The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Functional site class:
Phospholigands for MAGUK family Guanylate Kinase-like Domains
Functional site description:
The Membrane Associated Guanylate Kinase (MAGUK) family of proteins contain a Guanylate kinase-like (GK-like) domain that lost catalytic activity but gained the ability to bind phosphorylated proteins. In post-synaptic densities (PSDs), the PSD-95 family MAGUKs (also called Discs Large Homologue DLG family) function as molecular adaptors between glutamate receptors and intracellular signaling/cytoskeletal networks. The interaction between their GK-like domains and phosphorylated SAPAP proteins represents an essential link in the formation of the PSD-95/SAPAP/Shank postsynaptic core complex, but other GK-like domain partners have also been described.
ELM Description:
Based on structures and sequences, we found two alternative lengths for the GBR motif, which depend on the positioning of the C-terminal end of the motif helix in the binding groove. Most instances (including all SAPAPs) represent the longer version of the motif R..(S)[YFLM][^P][^P][ASG][LMVIQT] wherein a large hydrophobic residue in position +5 (from the phospho-serine) is preceded by a small residue, either alanine, glycine or serine. The homologs of the D. melanogaster protein Pins follow the shorter motif pattern where the large hydrophobic residue is shifted to position +4 and is only observed to be leucine R..(S)[YFLM][^P][^P][L]. There are multiple structures available for this phosphorylation-dependent interaction that confirm the validity of the above motif patterns. The phospho-LGN (3UAT), phospho-Pins (3TVT), phospho-LGL (3WP0) and phospho-SAPAP1-Repeat2 (5YPO) peptides all adopt a short α-helical conformation in the complex, occupying the concave groove clamped by the GMP-binding subdomain (β3, β4, β5 and β6) and the Core subdomain (α1 helix) of the GK-like domain. These structures confirm that the phosphate group of the pSer residue makes an extended network of charge-charge interactions plus H-bonds with several residues in the GK-like domain. This is reinforced by extensive hydrophobic contacts between the hydrophobic residues in the +1, +4 and +5 position with a conserved “hydrophobic helix binding groove” in the GK-like domain (Zhu,2014). Also, the side chain of Arg at the ‐3 position of p‐LGN forms salt bridges with Glu761 and Asp766 from the β3/β4‐loop of PSD-95 GK-like and a hydrogen bond with the phosphate group from pSer; therefore, replacement of Arg(‐3) with an Ala caused a 5‐fold decrease in affinity in p‐LGN's binding to PSD‐95 SH3‐GK (Zhu,2011). SIPA1L1 contains a Gly at +4 position, instead of a larger alanine or serine residue, accordingly, it was the partner with the lowest measured affinity among all.
Pattern: (R..(S)[YFLM][^P][^P][L])|(R..(S)[YFLM][^P][^P][ASG][LMVIQT])
Pattern Probability: 0.0000978
Present in taxon: Metazoa
Interaction Domain:
Guanylate_kin (PF00625) Guanylate kinase (Stochiometry: 1 : 1)
o See 14 Instances for LIG_DLG_GKlike_1
o Abstract
Post-synaptic densities (PSDs) are densely packed multi-protein structures orchestrating synaptic formation and function at the distal tip of dendritic spine heads (Carlin,1980 Chen,2008 Sheng,2011) that are enriched in neurotransmitter receptors, adhesion molecules, scaffold proteins, signalling enzymes, and cytoskeletal components. The spatial and temporal organization of scaffold protein-mediated protein complexes at the core of the PSD is pivotal for synaptic signalling and plasticity as those serve as bridges linking the upstream glutamate receptors (NMDA-type and AMPA-type glutamate receptors) with the downstream signalling complexes and the cytoskeleton (Won,2017 Zhu,2016). The PSD-95 family (also called discs large homologue, DLG family) of membrane-associated guanylate kinases (MAGUKs), including PSD-95, PSD-93, SAP102, and SAP97, are the most abundant scaffold proteins in PSDs. PSD-95 directly binds to Synapse-associated protein 90 (SAP90)/PSD-95-associated proteins (SAPAPs, also known as DLGAPs or GKAPs), which in turn bind to the Shank family proteins, forming the PSD-95/SAPAP/Shank core complex of PSD (Kim,1997 Naisbitt,1999). This core complex is thought to be critical for synaptic development and transmission. Loss of any of its components results in the loss of AMPAR-containing synapses and weaker synaptic transmissions (Zhu,2017).
MAGUKs contain a Guanylate kinase-like (GK-like) domain (InterPro: IPR008144) that diverged from guanylate kinase enzymes (which catalyze phosphoryl transfer from ATP to GMP) near the appearance of animals in the evolutionary record. These diverged MAGUK GK-like domains of animals have lost catalytic activity but gained the ability to bind phosphorylated segments of proteins (Johnston,2012), as the GMP-binding site of GK has evolved into a specific pSer/pThr-binding pocket (Zhu,2011).
The interaction between the DLG family members and phosphorylated SAPAP proteins represents an essential link in the formation of the PSD-95/SAPAP/Shank postsynaptic core complex. SAPAPs bind the guanylate kinase (GK) domains of the PSD-95 family proteins (Kim,1997 Takeuchi,1997 Zhu,2017 Zhu,2011) and MAGI2 (Hirao,1998) through very strictly conserved short repeats, referred to as GK-binding repeats (GBRs). GBRs were considered to match a R..(S)Y[LMVI][RK]A motif, with the serine residue required to be phosphorylated for binding. Studies also established that non-PSD-specific MAGUK proteins, for instance the zona occludens protein ZO-1, the peripheral plasma membrane protein CASK and the regulator of neutrophil polarity MPP1 do not specifically bind the SAPAP motif even though they also possess GK-like domains (Takeuchi,1997). Wide conservation of this interaction motif is underlined by the fact that the D. melanogaster homologue of mammalian MAGUKs, Dlg1 could also bind the rat SAPAP GBRs with similar affinity as mammalian PSD-95 family proteins (Takeuchi,1997).
Some other proteins also employ similar phosphorylated motifs to bind the GK-like domain, although they usually bind somewhat weaker than SAPAPs. These include members of diverse protein families, like the synaptic scaffold protein BEGAIN (Deguchi,1998), the Rap‐specific GTPase‐activating protein SPAR, the mitotic spindle regulatory protein LGN (Zhu,2011) and Lgl, a component of the evolutionarily conserved Scribble complex (Zhu,2014).
Interestingly, while in these interactions the peptide pSer could not be changed to glutamic/aspartic acid without losing/largely weakening the interaction (Zhu,2017 Zhu,2011), in one known case of MAP1A the complex revealed a unique target recognition mode, where an aspartic acid of MAP1A (D2117) could mimic phospho-serine and bind to the 'phospho-site' of the PSD-95 GK (Xia,2017).
o 15 selected references:

o 8 GO-Terms:

o 14 Instances for LIG_DLG_GKlike_1
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
642 650 EGPLSRVKSLKKSLRQSFRR TP 5 Homo sapiens (Human)
O43166 SIPA1L1
1629 1637 KSLPLRRPSYTLGMKSLHGE TP 1 Homo sapiens (Human)
Q8VDU0 Gpsm2
405 412 AGAKLGRRHSMENLELMKLT TP 3 Mus musculus (House mouse)
Q9VB22 pins
433 440 GRMVRVRRQSMEQLDLIKIT TP 2 Drosophila melanogaster (Fruit fly)
O88881 Begain
596 604 GSGLSRKDSLTKAQLYGTLL TP 3 Rattus norvegicus (Norway rat)
O95886 DLGAP3
393 401 PCRRMRSGSYIKAMGDEESG TP 3 Homo sapiens (Human)
O14490 DLGAP1
403 411 PKLQIRSHSYLRAVSEVSIN TP 1 Homo sapiens (Human)
O14490 DLGAP1
372 380 PKVAARRESYLKATQPSLTE TP 5 Homo sapiens (Human)
P97839 Dlgap4
394 402 PKTAARRQSYLRATQQSLGE TP 1 Rattus norvegicus (Norway rat)
P97838 Dlgap3
497 505 GCFRMRSHSYLRAIQAGCSQ TP 1 Rattus norvegicus (Norway rat)
P97837 Dlgap2
437 445 PCRRMRSGSYIKAMGDEESG TP 2 Rattus norvegicus (Norway rat)
P97836 Dlgap1
349 357 PCRRMRSGSYIKAMGDEDSG TP 8 Rattus norvegicus (Norway rat)
P97836 Dlgap1
409 417 PKLQIRSHSYLRAVSEVSIN TP 2 Rattus norvegicus (Norway rat)
P97836 Dlgap1
378 386 PKVAARRESYLKATQPSLTE TP 4 Rattus norvegicus (Norway rat)
Please cite: ELM — the eukaryotic linear motif resource in 2020. (PMID:31680160)

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