Structural insights into selective interaction between type IIa receptor protein tyrosine phosphatases and Liprin-α

Abstract

Synapse formation is induced by transsynaptic interaction of neuronal cell-adhesion molecules termed synaptic organizers. Type IIa receptor protein tyrosine phosphatases (IIa RPTPs) function as presynaptic organizers. The cytoplasmic domain of IIa RPTPs consists of two phosphatase domains, and the membrane-distal one (D2) is essential for synapse formation. Liprin-α, which is an active zone protein critical for synapse formation, interacts with D2 via its C-terminal domain composed of three tandem sterile alpha motifs (tSAM). Structural mechanisms of this critical interaction for synapse formation remain elusive. Here, we report the crystal structure of the complex between mouse PTPδ D2 and Liprin-α3 tSAM at 1.91 Å resolution. PTPδ D2 interacts with the N-terminal helix and the first and second SAMs (SAM1 and SAM2, respectively) of Liprin-α3. Structure-based mutational analyses in vitro and in cellulo demonstrate that the interactions with Liprin-α SAM1 and SAM2 are essential for the binding and synaptogenic activity.

Liprin-α-Mediated Assemblies and Their Roles in Synapse Formation

“…Specifically, SAM123 was found to interact with the CaM kinase domain (CaMK) of CASK and SAM123 of liprin-β1 simultaneously, indicating that SAM123 mediates protein assemblies by using different interfaces ( Figures 2B,C). This structural indication was further supported by two recent structural studies of liprin-α3 in complexes with the cytoplasmic phosphatase domains of two LAR-RPTP proteins, LAR and PTPδ (Wakita et al, 2020;Xie et al, 2020). The binding surface for LAR-RPTPs on SAM123 shows no overlap with that for either CASK or liprin-β ( Figures 2B,C).…”

“…Specifically, the phosphatase domains of LAR and PTPδ interact with a cleft between the two SAM domains, whereas a surface patch opposite to the cleft facilitates the binding of CASK to liprin-α. Serrapages et al, 1995;Serra-Pages et al, 1998;Kaufmann et al, 2002;Wyszynski et al, 2002;Ackley et al, 2005;Dunah et al, 2005;Astigarraga et al, 2010;Kiok et al, 2011;Joshi et al, 2014;Bomkamp et al, 2019;Wakita et al, 2020;Xie et al, 2020 CASK α1, 2, 3, 4 SAM123 Neurotransmitter release Olsen et al, 2005;Samuels et al, 2007;Wei et al, 2011;LaConte et al, 2016;Wu et al, 2016 Liprin Ko et al, 2003b;Dai et al, 2006;Kittelmann et al, 2013 GIT1 α1, 2, 3, 4 Dliprin-α SYD2 SAH AMPA receptor targeting, cell spreading Ko et al, 2003a,b;Totaro et al, 2007;Asperti et al, 2011;Liang et al, 2019;McDonald et al, for the liprin-α3_LCR/mDia_DID complex; 3TAC, 3TAD, 6KR4, and 6KIP for the SAM123 structures in complex with CASK_CaMK, liprin-β1_SAM123, LAR_D1D2, and PTPδ_D2, respectively; 1N7F for the liprin-α1_PBM/GRIP1_PDZ6 complex). The value curve at the bottom panel indicates sequence conservation of liprin-α proteins.…”

“…In addition to the SAM domains, some accessory elements in the SAM123 region are required for the complex formation between liprin-α and its specific binding partners ( Figures 1 , 2A ). In both the crystal structures of liprin-α3_SAM123 in complex with the two tandem phosphatase domains (D1D2) of LAR and with the second phosphatase domain (D2) of PTPδ, a loop at the N-terminal to the αN-helix was found to provide a second binding site for the D2 phosphatase domains of LAR and PTPδ, suggesting a conserved two-site binding mode between liprin-αs and LAR-RPTPs ( Figure 2B ) ( Wakita et al, 2020 ; Xie et al, 2020 ).…”

Roles of type IIa receptor protein tyrosine phosphatases as synaptic organizers

“…The structural mechanism of the interaction between Liprin-α and IIa RPTPs was recently elucidated by the complex structures of human Liprin-α3 tSAM with LAR D1-D2 and mouse Liprin-α3 tSAM with PTPδ D2 [75,76] ( Figure 4A). The tSAM domain of Liprin-α contains three SAM domains…”

“…The internal loop between SAM1 and SAM2 is responsible for binding to CASK but not for binding to the cytoplasmic domain of IIa RPTPs. The CASK-binding surface of Liprin-α is located on the opposite side of the IIa RPTP D2-binding surface [75][76][77]. Therefore, IIa RPTP and CASK can simultaneously bind to Liprin-α and form a ternary complex.…”