PKD2_ORYLA
ID PKD2_ORYLA Reviewed; 901 AA.
AC H2LRU7; B6EX24; E7FKV9;
DT 19-FEB-2014, integrated into UniProtKB/Swiss-Prot.
DT 19-FEB-2014, sequence version 2.
DT 03-AUG-2022, entry version 48.
DE RecName: Full=Polycystin-2;
DE AltName: Full=Polycystic kidney disease 2 protein homolog;
GN Name=pkd2;
OS Oryzias latipes (Japanese rice fish) (Japanese killifish).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Actinopterygii; Neopterygii; Teleostei; Neoteleostei; Acanthomorphata;
OC Ovalentaria; Atherinomorphae; Beloniformes; Adrianichthyidae; Oryziinae;
OC Oryzias.
OX NCBI_TaxID=8090;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
RC STRAIN=Orange-red;
RX PubMed=15954893; DOI=10.1111/j.1523-1755.2005.00378.x;
RA Mochizuki E., Fukuta K., Tada T., Harada T., Watanabe N., Matsuo S.,
RA Hashimoto H., Ozato K., Wakamatsu Y.;
RT "Fish mesonephric model of polycystic kidney disease in medaka (Oryzias
RT latipes) pc mutant.";
RL Kidney Int. 68:23-34(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), FUNCTION, SUBCELLULAR LOCATION,
RP INTERACTION WITH PKD1L1, DISRUPTION PHENOTYPE, AND TISSUE SPECIFICITY.
RX PubMed=21307098; DOI=10.1242/dev.058271;
RA Kamura K., Kobayashi D., Uehara Y., Koshida S., Iijima N., Kudo A.,
RA Yokoyama T., Takeda H.;
RT "Pkd1l1 complexes with Pkd2 on motile cilia and functions to establish the
RT left-right axis.";
RL Development 138:1121-1129(2011).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Hd-rR;
RX PubMed=17554307; DOI=10.1038/nature05846;
RA Kasahara M., Naruse K., Sasaki S., Nakatani Y., Qu W., Ahsan B., Yamada T.,
RA Nagayasu Y., Doi K., Kasai Y., Jindo T., Kobayashi D., Shimada A.,
RA Toyoda A., Kuroki Y., Fujiyama A., Sasaki T., Shimizu A., Asakawa S.,
RA Shimizu N., Hashimoto S., Yang J., Lee Y., Matsushima K., Sugano S.,
RA Sakaizumi M., Narita T., Ohishi K., Haga S., Ohta F., Nomoto H., Nogata K.,
RA Morishita T., Endo T., Shin-I T., Takeda H., Morishita S., Kohara Y.;
RT "The medaka draft genome and insights into vertebrate genome evolution.";
RL Nature 447:714-719(2007).
CC -!- FUNCTION: Component of a heteromeric calcium-permeable ion channel
CC formed by PKD1 and PKD2 that is activated by interaction between PKD1
CC and a Wnt family member, such as WNT3A and WNT9B. Can also form a
CC functional, homotetrameric ion channel (By similarity). Functions as
CC non-selective, voltage-gated cation channel. Required for normal
CC oscillation of Ca(2+) levels within cilia; these oscillations of the
CC intraciliary Ca(2+) levels can trigger cytoplasmic Ca(2+) signaling
CC cascades (By similarity). May contribute to the release of Ca(2+)
CC stores from the endoplasmic reticulum (By similarity). Plays a role in
CC fluid-flow mechanosensation: forms a complex with pkd1l1 in cilia to
CC facilitate flow detection in left/right patterning (PubMed:21307098).
CC Required for normal specification of the body left-right axis during
CC embryogenesis (PubMed:21307098). {ECO:0000250|UniProtKB:O35245,
CC ECO:0000250|UniProtKB:Q13563, ECO:0000250|UniProtKB:Q6IVV8,
CC ECO:0000269|PubMed:21307098}.
CC -!- ACTIVITY REGULATION: Channel activity is regulated by phosphorylation.
CC Channel activity is regulated by intracellular Ca(2+).
CC {ECO:0000250|UniProtKB:Q13563}.
CC -!- SUBUNIT: Homotetramer (By similarity). Heterotetramer with pkd1, giving
CC rise to a complex formed by one pkd1 chain and three pkd2 chains (By
CC similarity). Interacts with pkd1l1. {ECO:0000250|UniProtKB:Q13563,
CC ECO:0000269|PubMed:21307098}.
CC -!- SUBCELLULAR LOCATION: Cell projection, cilium membrane
CC {ECO:0000269|PubMed:21307098}; Multi-pass membrane protein
CC {ECO:0000269|PubMed:21307098}. Endoplasmic reticulum membrane
CC {ECO:0000250|UniProtKB:Q13563}; Multi-pass membrane protein
CC {ECO:0000250|UniProtKB:Q13563}. Cell membrane
CC {ECO:0000250|UniProtKB:Q13563}; Multi-pass membrane protein
CC {ECO:0000250|UniProtKB:Q13563}. Basolateral cell membrane
CC {ECO:0000250|UniProtKB:Q13563}. Cytoplasmic vesicle membrane
CC {ECO:0000250|UniProtKB:Q13563}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=H2LRU7-1; Sequence=Displayed;
CC Name=2;
CC IsoId=H2LRU7-2; Sequence=VSP_053721;
CC -!- TISSUE SPECIFICITY: Ubiquitously expressed. Expressed in Kupffer's
CC vesicle, an organ equivalent to the node.
CC {ECO:0000269|PubMed:21307098}.
CC -!- DOMAIN: The C-terminal coiled-coil domain is involved in
CC oligomerization. The coiled-coil domain binds calcium and undergoes a
CC calcium-induced conformation change (in vitro).
CC {ECO:0000250|UniProtKB:Q13563}.
CC -!- PTM: Phosphorylated. Phosphorylation is important for protein function;
CC a mutant human construct that lacks the N-terminal phosphorylation
CC sites cannot complement a zebrafish pkd2-deficient mutant.
CC {ECO:0000250|UniProtKB:Q13563}.
CC -!- PTM: N-glycosylated. The four subunits in a tetramer probably differ in
CC the extent of glycosylation; simultaneous glycosylation of all
CC experimentally validated sites would probably create steric hindrance.
CC {ECO:0000250|UniProtKB:Q13563}.
CC -!- DISRUPTION PHENOTYPE: Defects in left-right axis patterning.
CC {ECO:0000269|PubMed:21307098}.
CC -!- SIMILARITY: Belongs to the polycystin family. {ECO:0000305}.
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DR EMBL; AB365080; BAG75153.1; -; mRNA.
DR EMBL; AB573427; BAJ65630.1; -; mRNA.
DR RefSeq; NP_001129990.1; NM_001136518.1.
DR AlphaFoldDB; H2LRU7; -.
DR SMR; H2LRU7; -.
DR STRING; 8090.ENSORLP00000008801; -.
DR GeneID; 100192346; -.
DR KEGG; ola:100192346; -.
DR CTD; 5311; -.
DR eggNOG; KOG3599; Eukaryota.
DR InParanoid; H2LRU7; -.
DR OrthoDB; 426073at2759; -.
DR TreeFam; TF316484; -.
DR Proteomes; UP000001038; Unplaced.
DR Proteomes; UP000265180; Chromosome 9.
DR Proteomes; UP000265200; Chromosome 9.
DR GO; GO:0016323; C:basolateral plasma membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0034703; C:cation channel complex; ISS:UniProtKB.
DR GO; GO:0060170; C:ciliary membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0005929; C:cilium; IDA:UniProtKB.
DR GO; GO:0030659; C:cytoplasmic vesicle membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0005789; C:endoplasmic reticulum membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0005887; C:integral component of plasma membrane; ISS:UniProtKB.
DR GO; GO:0016020; C:membrane; IBA:GO_Central.
DR GO; GO:0005262; F:calcium channel activity; ISS:UniProtKB.
DR GO; GO:0005509; F:calcium ion binding; IBA:GO_Central.
DR GO; GO:0005261; F:cation channel activity; ISS:UniProtKB.
DR GO; GO:0051371; F:muscle alpha-actinin binding; IBA:GO_Central.
DR GO; GO:0015271; F:outward rectifier potassium channel activity; ISS:UniProtKB.
DR GO; GO:0005267; F:potassium channel activity; IBA:GO_Central.
DR GO; GO:0005102; F:signaling receptor binding; IBA:GO_Central.
DR GO; GO:0005245; F:voltage-gated calcium channel activity; IBA:GO_Central.
DR GO; GO:0005248; F:voltage-gated sodium channel activity; IBA:GO_Central.
DR GO; GO:0070588; P:calcium ion transmembrane transport; ISS:UniProtKB.
DR GO; GO:0198738; P:cell-cell signaling by wnt; ISS:UniProtKB.
DR GO; GO:0071277; P:cellular response to calcium ion; ISS:UniProtKB.
DR GO; GO:0050982; P:detection of mechanical stimulus; IMP:UniProtKB.
DR GO; GO:0003127; P:detection of nodal flow; IMP:UniProtKB.
DR GO; GO:0098662; P:inorganic cation transmembrane transport; ISS:UniProtKB.
DR GO; GO:0071805; P:potassium ion transmembrane transport; ISS:UniProtKB.
DR GO; GO:0051290; P:protein heterotetramerization; ISS:UniProtKB.
DR GO; GO:0051262; P:protein tetramerization; ISS:UniProtKB.
DR GO; GO:0034765; P:regulation of ion transmembrane transport; IEA:UniProtKB-KW.
DR GO; GO:0051209; P:release of sequestered calcium ion into cytosol; IBA:GO_Central.
DR GO; GO:0016055; P:Wnt signaling pathway; IEA:UniProtKB-KW.
DR Gene3D; 1.20.120.350; -; 1.
DR InterPro; IPR011992; EF-hand-dom_pair.
DR InterPro; IPR002048; EF_hand_dom.
DR InterPro; IPR013122; PKD1_2_channel.
DR InterPro; IPR003915; PKD_2.
DR InterPro; IPR027359; Volt_channel_dom_sf.
DR Pfam; PF08016; PKD_channel; 1.
DR PRINTS; PR01433; POLYCYSTIN2.
DR SUPFAM; SSF47473; SSF47473; 1.
DR PROSITE; PS50222; EF_HAND_2; 2.
PE 1: Evidence at protein level;
KW Alternative splicing; Calcium; Calcium channel; Calcium transport;
KW Cell membrane; Cell projection; Cilium; Coiled coil; Cytoplasmic vesicle;
KW Disulfide bond; Endoplasmic reticulum; Glycoprotein; Ion channel;
KW Ion transport; Membrane; Metal-binding; Phosphoprotein; Potassium;
KW Potassium channel; Potassium transport; Reference proteome; Repeat;
KW Transmembrane; Transmembrane helix; Transport; Voltage-gated channel;
KW Wnt signaling pathway.
FT CHAIN 1..901
FT /note="Polycystin-2"
FT /id="PRO_0000425549"
FT TOPO_DOM 1..161
FT /note="Cytoplasmic"
FT /evidence="ECO:0000250|UniProtKB:Q13563"
FT TRANSMEM 162..183
FT /note="Helical; Name=S1"
FT /evidence="ECO:0000250|UniProtKB:Q13563"
FT TOPO_DOM 184..410
FT /note="Extracellular"
FT /evidence="ECO:0000250|UniProtKB:Q13563"
FT TRANSMEM 411..431
FT /note="Helical; Name=S2"
FT /evidence="ECO:0000250|UniProtKB:Q13563"
FT TOPO_DOM 432..447
FT /note="Cytoplasmic"
FT /evidence="ECO:0000250|UniProtKB:Q13563"
FT TRANSMEM 448..468
FT /note="Helical; Name=S3"
FT /evidence="ECO:0000250|UniProtKB:Q13563"
FT TOPO_DOM 469..494
FT /note="Extracellular"
FT /evidence="ECO:0000250|UniProtKB:Q13563"
FT TRANSMEM 495..515
FT /note="Helical; Name=S4"
FT /evidence="ECO:0000250|UniProtKB:Q13563"
FT TOPO_DOM 516..539
FT /note="Cytoplasmic"
FT /evidence="ECO:0000250|UniProtKB:Q13563"
FT TRANSMEM 540..561
FT /note="Helical; Name=5"
FT /evidence="ECO:0000250|UniProtKB:Q13563"
FT TOPO_DOM 562..573
FT /note="Extracellular"
FT /evidence="ECO:0000250|UniProtKB:Q13563"
FT INTRAMEM 574..588
FT /note="Pore-forming"
FT /evidence="ECO:0000250|UniProtKB:Q13563"
FT TOPO_DOM 589..596
FT /note="Extracellular"
FT /evidence="ECO:0000250|UniProtKB:Q13563"
FT TRANSMEM 597..617
FT /note="Helical; Name=S6"
FT /evidence="ECO:0000250|UniProtKB:Q13563"
FT TOPO_DOM 618..901
FT /note="Cytoplasmic"
FT /evidence="ECO:0000250|UniProtKB:Q13563"
FT DOMAIN 692..727
FT /note="EF-hand 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00448"
FT DOMAIN 756..791
FT /note="EF-hand 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00448"
FT REGION 1..57
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 69..127
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 715..775
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 745..764
FT /note="Linker"
FT /evidence="ECO:0000250|UniProtKB:Q13563"
FT REGION 857..901
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 775..814
FT /evidence="ECO:0000250|UniProtKB:Q13563"
FT MOTIF 583..585
FT /note="Selectivity filter"
FT /evidence="ECO:0000250|UniProtKB:Q13563"
FT COMPBIAS 1..18
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 79..124
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 715..736
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 886..901
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 705
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000250|UniProtKB:Q13563"
FT BINDING 707
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000250|UniProtKB:Q13563"
FT BINDING 709
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000250|UniProtKB:Q13563"
FT BINDING 711
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000250|UniProtKB:Q13563"
FT CARBOHYD 241
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 247
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 270
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 304
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 317
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 483
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT DISULFID 273..286
FT /evidence="ECO:0000250|UniProtKB:Q13563"
FT VAR_SEQ 867..901
FT /note="VSHPQPATPIGPRPRPPSSLSTDGLDTSANGGTHV -> TASTRALTEEPTC
FT EDIRRNDLPKTVAGQMFHM (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:21307098"
FT /id="VSP_053721"
FT CONFLICT 68
FT /note="M -> V (in Ref. 1; BAG75153)"
FT /evidence="ECO:0000305"
FT CONFLICT 187
FT /note="N -> D (in Ref. 1; BAG75153)"
FT /evidence="ECO:0000305"
FT CONFLICT 295
FT /note="E -> G (in Ref. 1; BAG75153)"
FT /evidence="ECO:0000305"
FT CONFLICT 402
FT /note="L -> V (in Ref. 1; BAG75153)"
FT /evidence="ECO:0000305"
FT CONFLICT 467
FT /note="S -> N (in Ref. 1; BAG75153 and 2; BAJ65630)"
FT /evidence="ECO:0000305"
FT CONFLICT 573
FT /note="G -> D (in Ref. 1; BAG75153)"
FT /evidence="ECO:0000305"
FT CONFLICT 581
FT /note="I -> V (in Ref. 1; BAG75153)"
FT /evidence="ECO:0000305"
FT CONFLICT 793
FT /note="H -> N (in Ref. 1; BAG75153)"
FT /evidence="ECO:0000305"
FT CONFLICT 848
FT /note="E -> K (in Ref. 1; BAG75153)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 901 AA; 102439 MW; 3E90806F7439DC25 CRC64;
MSATRVRPQS QAGTDKPPRT LDSSEGIEME NIQHQDPGLG GVAGSPSPPS RQAWSRDNPV
FEPEEEIMQA DWPQASPGRR SAFTASGGSS CSSGHGGYTR AGSSTQIPRG GLYPTQTLNG
QQQDRHEHPG CMKRIFQNIR ILWGTELMED GDSNRERYLW NVLRELLTYI AFLITICILT
YGMISTNMYY YTKAMSQLFL DAPLSSENPK TFRSLSTMED FWKYTQGPFL GGMYWEVWYN
NQSLPGNQSF IYYENILLGV PRLRQVRVHN ETCSIHEDLR DEVQGCYGVY TPSNEDNSPF
GPQNGTAWVH TTESKMNAST HWGQVSKYGG GGYYQDLSRT REESGLQLQF LKDHLWLDRG
TRAIFLDFSV YNGNVNLVCI ARLLVEFPAT GGVLTSWQFQ TLRLIKYVSS WDYFVGVCEV
AFCLFVLYYV VEEVLEIHIH RLHYFKNLWN CLDVLIVTLS VVAIIMSITR AAMGGDLLKG
LENYTSHTSF DSLANLQVQF NNMAAVIVFF CWVKLFKFIN FNKTMSQLST TMSRCAKDLV
GFAIMFFIIF LAYAQLAYLV FGTQVNDFST FQGSVFTQFR IILGDFDFFE IKEANPVLGP
IYFITFVLFI FFILMNMFLA IINDTYSEVK ADMAQHRSEM EMTDFIKKGC TKALVKLRLK
KTTVDDISDS LRQAGGKLNY DELLQDLKEK GHTEAEIQAI FAKYDQDGDL ELTEHDHQQM
RDDLEKERED LDLERNSLTR PSSGRSFPRT QDDSEEDDDE DSGHSSRRRG SSSGGVSYEE
FQVLVRRVDR MEHSIGSIVS KIDAVIVKLE GMERAKLKRR DVLVRLLDGV MEDERLGRDA
DTHREQMERL VKEELERWET DDVASQVSHP QPATPIGPRP RPPSSLSTDG LDTSANGGTH
V
