TCDB is operated by the Saier Lab Bioinformatics Group
TCIDNameDomainKingdom/PhylumProtein(s)
1.A.5.1.1









Polycystin 1 (PKD1 or PC1) assembles with TRPP2 (Q86VP3) in a stoichiometry of 3TRPP2: 1PKD1, forming the receptor/ion channel complex (Yu et al., 2009). The C-terminal coiled-coil complex is critical for proper assembly (Zhu et al., 2011).  Missense mutations have been identified that affect membrane topogenesis (Nims et al. 2011). Biomarkers for polycystic kidney diseases have been identified (Hogan et al. 2015).  Extracellular divalent ions, including Ca2+, inhibit permeation of monovalent ions by directly blocking the TRPP2 channel pore. D643, a negatively charged amino acid in the pore, is crucial for channel permeability (Arif Pavel et al. 2016). Polycystin (TRPP/PKD) complexes, made of transient receptor potential channel polycystin (TRPP)4 and polycystic kidney disease (PKD) proteins, play key roles in coupling extracellular stimuli with intracellular Ca2+ signals. PKD1 and PKD2 form a complex, the structure of which has been solved in 3-dimensions at high resolution.  The complex consists of PKD1:PKD2 = 3:1. PKD1 consists of a voltage-gated ion channel fold that interacts with PKD2 to complete a domain-swapped TRP architecture with unique features (Su et al. 2018; Su et al. 2018). The C-terminal tail of PKD1 may play a role in the prognosis of renal disease (Higashihara et al. 2018). TRPP2 uses 2 gating charges found in its fourth TMS (S4) to control its conductive state (Ng et al. 2019). Rosetta structural predictions demonstrated that the S4 undergoes approximately 3- to 5-Å transitional and lateral movements during depolarization coupled to opening of the channel pore. Both gating charges form state-dependent cation-pi interactions within the voltage sensor domain (VSD) during membrane depolarization. The transfer of a single gating charge per channel subunit is required for voltage, temperature, and osmotic swell polymodal gating. Thus, TRPP2 channel opening is dependent on activation of its VSDs (Ng et al. 2019).  Polycystin-1 assembles with Kv channels to govern cardiomyocyte repolarization and contractility (Altamirano et al. 2019). Three-dimensional in vitro models answer questions about ADPKD cystogenesis (Dixon and Woodward 2018). The polycystin-1 subunit directly contributes to the channel pore, and its eleven TMSs are sufficient for its channel function (Wang et al. 2019).  Polycystin-1 inhibits cell proliferation through phosphatase PP2A/B56alpha (Tang et al. 2019). Polycystin-1 regulates cardiomyocyte mitophagy (Ramírez-Sagredo et al. 2021). Maser and Calvet 2020 reviewed structural and functional features shared by polycystin-1 and the adhesion GPCRs (TC# 9.A.14.6.2) and discussed the implications of such similarities for our understanding of the functions of these proteins. Mutations in PKD1 and PKD2 cause autosomal dominant polycystic kidney disease (ADPKD). Polycystins are expressed in the primary cilium, and disrupting cilia structure slows ADPKD progression following inactivation of polycystins. Dysregulation of cyclin-dependent kinase 1 (Cdk1) is an early driver of cyst cell proliferation in ADPKD due to Pkd1 inactivation (Zhang et al. 2021). Genetic removal of c-Jun N-terminal kinases, Jnk1 and Jnk2, suppresses the nuclear accumulation of phospho c-Jun, reduces proliferation and reduces the severity of cystic disease. While Jnk1 and Jnk2 are thought to have largely overlapping functions, Jnk1 loss is nearly as effective as the double loss of Jnk1 and Jnk2 (Smith et al. 2021). Polycystic kidney disease (PKD), comprising autosomal dominant polycystic kidney disease (ADPKD) and autosomal recessive polycystic kidney disease (ARPKD), is characterized by incessant cyst formation in the kidney and liver. ADPKD and ARPKD represent the leading genetic causes of renal disease in adults and children, respectively. ADPKD is caused by mutations in PKD1 encoding polycystin1 (PC1) and PKD2 encoding polycystin 2 (PC2). PC1/2 are multi-pass transmembrane proteins that form a complex localized in the primary cilium. Predominant ARPKD cases are caused by mutations in polycystic kidney (Ma 2021). The mechanism of tethered agonist-mediated signaling by polycystin-1 has been investigated (Pawnikar et al. 2022). PC1 is an 11 TMS protein encoded by the PKD1 gene. It has a complex posttranslational maturation process, with over five proteolytic cleavages, and is found at multiple cellular locations. The initial description of the binding and activation of heterotrimeric Galphai/o by the juxtamembrane region of the PC1 cytosolic C-terminal tail (C-tail) opened the door tothe possibility of potential functions as a novel G protein-coupled receptor (GPCR). Subsequent  assays supported an ability of the PC1 C-tail to bind numerous members of the Galpha protein family and to either inhibit or activate G protein-dependent pathways involved in the regulation of ion channel activity, transcription factor activation, and apoptosis. PC1-mediated G protein regulation prevents kidney cyst development. Similarities between PC1 and the adhesion class of 7-TMS GPCRs, most notably a conserved GPCR proteolysis site (GPS) before the first TM domain, which undergoes autocatalyzed proteolytic cleavage, suggest potential mechanisms for PC1-mediated regulation of G protein signaling.  reviewed the evidence supporting GPCR-like functions of PC1 and their relevance to cystic disease, discusses the involvement of GPS cleavage and potential ligands in regulating PC1 GPCR function, and explores potential connections between PC1 GPCR-like activity and regulation of the channel properties of the polycystin receptor-channel complex (Maser et al. 2022). Drug targets and repurposing candidates may effectively treat pre-cystic as well as cystic ADPKD (Wilk et al. 2023).

Eukaryota
Metazoa
Polycystin 1 of Homo sapiens
1.A.5.1.2









Polycystic kidney disease protein 1-like 3 (PC1-like 3 protein or PKD1L3) (Polycystin-1L3).  May particpate in formation of the TRP sour taste receptor (see 1.A.5.2.2) (Ishimaru et al. 2010). Mediates Ca2+ influx-operated Ca2+ entry that generates pronounced Ca2+ spikes. Triggered by rapid onset/offset of Ca2+, voltage, or acid stimuli, Ca2+-dependent activation amplifies a small Ca2+ influx via the channel which concurrently drives self-limiting negative feedback inactivation that is regulated by the Ca2+-binding EF hands of its partner protein, PKD2-L1 (Hu et al. 2015). Polycystin-1 inhibits eIF2alpha phosphorylation and cell apoptosis through a PKR-eIF2alpha pathway (Tang et al. 2017).

Eukaryota
Metazoa
PKD1L3 of Homo sapiens
1.A.5.1.3









Heteromeric polycystic kidney disease proteins 1 and 2-like 1 (PKD1L1/PKD2L1/PC2) cation (calcium) channel of kidney primary cilia (DeCaen et al. 2013).  PKD2L1 is probably orthologous to mouse TC# 1.A.5.2.2. The voltage dependence of PKD2L1 may reflect the charge state of the S4 domain (Numata et al. 2017). PKD2L1, (TRPP3) is involved in the sour sensation and other pH-dependent processes and is a nonselective cation channel that can be regulated by voltage, protons, and calcium. The 3-d structure has been determined by cryoEM at 3.4 Å resolution (Su et al. 2018). Unlike its ortholog PKD2, the pore helix and TMS6, which are involved in upper and lower-gate opening, adopt an open conformation. The pore domain dilation is coupled to conformational changes of voltage-sensing domains via a series of pi-pi interactions, suggesting a potential PKD2L1 gating mechanism (Su et al. 2018). Autosomal dominant polycystic kidney disease is caused by mutations in PKD1 or PKD2 genes; the latter encodes polycystin-2 (PC2, also known as TRPP2), a member of the transient receptor potential (TRP) ion channel family. Despite most pathogenic mutations in PKD2 being truncation variants, there are many point mutations, which cause small changes in protein sequences but dramatic changes in the in vivo function of PC2. Conformational consequences of these mutations based on the cryo-EM structures of PC2 provide insight into the structure and function of PC2 and the molecular mechanism of pathogenesis caused by these mutations (Wang et al. 2023).

 

Eukaryota
Metazoa
PKD1L1/PKD2L1 of Homo sapiens
1.A.5.1.4









One of 10 receptors for the egg jelly ligands (REJ, REJ1 or PKD-REJ1) inducing the acrosome reaction in sea urchin eggs. Could be a regulator of sperm ion channels (Gunaratne et al. 2007).

Eukaryota
Metazoa
REJ of Strongylocentrotus purpuratus (Purple sea urchin)
1.A.5.1.5









PKD-REJ4 of 2829 aas and 2 TMSs, one N-terminal and one C-terminal (Gunaratne et al. 2007). Shows homology with hydrophilic domains in human PKDs.

Eukaryota
Metazoa
REJ4 of Strongylocentrotus purpuratus (Purple sea urchin)
1.A.5.1.6









PKD-REJ3 of 2681 aas (Gunaratne et al. 2007). Polycystin-2 (TC# 1.A.5.2.3) associates with the polycystin-1 homolog, suREJ3, and localizes to the acrosomal region of sea urchin spermatozoa (Neill et al. 2004).

Eukaryota
Metazoa
REJ3 of Strongylocentrotus purpuratus (Purple sea urchin)
1.A.5.1.8









Polycystin-1L2 G-protein receptor of 2459 aas and about 18 TMSs in a 1 (N-terminal) + 6-8 + 3 + 7 ( C-terminal) TMS arrangement.  It probably functions as an ion-channel regulator as well as a G-protein-coupled receptor (Yuasa et al. 2004).

Eukaryota
Metazoa
Polycystin-1L2 of Homo sapiens
1.A.5.2.1









Polycystin 2 (PKD2, PC2 or TRPP2) of 968 aas and 8 or 9 TMSs (Anyatonwu and Ehrlich, 2005). It is regulated by α-actinin (AAC17470) by direct binding, influencing its channel activity (Li et al., 2007), and is also regulated also by diaphanous-related formin 1 (mDia1) (Bai et al., 2008). It has 8 TMSs with 6 TMSs in the channel domain with N- and C- termini inside (Hoffmeister et al., 2010).  PC2 interacts with the inositol 1,4,5-trisphosphate receptor (IP(3)R) to modulate Ca2+ signaling (Li et al. 2009). The PKD2 voltage-sensor domain retains two of four gating charges commonly found in voltage-gated ion channels. The PKD2 ion permeation pathway is constricted at the selectivity filter near the cytoplasmic end of S6, suggesting that two gates regulate ion conduction (Shen et al. 2016). 15% of cases of polycystic kidney disease result from mutations in the gene encoding this protein, while 85% are in PKD1 (Ghata and Cowley 2017). Topological changes between the closed and open sub-conductance states of the functional channel are observed with an inverse correlation between conductance and height of the channel. Intrinsic PC2 mechanosensitivity in response to external forces was also observed (Lal et al. 2018). PC2 is present in ciliary membranes of the kidney and shares a transmembrane fold with other TRP channels as well as an extracellular domain found in TRPP and TRPML channels. Wang et al. 2019 characterized the phosphatidylinositol biphosphate (PIP2) and cholesterol interactions with PC2. PC2 has  a PIP binding site close to the equivalent vanilloid/lipid binding site in the TRPV1 channel and a binding site for cholesterol. The two classes of lipid binding sites were compared with sites observed in other TRPs and in Kv channels, suggesting that PC2, in common with other ion channels, may be modulated by both PIPs and cholesterol (Wang et al. 2019). Genetic removal of c-Jun N-terminal kinases, Jnk1 and Jnk2, suppresses the nuclear accumulation of phospho c-Jun, reduces proliferation and reduces the severity of cystic disease. While Jnk1 and Jnk2 are thought to have largely overlapping functions, Jnk1 loss is nearly as effective as the double loss of Jnk1 and Jnk2 (Smith et al. 2021). Polycystin-2 (TRPP2): ion channel properties and regulation have been described (Del Rocío Cantero and Cantiello 2022). Regulation of the PKD2 channel by TACAN (TC# 1.A.119.1.2) has been described (Liu et al. 2022). The mouse ortholog is 90% identical to the human protein.

Eukaryota
Opisthokonta
Polycystin 2 of Homo sapiens (Q13563)
1.A.5.2.2









Polycystic kidney disease Z-like protein, TrpP3 or PKD2L1 (50% identical to Polycystin 2 (1.A.5.2.1); regulated by α-actinin (AAC17470) by direct binding; Li et al, 2007). May form a heterodimeric complex with PKD1L3 (1.A.5.1.2) to form the TRP sour taste channel receptor (Ishimaru et al., 2006; Ishimaru et al. 2010).  Polycystic kidney disease (PKD) protein 2 Like 1 (PKD2L1) is also called transient receptor potential polycystin-3 (TRPP3).  It regulates Ca2+-dependent hedgehog signalling in primary cilia, intestinal development and sour taste. Two intra-membrane residues, aspartic acid 349 (D349) and glutamic acid 356 (E356) in the third TMS are critical for PKD2L1 channel function which may itself sense acids (Hussein et al. 2015). Extracellular loops are involved in assemby of the complex (Salehi-Najafabadi et al. 2017). It Component of a heteromeric calcium-permeable ion channel formed by PKD1 and PKD2 that is activated by interaction between PKD1 and a Wnt family member, such as WNT3A and WNT9B. Can also form a functional, homotetrameric ion channel (PubMed:27214281). It functions as a cation channel involved in fluid-flow mechanosensation by the primary cilium in the renal epithelium (Nauli et al. 2003). It functions as outward-rectifying K+ channel, but is also permeable to Ca2+, and to a much lesser degree, to Na+ (Kleene and Kleene 2017). It
may contribute to the release of Ca2+ stores from the endoplasmic reticulum. Together with TRPV4, it forms mechano- and thermosensitive channels in cilia (Köttgen et al. 2008). The
PKD1 channel protein.  It is involved in left-right axis specification via its role in sensing nodal flow; forms a complex with PKD1L1 in cilia to facilitate flow detection in left-right patterning (Yoshiba et al. 2012 ; Katoh et al. 2023). Detection of asymmetric nodal flow gives rise to a Ca2+ signal that is required for normal, asymmetric expression of genes involved in the specification of body left-right laterality (Yoshiba et al. 2012).

Eukaryota
Metazoa
TrpP3 of Mus musculus (Q14B55)
1.A.5.2.3









Polycystin-2, PKD2 or PKD-REJ2 of 907 aas and 8 TMSs (Gunaratne et al. 2007). Polycystin-2 associates with the polycystin-1 homolog, suREJ3 (TC# 1.A.5.1.6), and localizes to the acrosomal region of sea urchin spermatozoa (Neill et al. 2004).

Eukaryota
Metazoa
REJ2 of Strongylocentrotus purpuratus (Purple sea urchin)
1.A.5.2.4









Polycystin-2 (CePc2) (Polycystic kidney disease 2 protein homologue)

Eukaryota
Metazoa
Pkd-2 of Caenorhabditis elegans
1.A.5.3.1









The lysosomal monovalent cation/Ca2+ channel, TRP-ML1 (Mucolipin-1) (associated with the human lipid storage disorder, mucolipidosis type IV (MLIV)) (Kiselyov et al., 2005; Luzio et al., 2007). TRPML1 is an endolysosomal iron release channel (Dong et al., 2008).  It interacts with TMEM163, a CDF heavy metal transporter (TC# 2.A.4.8.3).  Together these proteins function in Zn2+ homeostasis, possibly by exporting Zn2+ (Cuajungco et al. 2014).  The MLIV disease could result from Zn2+ overload.  TrpML1 is probably involved in Zn2+ uptake into lysosomes (Cuajungco and Kiselyov 2017). Asp residues within the luminal pore may control calcium/pH regulation. A synthetic agonist, ML-SA1, can bind to the pore region to force a direct dilation of the lower gate (Schmiege et al. 2018). This channel plays a role in vesicle contraction following phagocytosis or pinocytosis, allowing maintenance of cell volume (Freeman et al. 2020). A mutation gave rise to progressive psychomotor delay, and atrophy of the corpus callosum and cerebellum was observed on brain magnetic resonance images (Hayashi et al. 2020).

Eukaryota
Metazoa
TRP-ML1 (Mucolipin-1) of Homo sapiens (Q9GZU1)
1.A.5.3.2









The TRP-ML3 or TRPML3 or Mcoln3 (Mucolipin-3) inward rectifying cation channel; associated with the mouse Viartini-Waddler phenotype when mutant (A419P) (Kim et al., 2007; Cuajungco and Samie 2008). H+-regulated Ca2+ channel that shuttles between intracellular vesicular compartments and the plasma membrane (Kim et al., 2010).

Eukaryota
Metazoa
Trp-ML3 of Mus musculus
(Q8R4F0)
1.A.5.3.3









Mucolipin-2 (TRPML2) non-selective plasma membrane cation channel (Ca2+ permeable). Shows inward rectification like TRPML1 and TRPML3 (Lev et al., 2010). Induces cell degeneration. Causes embryonic lethality, pigmentation defects and deafness, and regulates the acidification of early endosomes (Noben-Trauth, 2011). Found in the plasma membrane and early- and late-endosomes as well as lysosomes.  Activated by a transient reduction of extracellular sodium followed by sodium replenishment, by small chemicals related to sulfonamides, and by PI(3,5)P2, a rare phosphoinositide that naturally accumulates in the membranes of endosomes and lysosomes, and thus could act as a physiologically relevant agonist (García-Añoveros and Wiwatpanit 2014).  TRPML2 can form heteromultimers with TRPML1 and TRPML3; in B-lymphocytes, TRPML2 and TRPML1 may play redundant roles.  TRPML2 may play a role in immune cell development and inflammatory responses (Cuajungco et al. 2015). The TRPML family hallmark is a large extracytosolic/lumenal domain (ELD) between TMSs S1 and S2. Viet et al. 2019 presented crystal structures of the tetrameric human TRPML2 ELD. The structures reveal structural responses to the conditions the TRPML2 ELD encounters as the channel traffics through the endolysosomal system.

Eukaryota
Metazoa
TRPML2 of Homo sapiens (Q8IZK6)
1.A.5.3.4









Mucolipin-3 (Mcoln3, TRPML3). Orthologue of 1.A.5.3.2.  Asp residues within the luminal pores of all mucolipins may function to control calcium/pH regulation. A synthetic agonist, ML-SA1, can bind to the pore region of TRPMLs to force a direct dilation of the lower gate. These proteins have multiple ligand binding sites (Schmiege et al. 2018).

Eukaryota
Metazoa
TRPML3 of Homo sapiens
1.A.5.3.5









Mucolipin of 496 aas and 7 TMSs in a 1 + 6 TMS arrangement.  There is a ~200 aa loop between TMSs 1 and 2, and TMS 1 may be a leader sequence.

Eukaryota
Kinetoplastida
Mucolipin of Trypanosoma grayi
1.A.5.3.6









Uncharacterized protein of 1844 aas and 5 - 6 TMSs. 

Eukaryota
Kinetoplastida
UP of Leishmania major
1.A.5.3.7









Mucolipin-1 or CUP-5 of 611 aas and 6 TMSs in a 1 + 5 TMS arrangement. This C. elegans ortholog of the human protein is required for lysosome biogenesis. Mutations in cup-5 result in the accumulation of large vacuoles in several cells, in increased cell death, and in embryonic lethality (Treusch et al. 2004).

Eukaryota
Opisthokonta; metazoans
CUP-5 of Caenorhabditis elegans
1.A.5.4.1









The algal PDK2 cation channel in Chlamydomonas reinhardii, involved in coupling flagellar adhesion at the beginning of mating to the increase in flagellar calcium required for subsequent steps in mating (Huang et al., 2007). (Residues 1278-1346 (the PKD domain) are 25% identical, 54% similar to residues 107-176 in CcaA (TC# 1.A.1.14.2))
Eukaryota
Viridiplantae
PDK2 of Chlamydomonas reinhardii (A9LE42)