The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Functional site class:
PP4 EVH1-binding docking motifs
Functional site description:
The PP4 holoenzyme uses two homologous substrate recruitment subunits PPP4R3A and PPP4R3.The PPP4R3 substrate recruitment subunits contain an EVH1 domain at their N-terminus that recognizes short hydrophobic and proline residue-containing motifs in PP4 substrates. The EVH1 domains have a conserved tryptophan residue in the motif-binding pocket that coordinates a proline residue in the binding partner. The human PPP4R3 EVH1 domain has two similar yet distinct consensi recognizing both FxxP- and MxPP-containing peptides. The binding mode of the PPP4R3 FxxP-like peptides matches the polyproline helix binding modes of EVH1 domains of WASP, SPRED, Homer and Ena/VASP. No structure was available for the MxPP-containing peptides bound to the PPP4R3 EVH1 domain. The PPP4R3 EVH1 domain is found throughout eukaryotes and the FxxP-binding pocket is largely conserved which emphasizes the general mechanism of PP4 binding. However, few of the characterised instances are conserved over large evolutionary distances.
ELMs with same func. site: DOC_PP4_FxxP_1  DOC_PP4_MxPP_1 
ELM Description:
Both FxxP and MxPP consensi bind with affinities in the low µM (1-10µM) range (Ueki,2019). Alanine scanning of the FxxP motif, revealed that mutation of the phenylalanine or proline abolishes binding. Further ITC studies showed that tryptophan and tyrosine are tolerated at the phenylalanine position but with weaker binding strength. No other mutations were tolerated at the defined FxxP positions. Positions 2 and 3 of the FxxP tolerate most substitutions with the exception of acidic residues in position 2. Phage display and ITC data showed that PP4 binding peptides have a preference for additional prolines at the C-terminus of the motif. It is possible that this contributes to the ability to form a polyproline helix structure observed in the bound state. Both characterised MxPP-like motif instances contain large stretches of prolines at their C-terminus suggesting the structural properties of the C-terminus can compensate for the weak methionine in the hydrophobic position. Overall, the enthalpic specificity determinants are quite poor. In the structure of the FxxP motif bound to the EVH1 domain, only two residues are significantly buried in the binding pocket. This would point to a large structural component in the binding of the peptides. The C-terminal proline preference and the polyproline helix formed when bound are in agreement with this possibility. Finally, phosphorylation of FxxP motifs in Cdc6 at position 5 can decrease the binding strength for PP4 from 6.7µM to 39.8µM. The mechanism of modulation is unclear as there are no clear steric or electrostatic clashes, however, the phosphorylated region does form a polyproline helix when bound so a structural conflict may drive the affinity change.
Pattern: F..P
Pattern Probability: 0.0017312
Present in taxons: Eukaryota Fungi Metazoa
Interaction Domain:
WH1 (PF00568) WH1 domain (Stochiometry: 1 : 1)
o See 15 Instances for DOC_PP4_FxxP_1
o Abstract
Reversible protein phosphorylation is an essential regulatory mechanism in eukaryotes. Phosphoprotein phosphatases (PPPs) catalyze protein dephosphorylation by hydrolyzing Ser/Thr-linked phosphate ester bonds and play the crucial role of counteracting the enzymatic activity of protein kinases. Phosphatase specificity is mainly achieved through docking interaction with their substrates. Numerous phosphatase docking motifs have now been characterised including the PP1-binding KVxF and SILK motifs, the PP2A-binding LxxIxE motif and the Calcineurin-binding PxIxIT and LxVP motifs. The PP4 docking motif was the most recent of the major human PPP docking motifs to be characterised. The PPP4R3 substrate recruitment subunit of the PP4 holoenzyme binds FxxP- and MxPP-containing peptides through its Enabled/VASP Homology 1 (EVH1) domain. The FxxP motif has been characterised in several human proteins including Coiled-coil domain-containing protein 6 (CCDC6), M-phase inducer phosphatase 1 (CDC25A), Wings apart-like protein homolog (WAPL) and Kanadaptin (SLC4A1AP) and in Drosophila melanogaster Centromeric protein-C (Cenp-C) (Ueki,2019). The MxPP type motif has been characterised in mRNA-capping enzyme (MCE1) and Transcription initiation factor TFIID subunit 1-like (TAF1L). Most PP4 docking motifs have not been functionally characterised to any depth. The phospho-regulated PP4 docking motif in CCDC6 controls its cellular distribution by regulating CCDC6 nucleocytoplasmic shuttling. The PP4 docking motif in WAPL regulates cohesin binding and release. In Drosophila, centromeric Cenp-C recruits PP4 to centromeres and this PP4 docking motif-dependent interaction is required for the integrity of the centromere during mitosis (Lipinszki,2015). It is likely that large amounts of interesting PP4 docking motif related biology remains to be uncovered.
o 2 selected references:

o 8 GO-Terms:

o 15 Instances for DOC_PP4_FxxP_1
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
Q9VHP9 Cenp-C
1057 1060 DESSADVVFKKPLAPAPRAK TP 1 Drosophila melanogaster (Fruit fly)
1579 1582 VKAADEDVFRKPGLPPPASK TP 1 Homo sapiens (Human)
P46937 YAP1
95 98 RLRKLPDSFFKPPEPKSHSR TP 1 Homo sapiens (Human)
596 599 PNQKDDGVFKAPAPPSKVIK TP 1 Homo sapiens (Human)
P15498 VAV1
765 768 LDTTLQFPFKEPEKRTISRP TP 1 Homo sapiens (Human)
74 77 ASQDLSGDFKKPALPVSPAA TP 2 Homo sapiens (Human)
767 770 GSGTNEFQFLKPVLPNIQGH TP 1 Homo sapiens (Human)
789 792 ASDGSDFTFLRPLSVQQPTA TP 1 Homo sapiens (Human)
Q15021 NCAPD2
1337 1340 ASTASDNDFVTPEPRRTTRR TP 1 Homo sapiens (Human)
Q14680 MELK
439 442 SAVKNEEYFMFPEPKTPVNK TP 2 Homo sapiens (Human)
Q92620 DHX38
39 42 SAASEQHVFKAPAPRPSLLG TP 2 Homo sapiens (Human)
771 774 PLAMASSLFRVPEPPSSHSQ TP 2 Homo sapiens (Human)
P30305 CDC25B
199 202 DKENDGFVFKMPWKPTHPSS TP 2 Homo sapiens (Human)
P30304 CDC25A
148 151 NKENEAFEFKKPVRPVSRGC TP 2 Homo sapiens (Human)
Q16204 CCDC6
423 426 RRSNSPDKFKRPTPPPSPNT TP 2 Homo sapiens (Human)
Please cite: The Eukaryotic Linear Motif resource: 2022 release. (PMID:34718738)

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