1.A.7 ATP-gated P2X Receptor Cation Channel (P2X Receptor) Family
Members of the P2X Receptor family respond to ATP, a functional neurotransmitter released by exocytosis from many types of neurons. They have been placed into seven groups (P2X1 - P2X7) based on their pharmacological properties. These channels, which function at neuron-neuron and neuron-smooth muscle junctions, may play roles in the control of blood pressure and pain sensation. Their structural-fuctional relationships have been examined (Mager et al. 2004), and they are expressed throughout the body, mediating a multitude of functions, including muscle contraction, neuronal excitability and bone formation (Vial et al. 2004). They may function in lymphocyte and platelet physiology. They are found only in eukaryotes. Their ATP binding sites are extracellular and involve residues near ile-67. ATP binding causes the channel to go from the closed to the open state (Kracun et al., 2010). The intracellular amino terminus plays a dominant role in desensitization of P2X receptor ion channels (Allsopp and Evans, 2011). Activation and regulation of purinergic P2X receptor channels has been reviewed by Caddou et al. (2011). The gating mechanism has been proposed (Du et al., 2012). The ion access pathway to the transmembrane pore in P2X receptor channels has been estimated (Kawate et al., 2011). P2X receptor channels show threefold symmetry in ionic charge selectivity and unitary conductance (Browne et al., 2011). The binding of ATP to trimeric P2X receptors (P2XR) causes an enlargement of the receptor extracellular vestibule, leading to opening of the cation-selective transmembrane pore, and specific roles of vestibule amino acid residues in receptor activation have been evaluated (Rokic et al. 2013).
The seven different P2X receptor types differ in their sensitivities to ATP and various ATP analogues as well as in their inactivation kinetics. ATP binding initially causes opening of the non-selective cation channel, allowing Ca2+ entry. Prolonged exposure of slowly inactivating forms to ATP leads to dilation of the pore, making it permeable to larger molecules (up to 1000 Da). Then it functions as a cytolytic pore that is permeable to organic cations such as ethidium and N-methyl-D-glucamine. Formation of this cytolytic pore is regulated by the C-terminal hydrophilic domain in at least one of these receptors (P2X7; Smart et al., 2003). The ion-conducting pathway is formed by three TMS 2 (TMS2) alpha-helices, each being provided by the three subunits of the trimer. P2X receptors are trimeric ATP-activated ion channels permeable to Na+, K+ and Ca+2. The seven P2X receptor subtypes are implicated in physiological processes that include modulation of synaptic transmission, contraction of smooth muscle, secretion of chemical transmitters and regulation of immune responses.
The zebrafish chalice-shaped, trimeric P2X(4) receptor (TC#1.A.7.1.4) is knit together by subunit-subunit contacts implicated in ion channel gating and receptor assembly. Extracellular domains, rich in beta-strands, have large acidic patches that may attract cations, through fenestrations, to vestibules near the ion channel. In the transmembrane pore, the 'gate' is defined by an approximately 8 Å slab of protein. There are three non-canonical, intersubunit ATP-binding sites. ATP binding may promote subunit rearrangement as well as ion channel opening (Kawate et al., 2009).
The P2X1 receptor is the dominant P2X type in smooth muscle neurons. P2X2/P2X3 heterooligomers mediate sensory signals in many other sensory neurons. P2X4 and P2X6 receptors are highly expressed in the central nervous system and probably form heterooligomers. P2X7 is expressed in cells of the immune system and of hematopoetic origin. These channels have a homo- or heterotrimeric architecture (Aschrafi et al., 2004). The carboxy termini influence the regulation of P2X1 receptors (Wen and Evans 2011).
The proteins of the P2X Receptor family are quite similar in sequence, but they possess 380-1000 amino acyl residues per subunit with variability in length localized primarily to the C-terminal domains. They possess two transmembrane spanners, one about 30-50 residues from their N-termini, the other near residues 320-340. The extracellular receptor domains between these two spanners (typically of about 270 residues) are well conserved with several conserved glycyl residues and 10 conserved cysteyl residues. The hydrophilic C-termini vary in length. Like epithelial Na+ channel (ENaC) proteins (TC #1.A.6), they possess (a) N- and C-termini localized intracellularly, (b) two putative transmembrane spanners, (c) a large extracellular loop domain, and (d) many conserved extracellular cysteyl residues. P2X receptor channels are probably hetero- or homomultimers of several subunits and transport small monovalent cations (Me+ and Me++). Some transport Ca2+, and after prolonged exposure to ATP, various metabolites as noted above.
The three-dimensional structure of a P2X receptor is known (Burnstock and Kennedy, 2011). When ATP binds, the pore opens within milliseconds, allowing the cations to flow. P2X receptors are expressed in both central and peripheral neurons where they are involved in neuromuscular and synaptic neurotransmission and neuromodulation. They are also expressed in most types of nonneuronal cells and mediate a wide range of actions, such as contraction of smooth muscle, secretion and immunomodulation. Changes in the expression of P2X receptors have been characterized in many pathological conditions of the cardiovascular, gastrointestinal, respiratory, and urinogenital systems and in the brain and special senses. The therapeutic potential of P2X receptor agonists and antagonists is currently being investigated in a range of disorders, including chronic neuropathic and inflammatory pain, depression, cystic fibrosis, dry eye, irritable bowel syndrome, interstitial cystitis, dysfunctional urinary bladder, and cancer.
Hattori and Gouaux (2012) reported the crystal structure of the zebrafish P2X(4) receptor in complex with ATP and a new structure of the apo receptor. The agonist-bound structure reveals an ATP-binding motif and an open ion channel. ATP binding induces cleft closure of the nucleotide-binding pocket, flexing of the lower body β-sheet and a radial expansion of the extracellular vestibule. The structural widening of the extracellular vestibule is directly coupled to the opening of the ion channel pore by way of an iris-like expansion of the transmembrane helices.
Phosphoinositides modulate the functions of most P2X receptor channels in neurons and glia. A dual polybasic motif has been shown to determine phosphoinositide binding and regulation in members of the P2X channel family (Bernier et al., 2012). Modeling has provided insight into the ligand-binding properties of P2X receptors (Dal Ben et al. 2015). Three distinct roles for P2X7 during adult neurogenesis have been demonstrated, and these depend on the extracellular ATP concentrations: (i) P2X7 receptors can form transmembrane pores leading to cell death,
(ii) P2X7 receptors can regulate rates of proliferation, likely via calcium signalling and
(iii) P2X7 can function as scavenger receptors in the absence of ATP, allowing neural progenitor cells (NPCs) to phagocytose apoptotic NPCs during neurogenesis (Leeson et al. 2018).
Cys loop, glutamate, and P2X receptors are ligand-gated ion channels (LGICs) with 5, 4, and 3 protomers, respectively. Agonists and competitive antagonists apparently induce opposite motions of the binding pocket (Du et al., 2012b). Agonists, usually small, induce closure of the binding pocket, leading to opening of the channel pore, whereas antagonists, usually large, induce opening of the binding pocket, thereby stabilizing the closed pore. Both P2XRs and 5-HT3Rs, are modulated by pharmacologically relevant concentrations of ethanol, with inhibition or stimulation of P2XR subtypes and stimulation of 5-HT3Rs, respectively (Davies et al. 2006).
The strong expression of ATP-gated P2X3 receptors by a subpopulation of sensory neurons indicates the important role of these membrane proteins in nociceptive signaling in health and disease, especially when the latter is accompanied by chronic pain syndromes. These receptors exist mainly as trimeric homomers, and, in part, as heteromers (assembly of two P2X3 subunits with one P2X2). Recent investigations have suggested distinct molecular determinants responsible for agonist binding and channel opening for transmembrane flux of sodium, calcium and potassium ions. Trimeric P2X3 receptors are rapidly activated by ATP and can be strongly desensitized in the continuous presence of the agonist. Endogenous substances, widely thought to be involved in triggering pain, especially in pathological conditions, can potently modulate the expression and function of P2X3 receptors, with differential changes in response amplitude, desensitization and recovery. Strong facilitation of P2X3 receptor function is induced by enodogenous substances like the neuropeptide calcitonin gene-related peptide and the neurotrophins nerve growth factor and brain-derived neurotrophic factor. These substances possess distinct mechanisms of action on P2X3 receptors, generally attributable to discrete phosphorylation of N- or C-terminal P2X3 domains (Fabbretti and Nistri, 2012).
Two structural classes of pore-opening mechanisms have been established: bending of pore-lining helices in the case of tetrameric cation channels, and tilting of such helices in mechanosensitive channels. Expansion of the gate region in the external pore in P2X receptors is accompanied by a narrowing of the inner pore, indicating that pore-forming helices straighten on ATP binding to open the channel (Li et al., 2010). This pore-opening mechanism has implications for the role of subunit interfaces in the gating mechanism and points to a role of the internal pore in ion permeation. Amino terminal residues are involved in lipid, cholesterol and lipid raft regulation of P2X1 (Allsopp et al. 2010).
P2X2 has a voltage-dependent gating property even though it lacks a canonical voltage sensor. It is a trimer in which each subunit has two transmembrane helices and a large extracellular domain. The three inter-subunit ATP binding sites are linked to the pore forming transmembrane (TM) domains by beta-strands. Structural rearrangements of the linker region of the P2X2 receptor channel are induced not only by ligand binding but also by membrane potential change (Keceli and Kubo 2014). Knowledge about P2X receptor activation, especially focusing on the mechanisms underlying ATP-binding, conformational changes in the extracellular domain, and channel gating and desensitization, has been reviewed (Kawate 2017).
Ectodomain shedding of integral membrane receptors results in the release of soluble molecules and modification of the transmembrane regions of these receptors to mediate or modulate extracellular and intracellular signalling. Ectodomain shedding is stimulated by a variety of mechanisms, including the activation of P2 receptors by extracellular nucleotides. P2 receptor-mediated shedding involves P2 receptors, P2X7 (TC# 1.A.7.1.3) and P2Y2 (TC# 9.A.14.13.16), and the sheddases, ADAM10 (Meprin A, 701 aas and 2 TMSs, N- and C-termini; Q16820) and ADAM17 (Disintegrin, 824 aas and 2 TMSs near the N- and C-termini; P78536; see subfamily 2 in TC Family 9.B.87) (Pupovac and Sluyter 2016).
The trimeric ATP-gated ion channel, the P2X receptor, has six TMSs, and three of them, the M2 helices, line the ion conduction pathway. Using molecular dynamics simulation, Li 2018 identified four conformational states of the TM domain that are associated with four types of packing between M2 helices. Packing in the extracellular half of the M2 helix produces closed conformations, while packing in the intracellular half produces both open and closed conformations. State transition is observed and supports a mechanism where iris-like twisting of the M2 helices switches the location of helical packing between the extracellular and intracellular halves of the helices. This twisting motion alters the position and orientation of residue side-chains relative to the pore and thereby influences the pore geometry and possibly ion permeation. Helical packing, on the other hand, may restrict the twisting motion and generate discrete conformational states (Li 2018).
P2X7 receptors are exceptionally versatile: in their canonical role they act as ATP-gated calcium channels and facilitate calcium-signaling cascades, exerting control over the cell via calcium-encoded sensory proteins and transcription factor activation. P2X7 also mediates transmembrane pore formation to regulate cytokine release and facilitate extracellular communication, and when persistently stimulated by high extracellular ATP levels, large P2X7 pores form, which induce apoptotic cell death through cytosolic ion dysregulation. As a scavenger receptor, P2X7 directly facilitates phagocytosis of the cellular debris that arises during neurogenesis (Leeson et al. 2019).
The generalized transport reaction is:
Me+ (out) Me+ (in).
ATP-gated cation channel (purinoceptor or ATP-neuroreceptor). Residues Glu52-Gly96 play roles in agonist binding and channel gating (Allsopp et al., 2011). The rat protein is 89% identical to the human ortholog. Mutations likely to confer ivermectin sensitivity to human P2X1 have been proposed (Pasqualetto et al. 2018).
P2X1 of Homo sapiens
Green algal ATP-gated cation channel receptor P2X4 of 384 aas, 2 TMSs (Fountain et al., 2008).
P2X4 of Ostreococcus lucimarinus
P2X5 ATP-activated receptor, P2X5R or P2RX5, of 422 aas and 2 TMSs, N- and C-terminal (Sun et al. 2019).
P2X5R of Homo sapiens
ATP-gated cation channel (purinoceptor or ATP-neuroreceptor), P2X2. His33 and Ser345 are proximal to each other across an intra-subunit interface, and the relative movement between the two TMSs is likely important for transmitting the action of ATP binding to the opening of the channel (Liang et al. 2013). Two processes contribute to receptor desensitization, one, bath calcium-independent and the other, bath calcium-dependent, the latter being more important (Coddou et al. 2015). ATP dissociation causes reduction in outer pore expansion compared to the ATP-bound state. Moreover, the inner and outer ends of adjacent pore-lining helices come closer during opening, likely through a hinge-bending motion (Habermacher et al. 2016). Hearing loss mutations alter the functional properties of human P2X2 receptor channels through more than one mechanism (George et al. 2019). Residues in TMSs of the P2X4 receptor that contribute to channel function and ethanol sensitivity have been identified (Popova et al. 2020). Self-assembly of mammalian cell membranes on bioelectronic devices with P2X2 channel has been achieved (Liu et al. 2020).
P2X2 of Rattus norvegicus
ATP-gated NaCl-regulated nonselective cation (Na+, K+ and Ca2+) channel, the P2X purinoreceptor 7, P2X7. It expands to accommodate large molecules such as NAD, N-methyl-D-glucamine and triethyl ammonium) (Li et al., 2005; Lu et al., 2007) and plays a role in changing pain thresholds. A region called ADSEG in all P2X receptors is located in the M2 domain which aligns with TMS 5 in VIC K+ channels (1.A.1). ADSEG from P2X(7)R forms cation-selective channels in artificial lipid bilayers and biological membranes similar to those of the full length protein (de Souza et al., 2011). Channel activity is regulated by calmodulin (Roger et al., 2008). P2XRs allow direct permeation of nanometer-sized dyes (Browne et al. 2013). Macrophage P2X7 receptors are modulated in response to infection with Leishmania amazonensis so that they become more permeable to anions and less permeable to cations (Marques-da-Silva et al. 2011). Residues involved in pore conductivity and agonist sensitivity have been identified (Jindrichova et al. 2015) as have residues involved in channel activation (Caseley et al. 2016). The channel opening extends from the pre-TMS2 region through the outer half of the trihelical TMS2 channel; the gate and the selectivity filter have been identified (Pippel et al. 2017). The purinergic receptors, P2RX4 and P2RX7, when mutated, affect susceptibility to multiple sclerosis (MS) (Sadovnick et al. 2017). P2X7 may serve as a receptor for the regulation of annexin secretion during macrophage polarization (de Torre-Minguela et al. 2016). These receptors can reduce salivary gland inflammation (Khalafalla et al. 2017). The P2X7 receptor forms ion channels dependent on lipids but independently of its cytoplasmic domain (Karasawa et al. 2017). A truncated naturally occurring variant of P2X7, P2X7-j of 258 aas, lacks the entire intracellular carboxyl terminus, the second TMS, and the distal third of the extracellular loops of the full-length P2X7 receptor. P2X7-j, expressed in the plasma membrane, failed to form pores and mediate apoptosis (Feng et al. 2006). P2X7-j formed heterooligomers with and blocked P2X7-mediated channel formation. Alternative splicing of P2X7 controls gating of the ion channel by ADP-ribosylation (Schwarz et al. 2012). Three distinct roles for P2X7 during adult neurogenesis have been demonstrated, and these depend on the extracellular ATP concentrations: (i) P2X7 receptors can form transmembrane pores leading to cell death, (ii) P2X7 receptors can regulate rates of proliferation, likely via calcium signalling, and (iii) P2X7 can function as scavenger receptors in the absence of ATP, allowing neural progenitor cells (NPCs) to phagocytose apoptotic NPCs during neurogenesis (Leeson et al. 2018). P2X7 also plays a role in purinergic vasotoxicity and cell death (Shibata et al. 2018). NAD+ covalently modifies the P2X7R of mouse T lymphocytes, thus lowering the ATP threshold for activation. Other structurally unrelated agents have been reported to activate P2X7R: (a) the antibiotic polymyxin B, possibly a positive allosteric P2X7R modulator, (b) the bactericidal peptide LL-37, (c) the amyloidogenic β peptide, and (d) serum amyloid A (Di Virgilio et al. 2018). Some agents, such as Alu-RNA, have been suggested to activate P2X7R, acting on the intracellular N- or C-terminal domains. P2X7R of enteric neurons may be involved in diabetes-induced nitrous oxide (NOS) neuron damage via combining with pannexin-1 to form transmembrane pores which transport macromolecular substances and calcium into the cells (Zhang et al. 2019). ATP-gated P2X7 receptors require chloride channels to promote inflammation in human macrophages (Janks et al. 2019). P2X7 overexpression is can be associated with cancer progression. P2X7 plays also an important role in glioma biology (Matyśniak et al. 2020).
P2X7 of Homo sapiens (Q99572)
The P2X4 receptor (P2X4R) of the zebrafish of 389 aas and 2 TMSs. The 3-d structure is known in its closed, resting state (Kawate et al., 2009). A hift of L340 packing between different sites may alter the side-chain orientation that frees or occludes the pore. L340, A344 and A347 may also gate the pore by a expansion-contraction mechanism (Li 2015). Ivermectin binds to the transmembrane domain while Zn2+ binds to the extracellular domain, but they exhbit additive cooperativity (Latapiat et al. 2017).
P2X(4) purinoceptor (ATP) gated ionotropic receptor, subunit 4 of Danio rerio (Q98TZ0)
The purinergic receptor, P2X4, is sensitive to the macrocyclic lactone, ivermectin, which allosterically modulates both ion conduction and channel gating (Samways et al., 2012). The secondary structure and gating rearrangements of TMSs in rat P2X4 receptor channels have been proposed (Silberberg et al. 2005). Bile acids inhibit the human P2X4 (Ilyaskin et al. 2019). The gating mechanism has been discussed (Du et al., 2012) and considered to be determined by the conformation of the transmembrane domain (Minato et al. 2016; Pierdominici-Sottile et al. 2016). The crystal structure of the ATP-gated P2X4 ion channel in the closed state has been reported (Kawate et al., 2009). Unobstructed lateral portals are preferentially used as access routes to the pores of P2X receptors (Samways et al., 2011). Activation is ATP-dependent and rapid, but desensitization occurs within seconds and is ATP-independent (Stojilkovic et al. 2010). Ectodomain cysteines play roles in agonist binding and channel gating (Rokic et al. 2010). Evermectin has distinct effects on opening and dilation of the channel pore, the first accounting for increased peak current amplitude, and the latter correlating with changes in the kinetics of receptor deactivation (Zemkova et al. 2014). Conserved amino acids within the regions linking the ectodomain with the pore-forming transmembrane domain may contribute to signal transduction and channel gating (Gao et al. 2015; Jelínkova et al. 2008). Binding of ATP produces distortions in the chains that eliminate restrictions on the interchain displacements, leading to the opening of the pore (Pierdominici-Sottile et al. 2016). The purinergic receptors, P2RX4 and P2RX7, affect susceptibility to multiple sclerosis (MS) (Sadovnick et al. 2017).
P2X4 of Homo sapiens (Q99571)
ATP-gated P2X3 receptor. Tyr-37 stabilizes desensitized states and restricts calcium permeability (Jindrichova et al., 2011). Exhibits "high affinity desensitization" but slow reactivation from the desensitized state (Giniatullin and Nistri 2013). An endogenous regulator of P2X3 in bladder is the Pirt protein (TC#8.A.64.1.1) Gao et al. 2015). X-ray crystal structures of the human P2X3 receptor in apo/resting, agonist-bound/open-pore, agonist-bound/closed-pore/desensitized and antagonist-bound/closed states have been determined (Mansoor et al. 2016). The open state structure harbours an intracellular motif termed the 'cytoplasmic cap', which stabilizes the open state of the ion channel pore and creates lateral, phospholipid-lined cytoplasmic fenestrations for water and ion egress.
P2X3 receptor of Homo sapiens (P56373)
P2X purinoceptor of Tetaodon nigroviridis
The p2X purinoreceptor 4a of 389 aas and 2 TMSs, P2X4a of 388 aas and 2 TMSs. A splice variant of 361 aas also exists and may form heterotrimers with P2RX4a (Townsend-Nicholson et al. 1999). Plays a role in alcoholism (Franklin et al. 2014). P2RX4 deficiency alleviates allergen-induced airway inflamation (Zech et al. 2016).
P2X4a of Mus musculus (Mouse)
Purinorepector, P2X7 (P2RX7) of 595 aas and 2 TMSs. The crystal structure in complex with a series of allosteric antagonists were published, giving insight into the mechanism of channel antagonism (Pasqualetto et al. 2018). A P2RX7 single nucleotide polymorphism haplotype promotes exon 7 and 8 skipping and disrupts receptor function (Skarratt et al. 2020).
P2X7 of Ailuropoda melanoleuca (Giant panda)
The osmoregulatory intracellular P2X receptor, P2XA gated by ATP (present in the osmoreulatory organelle, the contractile vacuole) (Fountain et al., 2007). One of five P2X receptors in D. discoideum is localized to the contractile vacuole with the ligand binding domain facing the lumen. Plays a role in Ca2+ signaling, but also is Cl- permeable. May function in osmoregulation (Ludlow et al., 2009). Four of the five receptors operate as ATP-gated channels (P2XA, P2XB, P2XD, and P2XE). For the P2XA receptor, ATP was the only effective agonist, but extracellular sodium, compared with potassium, strongly inhibited ATP responses in P2XB, P2XD, and P2XE receptors. Increasing the proton concentration (pH 6.2) accelerated desensitization at P2XA receptors and decreased currents at P2XD receptors, but increased the currents at P2XB and P2XE receptors. Dictyostelium lacking P2XA receptors showed an impaired regulatory volume decrease in hypotonic solution. This phenotype was rescued by overexpression of P2XA and P2XD receptors, partially rescued by P2XB and P2XE receptors, and not rescued by P2XC receptor which appeared to be inactive (Baines et al. 2013).
P2XA of Dictyostelium discoideum (Q55A88)
Partial seqence of a putative P2XR of 273 aas and 1 TMS at residue 150 in the protein.
Putative P2XR of an archaeon (phyllosphere metagenome)
Uncharacterized P2X recpetor of 399 aas and 2 TMSs/
UP of Guillardia theta
Uncharacterized P2X receptor of 524 aas and 2 TMSs.
UP of Emiliania huxleyi (Pontosphaera huxleyi)
Uncharacterized protein of 488 aas and 2 TMSs.
UP of Vitrella brassicaformis
P2X receptor E isoform X1 of 397 aas and 2 TMSs, N- and C-terminal.
P2XR of Nematostella vectensis
P2X receptor of 373 aas and 2 TMSs, N- and C-terminal.
P2XR of Planoprotostelium fungivorum
Uncharacterized P2X receptor of 458 aas and 2 TMSs, N- and C-terminal.
UP of Catenaria anguillulae
Uncharacterized protein of 396 aas and 2 TMSs, N- and C-terminal.
UP of Rhizophagus diaphanus
P2X receptor E of 1271 aas and 4 TMSs roughly equidistant from each other, at positions 311, 627, 918, and at the C-terminus. The region showing sequence similarity with other members of the P2XR family is residues 300 to 640, including TMSs 1 and 2 of the 3 distinct TMSs.
P2XR E of Symbiodinium microadriaticum
Uncharacterized protein of 653 aas and 1 centrally located TMS. This protein may be a fragment, but shows appreciable sequence identity with members of the P2X family.
UP of an archaeon (phyllosphere metagenome)