Graphical abstract
Abbreviations: BTK, ITK; SH3, SH2; PHTH, PRR; TEC, PLCγ; γSA, sPH; DAG, IP3; PIP3, IP4; SAXS, NMR
Highlights
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TEC kinases and PLCγ transition between autoinhibited state and active conformation.
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PLCγ structures reveal both autoinhibited form and active form of gamma specific array (γSA); the four regulatory domains unique to the PLCγ isozymes.
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Domain dynamics likely control activation mechanism.
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PLCγ phosphorylation triggers conformational switch.
Abstract
Cell surface receptors such as the T-cell receptor (TCR) and B-cell receptor (BCR) engage with external stimuli to transmit information into the cell and initiate a cascade of signaling events that lead to gene expression that drives the immune response. At the heart of controlling T- and B-cell cell signaling, phospholipase Cγ hydrolyzes membrane associated PIP2, leading to generation of the second messengers IP3 and DAG. These small molecules trigger mobilization of intracellular Ca2+ and promote transcription factor transport into the nucleus launching the adaptive immune response. The TEC family kinases are responsible for phosphorylating and activating PLCγ, and our group aims to understand mechanisms that regulate immune cell signal transduction by focusing on this kinase/phospholipase axis in T-cells and B-cells. Here, we review the current molecular level understanding of how the TEC kinases (ITK and BTK) and PLCγ1/2 are autoinhibited prior to activation of cell surface receptors, how TEC kinases are activated to specifically recognize the PLCγ substrate, and how conformational changes induced by phosphorylation trigger PLCγ activation.
Introduction
TEC kinases and phospholipases (Fig. 1)
Tyrosine kinases are first responders that propagate cellular signals immediately following membrane receptor engagement. In a subset of immune cells including T- and B-cells, the TEC family kinases are the third in a series of proximal non-receptor tyrosine kinases that are activated by phosphorylation. Activated TEC family kinases ITK and BTK are assembled within the membrane associated scaffolding protein complex and phosphorylate their substrate phospholipase Cγ (PLCγ) (Fig. 1a). In the absence of activating stimuli, TEC kinases adopt an autoinhibited conformation that limits unwarranted catalytic activity. TEC family kinases have been notoriously resistant to crystallizing in their full-length form leaving open many questions regarding the molecular details of regulation.
PLC’s are a central node in controlling many aspects of cell signaling and gene expression. The PLCγ subtype consists of PLCγ1 and PLCγ2 isoforms that are expressed in T-cells and B-cells respectively among other cell types. Activated PLCγ1/2 hydrolyzes phosphatidylinositol 4,5-bisphosphate (PIP2) to generate the second messengers inositol trisphosphate (IP3) and diacylglycerol (DAG) (Fig. 1b) triggering further signaling events that ultimately result in changes in gene transcription, that for T- and B-cells, result in activation of the adaptive immune response.
This graphical review directs its attention to the conformational changes and molecular binding events that control the transition between autoinhibited and activated TEC kinases and phospholipase Cγ. Throughout, we highlight available data to build a structural understanding of the molecular events that regulate the TEC kinases and the phospholipase C gamma family; sequence and structural homology between BTK and ITK, as well as PLCγ1 and PLCγ2, suggest that structural features determined for one family member are likely shared across the protein family.
Tec family kinase autoinhibition (Fig. 2)
Non-receptor tyrosine kinases (NRTKs) are cytosolic enzymes that are activated following receptor engagement. The well-studied SRC family kinases are the prototypical example of NRTKs and make up the largest family of NRTKs with 9 distinct kinases. The SRC kinase sequences all include a conserved C-terminal regulatory tail that contains an inhibitory tyrosine phosphorylation site (Y527 in SRC). The precise regulatory role of SRC Y527 became clear when the first SRC kinase was crystalized in 1997 (Xu et al., 1997). Phosphorylated Y527 (pY527) interacts with the SH2 domain in the same molecule stabilizing the compact autoinhibitory state. Loss of the Y527 hydroxyl (mutation of Y527 to phenylalanine) results in increased propensity for the SRC kinase to adopt an open, active conformation.
The second largest family of NRTKs are the TEC kinases. The five members of the TEC family (ITK, BTK, TXK (RLK), TEC & BMX) are expressed primarily in cells of hematopoietic lineage and none of the TEC kinases contain the C-terminal regulatory phosphorylation site that is so critical in controlling the function of the SRC family kinases. To date, a crystal structure of any full-length autoinhibited TEC kinase is lacking but in 2015, a fragment containing just three of the domains in the TEC family kinase BTK was crystallized (Wang et al., 2015) representing the first glimpse into how the TEC kinase domains are arranged in three-dimensional space (Fig. 2a,b). The SRC-module (SH3-SH2-kinase fragment) crystallized as a domain swapped dimer with domain swapping occurring in the SH2 domain. While the functional significance of the domain swapped dimer is unknown, each half of the domain swapped dimer adopts an autoinhibitory conformation quite similar to that observed for the SRC family. The SH3 and SH2 domains assemble on the ‘back’ of the kinase domain with the SH2-linker region contacting both the SH3 and kinase domain N-lobe (Fig. 2a,i,ii). This domain arrangement is similar to SRC kinases despite the absence of the SRC regulatory tail in the TEC family. Solution studies of BTK (Joseph et al., 2017), revealed the negatively charged side-chain D656 fills the role of SRC pY527 by mediating inhibitory contacts between the end of the kinase domain and the BTK SH2 domain (Fig. 2a,iii). In addition, interactions between the SH2-kinase linker and the N-lobe of the kinase assemble a hydrophobic stack (Fig. 2a, ii) which stabilizes the autoinhibited structure and also allosterically communicates with the active site; formation of the inhibitory hydrophobic stack leads to selective binding of ADP over ATP in the kinase domain, an observation first established with ITK and SRC (von Raussendorf et al., 2017). This work provided a clear link between the regulatory interactions of the SH3/SH2-linker region and the catalytic function of the active site (von Raussendorf et al., 2017).
A distinguishing feature of the TEC family is the Pleckstrin-Homology Tec-Homology (PHTH) domain followed by a long linker region that contains a proline-rich region (PRR) that matches the canonical SH3 ligand sequence (Fig. 2, center). Accurately defining the autoinhibitory contacts for the PHTH domain and the role of the PRR has been challenging (Wang et al., 2015, Amatya et al., 2019). A crystal structure of the PHTH domain tethered directly to the kinase domain via a Ala-Ala dipeptide has been solved (Fig. 2c) and reveals a contact between the PHTH α2 helix and N-lobe of the kinase domain (Wang et al., 2015). The position of the PHTH domain in the tethered crystal structure (Fig. 2c) partially overlaps with the SH3 domain in the structure of the autoinhibited SRC module of BTK (Fig. 2a) and so these structures are mutually exclusive. It is possible that this binding mode represents an intermediate on the activation pathway instead of a stable autoinhibited structure. An alternative autoinhibitory position for the PHTH domain (Fig. 2d) has been characterized based on nuclear magnetic resonance (NMR) data and hydrogen–deuterium exchange applied to the full-length BTK molecule (Amatya et al., 2019, Devkota et al., 2017). These solution-based approaches suggest that the β3-β4 loop of the PHTH domain mediates an autoinhibitory contact with the catalytic face of the C-lobe kinase domain stabilizing the autoinhibited state of the kinase domain. Given the multiple interdomain contacts observed between the PHTH and kinase domain (Fig. 2c,d) it is likely that the PHTH domain is dynamic and possibly sampling a range of conformational states with respect to the autoinhibited SRC module (Fig. 2e).
Current models of autoinhibited full-length BTK do not resolve the proline-rich region (PRR). Available data suggest that this long linear motif situated between PHTH and SH3 domains (Fig. 2, center) might serve to ‘prime’ the full-length kinase for activation (Devkota et al., 2015). The canonical SH3 ligand sequence within the PRR binds to the adjacent SH3 domain in a manner that competes with the autoinhibitory contact between the SH3 binding groove and the SH2-kinase linker. Mutation of the PRR results in a more stable autoinhibited state and lower catalytic activity in vitro (Joseph et al., 2017). It is also likely that the PRR of the TEC kinases serves as a docking site for other SH3 containing signaling proteins during signaling; in fact, the BTK PRR contains two consecutive SH3 ligands setting it apart from the other kinases in the family.
PLCγ autoinhibition (Fig. 3)
Studies have shown that mutants of both PLCγ1 and PLCγ2 have been implicated in driving human diseases such as leukemias and lymphomas, as well as being associated with dysregulated immune responses and resistance to inhibitors. Therefore, numerous experimental approaches have been carried out to structurally characterize the PLCγ isozyme (Bunney et al., 2012, Hajicek et al., 2019).
Some of the first structural work on PLCγ involved determination of two crystal structures for the tandem nSH2-cSH2-linker region; one phosphorylated on Y783 and the other without phosphorylation (Bunney et al., 2012). The structure of phosphorylated nSH2-cSH2-linker reveals a canonical pY/SH2 interaction between pY783 and the arginine lined binding pocket of cSH2 (Fig. 3a). The cSH2 binding pocket also showed electron density for the structure of unphosphorylated PLCγ1 nSH2-cSH2-linker, which the authors suggest that the Y783 containing linker binds to the cSH2 domain even in the absence of phosphorylation. Using a combination of NMR and small angle X-ray scattering (SAXS), the same authors produced a structural model of the entire γSA. In this model, the sPH-SH3 segment contacts the cSH2 domain (via an sPH/cSH2 interface) involving the βD-βE strands of the cSH2 domain (Fig. 3b,c). Split PH domains are characterized by insertions of one or more autonomously folded protein modules in the middle of pH domain sequences, which is an uncommon feature for PH domains making split PH domains quite unique (Wen et al., 2006).
Advances in cryoEM and success in crystallizing the full-length PLCγ1 enzyme (Hajicek et al., 2019, Liu et al., 2020) yielded the first glimpse of the complete autoinhibitory structure of this class of phospholipase. The autoinhibited structure shows that the sPH and cSH2 domains both form extensive autoinhibitory contacts with the core of PLCγ1 (Fig. 3d,e). These inhibitory interfaces latch the γSA to the top of the catalytic core and block access to the PIP2 substrate. The cSH2-linker region of PLCγ1 is not evident in the full-length crystal structure and was in fact shortened considerably in order to obtain crystals of the full-length PLCγ1. The cSH2/core interface is coincident with the binding site of the phosphorylated Y783 linker suggesting that release of the cSH2 domain from the core is triggered upon phosphorylation. In addition, the association of the non-phosphorylated Y783 containing linker with cSH2 (Bunney et al., 2012) suggests that autoinhibited PLCγ1 samples an open conformation prior to Y783 phosphorylation-induced activation. In fact, any mechanism that competes with the stable, latched γSA/core interaction will shift the equilibrium away from the autoinhibited form and result in increased accessibility to PIP2 substrate and thus increased activity of the enzyme. For example, mutations in PLCγ2 drive drug resistance in part by shifting the optimal equilibrium away from autoinhibited enzyme (Joseph et al., 2021).
Comparison of the two available structural models for the PLCγ1 γSA region (Fig. 3f) show two distinct arrangements of the sPH/SH3 cassette with respect to the nSH2-cSH2 segment. It is suggested that a large conformational change occurs in the γSA region upon PLCγ1 activation (Gresset et al., 2010) and so the conformational states revealed to date by structural biology approaches may represent the autoinhibited form (as confirmed by the full-length structure, Fig. 3d) and the putative active state (captured by solution methods focused on the isolated γSA region, Fig. 3b). In essence, the models suggest that activation via phosphorylation of Y783 competes with the cSH2/core interaction allowing the sPH/SH3 domains to swing down and interact with a different surface on cSH2. The conformational adjustment initiated by pY783 binding to the cSH2 domain would result in release of γSA from the PLCγ core followed by steric occlusion of the autoinhibitory surface of γSA. This activation mechanism may, in part, serve to prevent re-association of cSH2 with the PLCγ core to maintain the active state of PLCγ as it encounters its substrate at the membrane. Additional experiments are needed to test this idea and gain a deeper appreciation for the dynamics that control activation/autoinhibition of the PLCγ family.
Adaptor proteins/ membrane association/substrate priming and docking (Fig. 4, Fig. 5)
Interactions of the regulatory domains of TEC kinases with their ligands leads to activation and recruitment to the receptor signaling complex (Fig. 4a). As depicted in Fig. 2e, the PHTH domain may be visiting multiple isoenergetic conformational states in the autoinhibited kinase. Crystal structures, biophysical approaches and molecular dynamic simulations of the BTK PHTH domain bound to PIP3, the headgroup of PIP3, IP4 or the soluble phosphoinositol IP6 (Wang et al., 2015, Wang et al., 2019, Chung et al., 2019), show that PHTH dimerization can occur and that the BTK PHTH domain harbors two sites for membrane interaction (Fig. 4b). BTK dimerization and the presence of multiple ligand binding sites may confer a switch-like activation of BTK (Chung et al., 2019) by requiring a threshold concentration of PIP3 to generate membrane associated active BTK. Binding of the BTK PHTH domain to membrane associated PIP3 also promotes conformational changes throughout the full-length BTK molecule. Hydrogen deuterium exchange mass spectrometry reveals increased exposure to solvent in all domains of BTK upon association with PIP3 containing liposomes (Joseph et al., 2017). The active conformation of BTK at the membrane has not been experimentally determined but early SAXS analysis (Marquez et al., 2003) revealed an elongated conformation that would be compatible with the PHTH dimer at the membrane and binding of the SH3 and SH2 domains to adaptor protein sequences (Fig. 4a, 5).
SH3 ligands (PXXP motifs) within the adaptor proteins can displace the SH2-kinase linker bound to the SH3 domain in the autoinhibited conformation stabilizing the active kinase within the signaling complex (Fig. 4a,c). Receptor activation also leads to phosphorylation of adaptor proteins such as SLP-76 (pY145) which recruits ITK into the scaffolded complex via a canonical ITK SH2/pY145 interaction that disrupts the autoinhibitory interaction between SH2 and kinase domain (Fig. 4a,d).
Interestingly, BTK is the target of Ibrutinib and other second-generation inhibitors used in the treatment of B-cell chronic lymphocytic leukemia (CLL). BTK is prone to mutations that elicit drug resistance and in at least one case the mutation shifts the conformational equilibrium toward the active state of the kinase thereby increasing cellular BTK activity promoting escape from drug induced inhibition (Joseph et al., 2020). As well, different active site inhibitors of BTK show markedly different effects on the conformational equilibrium of the full-length enzyme; Ibrutinib destabilizes the compact autoinhibited form of BTK while GDC0853 has no effect on the conformational preferences of BTK outside of the kinase domain (Joseph et al., 2020). The extent to which drug induced changes in the conformational equilibrium of BTK affect signaling processes is not yet known.
Once activated, BTK/ITK is assembled within the membrane associated adaptor protein complex. Into this environment enters PLCγ1/2, which exits its autoinhibited conformation to associate with the kinase domain and specific regions of adaptor/scaffold proteins (Fig. 5). Here, TEC family kinase mediated activation of PLCγ occurs and active PLCγ promotes hydrolysis of PIP2 (Fig. 5). The next stage of signaling can commence: action of PIP2 derived second messengers IP3 and DAG on calcium channels and the PKC/Ras pathway drive changes in cell morphology and gene transcription ultimately generating the adaptive immune response.
Declaration of Competing Interest
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
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