The structure of SALM5 suggests a dimeric assembly for the presynaptic RPTP ligand recognition

Abstract

Synaptic adhesion molecules play a crucial role in the regulation of synapse development and maintenance. Recently, several families of leucine-rich repeat (LRR) domain-containing neuronal adhesion molecules have been characterised, including netrin-G ligands, LRRTMs and the synaptic adhesion-like molecule (SALM) family proteins. Most of these are expressed at the excitatory glutamatergic synapses, and dysfunctions of these genes are genetically linked with cognitive disorders, such as autism spectrum disorders and schizophrenia. The SALM family proteins SALM3 and SALM5, similar to SLITRKs, have been shown to bind to the presynaptic receptor protein tyrosine phosphatase (RPTP) family ligands. Here, we present the 3.1 Å crystal structure of the SALM5 LRR-Ig-domain construct and biophysical studies that verify the crystallographic results. We show that SALM1, SALM3 and SALM5 form similar dimeric structures, in which the LRR domains form the dimer interface. Both SALM3 and SALM5 bind to RPTP immunoglobulin domains with micromolar affinity. SALM3 shows a clear preference for the RPTP ligands with the meB splice insert. Our structural studies and sequence conservation analysis suggests a ligand-binding site and mechanism for RPTP binding via the dimeric LRR domain region.

Structural basis of SALM3 dimerization and synaptic adhesion complex formation with PTPσ

“…Dimerization through the LRR domain is a defining feature of the SALM family. The SALM3 LRR domain forms a dimer similar to those observed for SALM5 and SALM2 crystal structures 17,18,20 (Fig. 1).…”

“…2). The dimer species is however very stable in solution for both SALM3 and SALM5, and also SALM1 based on our observations 20 . Monomeric species have not been observed in vitro.…”

“…1). It appears that the SALMs form a highly conserved dimeric structure based on the known structures of SALM2, SALM3 and SALM5 and our data on SALM1 oligomerization 20 , and the overall sequence conservation of the interface residues in the protein family ( Supplementary Fig. S2, Table S1).…”

Splice‐dependent trans‐synaptic PTP δ– IL 1 RAPL 1 interaction regulates synapse formation and non‐ REM sleep

“…To further explore the possibility that PTPδ trans‐synaptically regulates pTyr levels of IL1RAPL1, we generated another transgenic mouse line ( Ptprd‐meA −/− ) in which the PTPδ–IL1RAPL1 interaction was selectively abolished by deleting the meA splice insert (9 aa‐long) of PTPδ, encoded by exons 15 and 16 (Fig C and D). The PTPδ‐meA insert is critical for the PTPδ–IL1RAPL1 interaction but not interactions of PTPδ with other postsynaptic CAMs (NGL‐3, Slitrks, IL1RAcP, SALM3/5, and IL‐1RAcP) (Yoshida et al , ; Takahashi et al , ; Um et al , ; Li et al , ; Yamagata et al , ,b; Choi et al , ; Goto‐Ito et al , ; Karki et al , ; Lin et al , ).…”

“…LAR‐RPTPs have been suggested to regulate synapse development and function by acting as presynaptic organizers that trans‐synaptically interact with multiple postsynaptic CAMs, including NGL‐3 (netrin‐G ligand‐3), TrkC, Slitrks, IL1RAPL1 (interleukin 1 receptor accessory protein like 1), IL‐1RAcP (interleukin 1 receptor accessory protein), and SALM3/5 (cell adhesion‐like molecule 3/5, also known as LRFN4/5 for leucine‐rich repeat and fibronectin type III domain) (Woo et al , ; Kwon et al , ; Takahashi et al , , ; Valnegri et al , ; Yoshida et al , , ; Yim et al , ; Li et al , ; Choi et al , ). These interactions are frequently regulated by splice inserts located on the extracellular regions of LAR‐RPTPs; related molecular details have been clarified by biochemical, cell biological, and X‐ray crystallographic studies (Coles et al , ; Um et al , ; Yamagata et al , 2015a; Won et al , ; Goto‐Ito et al , ; Karki et al , ; Lin et al , ). For instance, PTPδ requires the miniexon A (meA) splice insert to interact with IL1RAPL1 (Yoshida et al , ; Yamagata et al , 2015b), a postsynaptic CAM that critically regulates synaptic and neuronal functions (Montani et al , ), whereas PTPδ requires the miniexon B (meB) to interact with Slitrks, SALM3/5, and IL‐1RAcP (Takahashi et al , ; Yoshida et al , ; Yim et al , ; Um et al , ; Li et al , ; Yamagata et al , ,b; Choi et al , ).…”