)

ELM data can be downloaded & distributed for non-commercial use according to the ELM Software License Agreement