The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Functional site class:
Calcineurin (PP2B)-docking motif LxvP
Functional site description:
Calcineurin (PP2B) is a Ca2+- and calmodulin-regulated serine/threonine protein phosphatase known to affect cell biological function mainly in yeast and mammalian systems but is found in all Eukaryotes. It regulates a number of different pathways, including activation of the NFAT family of transcription factors, regulation of axonal guidance, the Ca2+-dependent migration of neutrophils, synaptic plasticity, and apoptosis. The effectiveness of dephosphorylation depends not only on the proximal position of calcineurin-binding site to the dephosphorylation site but also on the flexibility of the calcineurin active site. Calcineurin has been shown to interact with two distinct linear motifs: one docking motif (DOC_PP2B_PxIxI_1) that directly interacts with the catalytic subunit A (CNA) of calcineurin, and a second docking motif (DOC_PP2B_LxvP_1) that binds to both CNA and calcineurin B (CNB), the regulatory Ca2+-binding subunit of calcineurin.
ELMs with same tags:
ELM Description:
This PP2B-docking motif is defined by four amino acids. There is an absolute requirement for leucine in the first position of the motif and for proline in the last position. However, the viral protein A238L (O36972), which has been shown to prevent recognition of LxvP-containing substrates by calcineurin, contains a lysine residue instead of a proline in the last position (4F0Z) (Grigoriu,2013). The second position can accommodate a variety of amino acids. The third position generally contains a valine, but other hydrophobic residues have also been observed. Some motif instances are immediately preceded by an aromatic residue, which can further strengthen the interaction. Upon binding of Ca2+, the CNA subunit undergoes a conformational change, exposing the hydrophobic motif-binding pocket that is located at the interface of the CNA and CNB subunits. Therefore, LxvP sites can only interact with activated calcineurin. The hydrophobic pocket includes two CNA residues (W352, F356) and three CNB residues (L115, M118, V119), which mediate binding to substrates containing an LxvP motif. Immunosuppressants have been shown to bind to the hydrophobic pocket in a similar way. Upon binding to the hydrophobic pocket, the motif adopts a conformation in which it is almost parallel to the α-helix of CNA binding to CNB. The proline in the motif is predicted to interact with the aromatic residues in CNA.
Pattern: L.[LIVAPM]P
Pattern Probability: 0.0022964
Present in taxon: Eukaryota
Interaction Domains:
o See 8 Instances for DOC_PP2B_LxvP_1
o Abstract
The Ca2+-dependent phosphatase calcineurin, also known as protein phosphatase 2B (PP2B), is involved in a number of diverse signaling pathways in cells of different tissues. However, dephosphorylation by calcineurin is not used as broadly in cell regulation as the PP1 phosphatase. Calcineurin is evolutionarily conserved across Eukaryotes and seems to be ubiquitously expressed (Rusnak,2000). It participates in signal transduction pathways governing the development and function of the immune, nervous, cardiovascular and musculoskeletal systems (Aramburu,2004). The best-studied cellular function of calcineurin involves the regulation of T cell gene expression via dephosphorylation of NFAT family transcription factors, enabling NFAT nuclear translocation (reported in complex with calcineurin) and activation of interleukin IL-2. In yeast, the localization of PP2B substrates is dispersed, with examples of PP2B substrates present in the nucleus (Stathopoulos-Gerontides,1999), on the cytosolic side of the plasma membrane (Bultynck,2006) and cytosolic tail-anchored proteins of the endoplasmic reticulum (Heath,2004). The function of PP2B substrates in yeast is associated with various environmental stimuli that are stressful to the cell (unstressed PP2B-minus cells are viable in the laboratory) (Boustany,2002). Survival responses include correct organization of the actin cytoskeleton.
Calcineurin is a heterodimeric protein consisting of calcineurin A (CNA), the catalytic subunit, and calcineurin B (CNB), the Ca2+-binding subunit. In addition to the phosphatase domain, the CNA subunit contains three regulatory domains including a CNB-binding domain, a calmodulin-binding domain, and an auto-inhibitory domain. The auto-inhibitory domain can bind to the substrate-binding pocket of the catalytic subunit, resulting in basal auto-inhibition. The CNB subunit contains four Ca2+-binding EF-hand motifs. Binding of Ca2+/calmodulin to the enzyme results in a conformational change that averts auto-inhibition and leads to activation of the phosphatase (Rusnak,2000). Activated calcineurin then dephosphorylates target S/T phosphorylation sites. Calcineurin does not necessarily dephosphorylate all sites on the substrate. Most of the residues dephosphorylated by calcineurin are in SP or TP sites, possibly explaining the associated proline isomerase.
Calcineurin signaling can be effectively blocked by cyclosporin A and tacrolimus (FK506), which form a complex with a specific immunophilin binding protein (the proline isomerases cyclophilin or FKBP, respectively). Stable drug-immunophilin complexes can then block nuclear translocation of NFATs, thereby suppressing T cell activation (Lai,1998). These immunosuppressant drugs find use after organ transplantations and, in the case of tacrolimus, for ectopic treatment in atopic dermatitis.
There are two independent calcineurin-binding regions called CNBR1 (DOC_PP2B_PxIxI_1) and 2 (DOC_PP2B_LxvP_1), both first reported in the N-terminal domain of NFAT. The secondary contact site LxvP contributes to the overall affinity of a substrate to calcineurin in addition to the primary PxIxI site. Recently it has been shown that both docking motifs in NFAT proteins cooperate and are required for the phosphatase activity of calcineurin (Rodriguez,2009).
o 5 selected references:

o 10 GO-Terms:

o 8 Instances for DOC_PP2B_LxvP_1
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
O35303 Dnm1l
645 648 QKGHAVNLLDVPVPVARKLS TP 5 Rattus norvegicus (Norway rat)
393 396 EANFSANTLSVPRWSPQIPR TP 5 Homo sapiens (Human)
P00515 PRKAR2A
83 86 SESEDEEDLDVPIPGRFDRR TP 1 Bos taurus (Cattle)
P36054 RCN1
101 104 QRNLTKQYLKVPESEKMFLI TP 4 Saccharomyces cerevisiae S288c
Q14934 NFATC4
378 381 KEVAGMDYLAVPSPLAWSKA TP 4 Homo sapiens (Human)
Q12968 NFATC3
393 396 KDSCGDQFLSVPSPFTWSKP TP 8 Homo sapiens (Human)
Q13469 NFATC2
369 372 RNSAPESILLVPPTWPKPLV TP 6 Homo sapiens (Human)
O95644 NFATC1
387 390 KGGFCDQYLAVPQHPYQWAK TP 14 Homo sapiens (Human)
Please cite: The Eukaryotic Linear Motif resource: 2022 release. (PMID:34718738)

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