PZRN3_HUMAN
ID PZRN3_HUMAN Reviewed; 1066 AA.
AC Q9UPQ7; A7MCZ6; Q8N2N7; Q96CC2; Q9NSQ2;
DT 01-FEB-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-2005, sequence version 2.
DT 03-AUG-2022, entry version 185.
DE RecName: Full=E3 ubiquitin-protein ligase PDZRN3;
DE EC=2.3.2.27;
DE AltName: Full=Ligand of Numb protein X 3;
DE AltName: Full=PDZ domain-containing RING finger protein 3;
DE AltName: Full=RING-type E3 ubiquitin transferase PDZRN3 {ECO:0000305};
DE AltName: Full=Semaphorin cytoplasmic domain-associated protein 3;
DE Short=Protein SEMACAP3;
GN Name=PDZRN3; Synonyms=KIAA1095, LNX3, SEMCAP3;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), AND TISSUE SPECIFICITY.
RC TISSUE=Brain;
RX PubMed=10470851; DOI=10.1093/dnares/6.3.197;
RA Kikuno R., Nagase T., Ishikawa K., Hirosawa M., Miyajima N., Tanaka A.,
RA Kotani H., Nomura N., Ohara O.;
RT "Prediction of the coding sequences of unidentified human genes. XIV. The
RT complete sequences of 100 new cDNA clones from brain which code for large
RT proteins in vitro.";
RL DNA Res. 6:197-205(1999).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
RC TISSUE=Skin;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 405-729 (ISOFORM 3).
RX PubMed=14702039; DOI=10.1038/ng1285;
RA Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
RA Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
RA Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
RA Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
RA Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H.,
RA Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M.,
RA Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K.,
RA Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T.,
RA Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M.,
RA Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S.,
RA Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H.,
RA Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K.,
RA Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N.,
RA Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
RA Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
RA Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
RA Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
RA Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y.,
RA Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K.,
RA Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T.,
RA Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T.,
RA Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y.,
RA Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H.,
RA Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y.,
RA Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H.,
RA Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O.,
RA Isogai T., Sugano S.;
RT "Complete sequencing and characterization of 21,243 full-length human
RT cDNAs.";
RL Nat. Genet. 36:40-45(2004).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 587-1066 (ISOFORM 1), AND VARIANT
RP VAL-783.
RC TISSUE=Testis;
RX PubMed=17974005; DOI=10.1186/1471-2164-8-399;
RA Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U.,
RA Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H., Heubner D.,
RA Hoerlein A., Michel G., Wedler H., Koehrer K., Ottenwaelder B., Poustka A.,
RA Wiemann S., Schupp I.;
RT "The full-ORF clone resource of the German cDNA consortium.";
RL BMC Genomics 8:399-399(2007).
RN [5]
RP IDENTIFICATION.
RX PubMed=15010864;
RA Katoh M., Katoh M.;
RT "Identification and characterization of PDZRN3 and PDZRN4 genes in
RT silico.";
RL Int. J. Mol. Med. 13:607-613(2004).
RN [6]
RP TISSUE SPECIFICITY.
RX PubMed=15305371; DOI=10.1002/ijc.20408;
RA Santin A.D., Zhan F., Bellone S., Palmieri M., Cane S., Bignotti E.,
RA Anfossi S., Gokden M., Dunn D., Roman J.J., O'Brien T.J., Tian E.,
RA Cannon M.J., Shaughnessy J. Jr., Pecorelli S.;
RT "Gene expression profiles in primary ovarian serous papillary tumors and
RT normal ovarian epithelium: identification of candidate molecular markers
RT for ovarian cancer diagnosis and therapy.";
RL Int. J. Cancer 112:14-25(2004).
RN [7]
RP TISSUE SPECIFICITY.
RX PubMed=17118964; DOI=10.1242/jcs.03290;
RA Ko J.A., Kimura Y., Matsuura K., Yamamoto H., Gondo T., Inui M.;
RT "PDZRN3 (LNX3, SEMCAP3) is required for the differentiation of C2C12
RT myoblasts into myotubes.";
RL J. Cell Sci. 119:5106-5113(2006).
RN [8]
RP STRUCTURE BY NMR OF 271-377.
RG RIKEN structural genomics initiative (RSGI);
RT "Solution structure of RSGI RUH-005, a PDZ domain in human cDNA,
RT KIAA1095.";
RL Submitted (JAN-2004) to the PDB data bank.
RN [9]
RP STRUCTURE BY NMR OF 404-515.
RG RIKEN structural genomics initiative (RSGI);
RT "Solution structure of the fourth PDZ domain of KIAA1095 protein.";
RL Submitted (NOV-2004) to the PDB data bank.
CC -!- FUNCTION: E3 ubiquitin-protein ligase. Plays an important role in
CC regulating the surface level of MUSK on myotubes. Mediates the
CC ubiquitination of MUSK, promoting its endocytosis and lysosomal
CC degradation. Might contribute to terminal myogenic differentiation.
CC {ECO:0000250|UniProtKB:Q69ZS0}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine +
CC [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-
CC cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.;
CC EC=2.3.2.27;
CC -!- PATHWAY: Protein modification; protein ubiquitination.
CC -!- SUBUNIT: Interacts with NLGN1 and EFNB2. Interacts with UBE2D2 and with
CC MUSK via the first PDZ domain. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Synapse {ECO:0000250|UniProtKB:Q69ZS0}. Cytoplasm
CC {ECO:0000250|UniProtKB:E7FDW2}. Note=Localizes to the postsynaptic
CC region of neuromuscular junctions. {ECO:0000250|UniProtKB:Q69ZS0}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=3;
CC Name=1;
CC IsoId=Q9UPQ7-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9UPQ7-2; Sequence=VSP_012606, VSP_012607;
CC Name=3;
CC IsoId=Q9UPQ7-3; Sequence=VSP_012608, VSP_012609;
CC -!- TISSUE SPECIFICITY: Widely expressed, including in the heart, skeletal
CC muscle and liver and, at lower levels, in the brain, colon, small
CC intestine, placenta and lung. Down-regulated in ovarian serous
CC papillary tumors. {ECO:0000269|PubMed:10470851,
CC ECO:0000269|PubMed:15305371, ECO:0000269|PubMed:17118964}.
CC -!- DOMAIN: The RING-type zinc finger domain is required for E3 ligase
CC activity. {ECO:0000250}.
CC -!- PTM: Auto-ubiquitinated. {ECO:0000250}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAA83047.1; Type=Erroneous initiation; Evidence={ECO:0000305};
CC Sequence=BAC11068.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; AB029018; BAA83047.1; ALT_INIT; mRNA.
DR EMBL; BC014432; AAH14432.1; -; mRNA.
DR EMBL; BC152417; AAI52418.1; -; mRNA.
DR EMBL; AK074573; BAC11068.1; ALT_INIT; mRNA.
DR EMBL; AL157498; CAB75679.1; -; mRNA.
DR CCDS; CCDS33789.1; -. [Q9UPQ7-1]
DR PIR; T46925; T46925.
DR RefSeq; NP_001290068.1; NM_001303139.1.
DR RefSeq; NP_001290069.1; NM_001303140.1.
DR RefSeq; NP_001290070.1; NM_001303141.1.
DR RefSeq; NP_001290071.1; NM_001303142.1.
DR RefSeq; NP_055824.1; NM_015009.2. [Q9UPQ7-1]
DR PDB; 1UHP; NMR; -; A=246-339.
DR PDB; 1WH1; NMR; -; A=405-515.
DR PDBsum; 1UHP; -.
DR PDBsum; 1WH1; -.
DR AlphaFoldDB; Q9UPQ7; -.
DR BMRB; Q9UPQ7; -.
DR SMR; Q9UPQ7; -.
DR BioGRID; 116664; 40.
DR IntAct; Q9UPQ7; 8.
DR STRING; 9606.ENSP00000263666; -.
DR iPTMnet; Q9UPQ7; -.
DR PhosphoSitePlus; Q9UPQ7; -.
DR BioMuta; PDZRN3; -.
DR DMDM; 62288903; -.
DR EPD; Q9UPQ7; -.
DR jPOST; Q9UPQ7; -.
DR MassIVE; Q9UPQ7; -.
DR MaxQB; Q9UPQ7; -.
DR PaxDb; Q9UPQ7; -.
DR PeptideAtlas; Q9UPQ7; -.
DR PRIDE; Q9UPQ7; -.
DR ProteomicsDB; 85416; -. [Q9UPQ7-1]
DR ProteomicsDB; 85417; -. [Q9UPQ7-2]
DR ProteomicsDB; 85418; -. [Q9UPQ7-3]
DR Antibodypedia; 31945; 110 antibodies from 16 providers.
DR DNASU; 23024; -.
DR Ensembl; ENST00000263666.9; ENSP00000263666.4; ENSG00000121440.15. [Q9UPQ7-1]
DR Ensembl; ENST00000308537.4; ENSP00000308831.4; ENSG00000121440.15. [Q9UPQ7-2]
DR GeneID; 23024; -.
DR KEGG; hsa:23024; -.
DR MANE-Select; ENST00000263666.9; ENSP00000263666.4; NM_015009.3; NP_055824.1.
DR UCSC; uc003dpl.2; human. [Q9UPQ7-1]
DR CTD; 23024; -.
DR DisGeNET; 23024; -.
DR GeneCards; PDZRN3; -.
DR HGNC; HGNC:17704; PDZRN3.
DR HPA; ENSG00000121440; Low tissue specificity.
DR MIM; 609729; gene.
DR neXtProt; NX_Q9UPQ7; -.
DR OpenTargets; ENSG00000121440; -.
DR PharmGKB; PA134931098; -.
DR VEuPathDB; HostDB:ENSG00000121440; -.
DR eggNOG; KOG0297; Eukaryota.
DR eggNOG; KOG0312; Eukaryota.
DR GeneTree; ENSGT00950000183062; -.
DR HOGENOM; CLU_058306_0_0_1; -.
DR InParanoid; Q9UPQ7; -.
DR OMA; HAGCGQL; -.
DR OrthoDB; 631580at2759; -.
DR PhylomeDB; Q9UPQ7; -.
DR TreeFam; TF315909; -.
DR PathwayCommons; Q9UPQ7; -.
DR SignaLink; Q9UPQ7; -.
DR UniPathway; UPA00143; -.
DR BioGRID-ORCS; 23024; 10 hits in 1107 CRISPR screens.
DR ChiTaRS; PDZRN3; human.
DR EvolutionaryTrace; Q9UPQ7; -.
DR GeneWiki; PDZRN3; -.
DR GenomeRNAi; 23024; -.
DR Pharos; Q9UPQ7; Tbio.
DR PRO; PR:Q9UPQ7; -.
DR Proteomes; UP000005640; Chromosome 3.
DR RNAct; Q9UPQ7; protein.
DR Bgee; ENSG00000121440; Expressed in blood vessel layer and 196 other tissues.
DR ExpressionAtlas; Q9UPQ7; baseline and differential.
DR Genevisible; Q9UPQ7; HS.
DR GO; GO:0070161; C:anchoring junction; IEA:UniProtKB-KW.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0031594; C:neuromuscular junction; IBA:GO_Central.
DR GO; GO:0061630; F:ubiquitin protein ligase activity; IBA:GO_Central.
DR GO; GO:0004842; F:ubiquitin-protein transferase activity; ISS:UniProtKB.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0007528; P:neuromuscular junction development; IBA:GO_Central.
DR GO; GO:0016567; P:protein ubiquitination; ISS:UniProtKB.
DR Gene3D; 2.30.42.10; -; 2.
DR Gene3D; 3.30.40.10; -; 2.
DR InterPro; IPR001478; PDZ.
DR InterPro; IPR036034; PDZ_sf.
DR InterPro; IPR001841; Znf_RING.
DR InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR InterPro; IPR017907; Znf_RING_CS.
DR InterPro; IPR001293; Znf_TRAF.
DR Pfam; PF00595; PDZ; 2.
DR SMART; SM00228; PDZ; 2.
DR SMART; SM00184; RING; 1.
DR SUPFAM; SSF50156; SSF50156; 2.
DR PROSITE; PS50106; PDZ; 2.
DR PROSITE; PS00518; ZF_RING_1; 1.
DR PROSITE; PS50089; ZF_RING_2; 1.
DR PROSITE; PS50145; ZF_TRAF; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Alternative splicing; Coiled coil; Cytoplasm; Metal-binding;
KW Phosphoprotein; Reference proteome; Repeat; Synapse; Transferase;
KW Ubl conjugation; Ubl conjugation pathway; Zinc; Zinc-finger.
FT CHAIN 1..1066
FT /note="E3 ubiquitin-protein ligase PDZRN3"
FT /id="PRO_0000055917"
FT DOMAIN 249..339
FT /note="PDZ 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00143"
FT DOMAIN 419..503
FT /note="PDZ 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00143"
FT ZN_FING 18..56
FT /note="RING-type; degenerate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00175"
FT ZN_FING 100..158
FT /note="TRAF-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00207"
FT REGION 545..603
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 744..778
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 808..863
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 679..704
FT /evidence="ECO:0000255"
FT COILED 975..1025
FT /evidence="ECO:0000255"
FT COMPBIAS 568..586
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 589..603
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 753..774
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 812..830
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 427
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q69ZS0"
FT VAR_SEQ 307..360
FT /note="VNGRDLSRATHDQAVEAFKTAKEPIVVQVLRRTPRTKMFTPPSESQLVDTGT
FT QT -> MRKLELRTVKLPKAHSQDSNAGFIPQLLSLHTPPLSCEKGGGHLACGGAYLNC
FT I (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:15489334"
FT /id="VSP_012606"
FT VAR_SEQ 361..1066
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:15489334"
FT /id="VSP_012607"
FT VAR_SEQ 641..729
FT /note="DECERFRELLELKCQVKSATPYGLYYPSGPLDAGKSDPESVDKELELLNEEL
FT RSIELECLSIVRAHKMQQLKEQYRESWMLHNSGFRNY -> EGEDPQRRDALHHQEARA
FT GPPAAGARPEDPGRAQRHDHRRRRGERDEDGALLEQGGEEAAPGEGQGAAAAARVHDAE
FT QVGLSQGAASSR (in isoform 3)"
FT /evidence="ECO:0000303|PubMed:14702039"
FT /id="VSP_012608"
FT VAR_SEQ 730..1066
FT /note="Missing (in isoform 3)"
FT /evidence="ECO:0000303|PubMed:14702039"
FT /id="VSP_012609"
FT VARIANT 783
FT /note="A -> V (in dbSNP:rs3205537)"
FT /evidence="ECO:0000269|PubMed:17974005"
FT /id="VAR_020965"
FT STRAND 245..252
FT /evidence="ECO:0007829|PDB:1UHP"
FT STRAND 255..257
FT /evidence="ECO:0007829|PDB:1UHP"
FT STRAND 260..264
FT /evidence="ECO:0007829|PDB:1UHP"
FT STRAND 273..276
FT /evidence="ECO:0007829|PDB:1UHP"
FT STRAND 282..286
FT /evidence="ECO:0007829|PDB:1UHP"
FT STRAND 288..290
FT /evidence="ECO:0007829|PDB:1UHP"
FT HELIX 291..294
FT /evidence="ECO:0007829|PDB:1UHP"
FT STRAND 303..307
FT /evidence="ECO:0007829|PDB:1UHP"
FT HELIX 317..326
FT /evidence="ECO:0007829|PDB:1UHP"
FT STRAND 329..337
FT /evidence="ECO:0007829|PDB:1UHP"
FT STRAND 433..436
FT /evidence="ECO:0007829|PDB:1WH1"
FT STRAND 447..452
FT /evidence="ECO:0007829|PDB:1WH1"
FT STRAND 454..456
FT /evidence="ECO:0007829|PDB:1WH1"
FT HELIX 457..460
FT /evidence="ECO:0007829|PDB:1WH1"
FT STRAND 469..475
FT /evidence="ECO:0007829|PDB:1WH1"
FT HELIX 481..488
FT /evidence="ECO:0007829|PDB:1WH1"
FT STRAND 498..502
FT /evidence="ECO:0007829|PDB:1WH1"
SQ SEQUENCE 1066 AA; 119596 MW; EE837EF3B5B0C808 CRC64;
MGFELDRFDG DVDPDLKCAL CHKVLEDPLT TPCGHVFCAG CVLPWVVQEG SCPARCRGRL
SAKELNHVLP LKRLILKLDI KCAYATRGCG RVVKLQQLPE HLERCDFAPA RCRHAGCGQV
LLRRDVEAHM RDACDARPVG RCQEGCGLPL THGEQRAGGH CCARALRAHN GALQARLGAL
HKALKKEALR AGKREKSLVA QLAAAQLELQ MTALRYQKKF TEYSARLDSL SRCVAAPPGG
KGEETKSLTL VLHRDSGSLG FNIIGGRPSV DNHDGSSSEG IFVSKIVDSG PAAKEGGLQI
HDRIIEVNGR DLSRATHDQA VEAFKTAKEP IVVQVLRRTP RTKMFTPPSE SQLVDTGTQT
DITFEHIMAL TKMSSPSPPV LDPYLLPEEH PSAHEYYDPN DYIGDIHQEM DREELELEEV
DLYRMNSQDK LGLTVCYRTD DEDDIGIYIS EIDPNSIAAK DGRIREGDRI IQINGIEVQN
REEAVALLTS EENKNFSLLI ARPELQLDEG WMDDDRNDFL DDLHMDMLEE QHHQAMQFTA
SVLQQKKHDE DGGTTDTATI LSNQHEKDSG VGRTDESTRN DESSEQENNG DDATASSNPL
AGQRKLTCSQ DTLGSGDLPF SNESFISADC TDADYLGIPV DECERFRELL ELKCQVKSAT
PYGLYYPSGP LDAGKSDPES VDKELELLNE ELRSIELECL SIVRAHKMQQ LKEQYRESWM
LHNSGFRNYN TSIDVRRHEL SDITELPEKS DKDSSSAYNT GESCRSTPLT LEISPDNSLR
RAAEGISCPS SEGAVGTTEA YGPASKNLLS ITEDPEVGTP TYSPSLKELD PNQPLESKER
RASDGSRSPT PSQKLGSAYL PSYHHSPYKH AHIPAHAQHY QSYMQLIQQK SAVEYAQSQM
SLVSMCKDLS SPTPSEPRME WKVKIRSDGT RYITKRPVRD RLLRERALKI REERSGMTTD
DDAVSEMKMG RYWSKEERKQ HLVKAKEQRR RREFMMQSRL DCLKEQQAAD DRKEMNILEL
SHKKMMKKRN KKIFDNWMTI QELLTHGTKS PDGTRVYNSF LSVTTV