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Protein

E3 ubiquitin-protein ligase PDZRN3

Gene

PDZRN3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

E3 ubiquitin-protein ligase. Plays an important role in regulating the surface level of MUSK on myotubes. Mediates the ubiquitination of MUSK, promoting its endocytosis and lysosomal degradation. Might contribute to terminal myogenic differentiation (By similarity).By similarity

Pathwayi: protein ubiquitination

This protein is involved in the pathway protein ubiquitination, which is part of Protein modification.
View all proteins of this organism that are known to be involved in the pathway protein ubiquitination and in Protein modification.

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri18 – 56RING-type; degeneratePROSITE-ProRule annotationAdd BLAST39
Zinc fingeri100 – 158TRAF-typePROSITE-ProRule annotationAdd BLAST59

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

Ubl conjugation pathway

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

UniPathwayiUPA00143.

Names & Taxonomyi

Protein namesi
Recommended name:
E3 ubiquitin-protein ligase PDZRN3 (EC:6.3.2.-)
Alternative name(s):
Ligand of Numb protein X 3
PDZ domain-containing RING finger protein 3
Semaphorin cytoplasmic domain-associated protein 3
Short name:
Protein SEMACAP3
Gene namesi
Name:PDZRN3
Synonyms:KIAA1095, LNX3, SEMCAP3
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 3

Organism-specific databases

HGNCiHGNC:17704. PDZRN3.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Pathology & Biotechi

Organism-specific databases

DisGeNETi23024.
OpenTargetsiENSG00000121440.
PharmGKBiPA134931098.

Polymorphism and mutation databases

BioMutaiPDZRN3.
DMDMi62288903.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000559171 – 1066E3 ubiquitin-protein ligase PDZRN3Add BLAST1066

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei427PhosphoserineBy similarity1

Post-translational modificationi

Auto-ubiquitinated.By similarity

Keywords - PTMi

Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ9UPQ7.
PaxDbiQ9UPQ7.
PeptideAtlasiQ9UPQ7.
PRIDEiQ9UPQ7.

PTM databases

iPTMnetiQ9UPQ7.
PhosphoSitePlusiQ9UPQ7.

Expressioni

Tissue specificityi

Widely expressed, including in the heart, skeletal muscle and liver and, at lower levels, in the brain, colon, small intestine, placenta and lung. Down-regulated in ovarian serous papillary tumors.3 Publications

Gene expression databases

BgeeiENSG00000121440.
CleanExiHS_PDZRN3.
ExpressionAtlasiQ9UPQ7. baseline and differential.
GenevisibleiQ9UPQ7. HS.

Organism-specific databases

HPAiHPA038822.

Interactioni

Subunit structurei

Interacts with NLGN1 and EFNB2. Interacts with UBE2D2 and with MUSK via the first PDZ domain.By similarity

Protein-protein interaction databases

BioGridi116664. 12 interactors.
IntActiQ9UPQ7. 2 interactors.
STRINGi9606.ENSP00000263666.

Structurei

Secondary structure

11066
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi246 – 252Combined sources7
Beta strandi255 – 257Combined sources3
Beta strandi260 – 264Combined sources5
Beta strandi273 – 276Combined sources4
Beta strandi282 – 286Combined sources5
Beta strandi288 – 290Combined sources3
Helixi291 – 294Combined sources4
Beta strandi303 – 307Combined sources5
Helixi317 – 326Combined sources10
Beta strandi329 – 337Combined sources9
Beta strandi433 – 436Combined sources4
Beta strandi447 – 452Combined sources6
Beta strandi454 – 456Combined sources3
Helixi457 – 460Combined sources4
Beta strandi469 – 475Combined sources7
Helixi481 – 488Combined sources8
Beta strandi498 – 502Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1UHPNMR-A246-339[»]
1WH1NMR-A405-515[»]
ProteinModelPortaliQ9UPQ7.
SMRiQ9UPQ7.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9UPQ7.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini249 – 339PDZ 1PROSITE-ProRule annotationAdd BLAST91
Domaini419 – 503PDZ 2PROSITE-ProRule annotationAdd BLAST85

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili679 – 704Sequence analysisAdd BLAST26
Coiled coili975 – 1025Sequence analysisAdd BLAST51

Domaini

The RING-type zinc finger domain is required for E3 ligase activity.By similarity

Sequence similaritiesi

Contains 2 PDZ (DHR) domains.PROSITE-ProRule annotation
Contains 1 RING-type zinc finger.PROSITE-ProRule annotation
Contains 1 TRAF-type zinc finger.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri18 – 56RING-type; degeneratePROSITE-ProRule annotationAdd BLAST39
Zinc fingeri100 – 158TRAF-typePROSITE-ProRule annotationAdd BLAST59

Keywords - Domaini

Coiled coil, Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG0297. Eukaryota.
KOG0312. Eukaryota.
ENOG4111S26. LUCA.
GeneTreeiENSGT00510000046421.
HOGENOMiHOG000231379.
HOVERGENiHBG053554.
InParanoidiQ9UPQ7.
KOiK15682.
OMAiGDIHQEM.
OrthoDBiEOG091G0GKE.
PhylomeDBiQ9UPQ7.
TreeFamiTF315909.

Family and domain databases

Gene3Di2.30.42.10. 2 hits.
3.30.40.10. 1 hit.
3.90.890.10. 1 hit.
InterProiIPR001478. PDZ.
IPR013323. SIAH-type.
IPR008974. TRAF-like.
IPR001841. Znf_RING.
IPR013083. Znf_RING/FYVE/PHD.
IPR017907. Znf_RING_CS.
IPR001293. Znf_TRAF.
[Graphical view]
PfamiPF00595. PDZ. 2 hits.
[Graphical view]
SMARTiSM00228. PDZ. 2 hits.
SM00184. RING. 1 hit.
[Graphical view]
SUPFAMiSSF49599. SSF49599. 1 hit.
SSF50156. SSF50156. 2 hits.
PROSITEiPS50106. PDZ. 2 hits.
PS00518. ZF_RING_1. 1 hit.
PS50089. ZF_RING_2. 1 hit.
PS50145. ZF_TRAF. 1 hit.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9UPQ7-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MGFELDRFDG DVDPDLKCAL CHKVLEDPLT TPCGHVFCAG CVLPWVVQEG
60 70 80 90 100
SCPARCRGRL SAKELNHVLP LKRLILKLDI KCAYATRGCG RVVKLQQLPE
110 120 130 140 150
HLERCDFAPA RCRHAGCGQV LLRRDVEAHM RDACDARPVG RCQEGCGLPL
160 170 180 190 200
THGEQRAGGH CCARALRAHN GALQARLGAL HKALKKEALR AGKREKSLVA
210 220 230 240 250
QLAAAQLELQ MTALRYQKKF TEYSARLDSL SRCVAAPPGG KGEETKSLTL
260 270 280 290 300
VLHRDSGSLG FNIIGGRPSV DNHDGSSSEG IFVSKIVDSG PAAKEGGLQI
310 320 330 340 350
HDRIIEVNGR DLSRATHDQA VEAFKTAKEP IVVQVLRRTP RTKMFTPPSE
360 370 380 390 400
SQLVDTGTQT DITFEHIMAL TKMSSPSPPV LDPYLLPEEH PSAHEYYDPN
410 420 430 440 450
DYIGDIHQEM DREELELEEV DLYRMNSQDK LGLTVCYRTD DEDDIGIYIS
460 470 480 490 500
EIDPNSIAAK DGRIREGDRI IQINGIEVQN REEAVALLTS EENKNFSLLI
510 520 530 540 550
ARPELQLDEG WMDDDRNDFL DDLHMDMLEE QHHQAMQFTA SVLQQKKHDE
560 570 580 590 600
DGGTTDTATI LSNQHEKDSG VGRTDESTRN DESSEQENNG DDATASSNPL
610 620 630 640 650
AGQRKLTCSQ DTLGSGDLPF SNESFISADC TDADYLGIPV DECERFRELL
660 670 680 690 700
ELKCQVKSAT PYGLYYPSGP LDAGKSDPES VDKELELLNE ELRSIELECL
710 720 730 740 750
SIVRAHKMQQ LKEQYRESWM LHNSGFRNYN TSIDVRRHEL SDITELPEKS
760 770 780 790 800
DKDSSSAYNT GESCRSTPLT LEISPDNSLR RAAEGISCPS SEGAVGTTEA
810 820 830 840 850
YGPASKNLLS ITEDPEVGTP TYSPSLKELD PNQPLESKER RASDGSRSPT
860 870 880 890 900
PSQKLGSAYL PSYHHSPYKH AHIPAHAQHY QSYMQLIQQK SAVEYAQSQM
910 920 930 940 950
SLVSMCKDLS SPTPSEPRME WKVKIRSDGT RYITKRPVRD RLLRERALKI
960 970 980 990 1000
REERSGMTTD DDAVSEMKMG RYWSKEERKQ HLVKAKEQRR RREFMMQSRL
1010 1020 1030 1040 1050
DCLKEQQAAD DRKEMNILEL SHKKMMKKRN KKIFDNWMTI QELLTHGTKS
1060
PDGTRVYNSF LSVTTV
Length:1,066
Mass (Da):119,596
Last modified:February 1, 2005 - v2
Checksum:iEE837EF3B5B0C808
GO
Isoform 2 (identifier: Q9UPQ7-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     307-360: VNGRDLSRAT...SQLVDTGTQT → MRKLELRTVK...ACGGAYLNCI
     361-1066: Missing.

Note: No experimental confirmation available.
Show »
Length:360
Mass (Da):38,931
Checksum:i451BC8AF39408341
GO
Isoform 3 (identifier: Q9UPQ7-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     641-729: DECERFRELL...MLHNSGFRNY → EGEDPQRRDA...GLSQGAASSR
     730-1066: Missing.

Note: No experimental confirmation available.
Show »
Length:729
Mass (Da):80,006
Checksum:i24509433F18C9CFA
GO

Sequence cautioni

The sequence BAA83047 differs from that shown. Reason: Erroneous initiation.Curated
The sequence BAC11068 differs from that shown. Reason: Erroneous initiation.Curated

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_020965783A → V.1 PublicationCorresponds to variant rs3205537dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_012606307 – 360VNGRD…TGTQT → MRKLELRTVKLPKAHSQDSN AGFIPQLLSLHTPPLSCEKG GGHLACGGAYLNCI in isoform 2. 1 PublicationAdd BLAST54
Alternative sequenceiVSP_012607361 – 1066Missing in isoform 2. 1 PublicationAdd BLAST706
Alternative sequenceiVSP_012608641 – 729DECER…GFRNY → EGEDPQRRDALHHQEARAGP PAAGARPEDPGRAQRHDHRR RRGERDEDGALLEQGGEEAA PGEGQGAAAAARVHDAEQVG LSQGAASSR in isoform 3. 1 PublicationAdd BLAST89
Alternative sequenceiVSP_012609730 – 1066Missing in isoform 3. 1 PublicationAdd BLAST337

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB029018 mRNA. Translation: BAA83047.1. Different initiation.
BC014432 mRNA. Translation: AAH14432.1.
BC152417 mRNA. Translation: AAI52418.1.
AK074573 mRNA. Translation: BAC11068.1. Different initiation.
AL157498 mRNA. Translation: CAB75679.1.
CCDSiCCDS33789.1. [Q9UPQ7-1]
PIRiT46925.
RefSeqiNP_001290068.1. NM_001303139.1.
NP_001290069.1. NM_001303140.1.
NP_001290070.1. NM_001303141.1.
NP_001290071.1. NM_001303142.1.
NP_055824.1. NM_015009.2. [Q9UPQ7-1]
UniGeneiHs.660347.
Hs.662049.
Hs.666839.
Hs.743998.

Genome annotation databases

EnsembliENST00000263666; ENSP00000263666; ENSG00000121440. [Q9UPQ7-1]
ENST00000308537; ENSP00000308831; ENSG00000121440. [Q9UPQ7-2]
GeneIDi23024.
KEGGihsa:23024.
UCSCiuc003dpl.2. human. [Q9UPQ7-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB029018 mRNA. Translation: BAA83047.1. Different initiation.
BC014432 mRNA. Translation: AAH14432.1.
BC152417 mRNA. Translation: AAI52418.1.
AK074573 mRNA. Translation: BAC11068.1. Different initiation.
AL157498 mRNA. Translation: CAB75679.1.
CCDSiCCDS33789.1. [Q9UPQ7-1]
PIRiT46925.
RefSeqiNP_001290068.1. NM_001303139.1.
NP_001290069.1. NM_001303140.1.
NP_001290070.1. NM_001303141.1.
NP_001290071.1. NM_001303142.1.
NP_055824.1. NM_015009.2. [Q9UPQ7-1]
UniGeneiHs.660347.
Hs.662049.
Hs.666839.
Hs.743998.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1UHPNMR-A246-339[»]
1WH1NMR-A405-515[»]
ProteinModelPortaliQ9UPQ7.
SMRiQ9UPQ7.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi116664. 12 interactors.
IntActiQ9UPQ7. 2 interactors.
STRINGi9606.ENSP00000263666.

PTM databases

iPTMnetiQ9UPQ7.
PhosphoSitePlusiQ9UPQ7.

Polymorphism and mutation databases

BioMutaiPDZRN3.
DMDMi62288903.

Proteomic databases

EPDiQ9UPQ7.
PaxDbiQ9UPQ7.
PeptideAtlasiQ9UPQ7.
PRIDEiQ9UPQ7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000263666; ENSP00000263666; ENSG00000121440. [Q9UPQ7-1]
ENST00000308537; ENSP00000308831; ENSG00000121440. [Q9UPQ7-2]
GeneIDi23024.
KEGGihsa:23024.
UCSCiuc003dpl.2. human. [Q9UPQ7-1]

Organism-specific databases

CTDi23024.
DisGeNETi23024.
GeneCardsiPDZRN3.
H-InvDBHIX0163446.
HGNCiHGNC:17704. PDZRN3.
HPAiHPA038822.
MIMi609729. gene.
neXtProtiNX_Q9UPQ7.
OpenTargetsiENSG00000121440.
PharmGKBiPA134931098.
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0297. Eukaryota.
KOG0312. Eukaryota.
ENOG4111S26. LUCA.
GeneTreeiENSGT00510000046421.
HOGENOMiHOG000231379.
HOVERGENiHBG053554.
InParanoidiQ9UPQ7.
KOiK15682.
OMAiGDIHQEM.
OrthoDBiEOG091G0GKE.
PhylomeDBiQ9UPQ7.
TreeFamiTF315909.

Enzyme and pathway databases

UniPathwayiUPA00143.

Miscellaneous databases

ChiTaRSiPDZRN3. human.
EvolutionaryTraceiQ9UPQ7.
GeneWikiiPDZRN3.
GenomeRNAii23024.
PROiQ9UPQ7.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000121440.
CleanExiHS_PDZRN3.
ExpressionAtlasiQ9UPQ7. baseline and differential.
GenevisibleiQ9UPQ7. HS.

Family and domain databases

Gene3Di2.30.42.10. 2 hits.
3.30.40.10. 1 hit.
3.90.890.10. 1 hit.
InterProiIPR001478. PDZ.
IPR013323. SIAH-type.
IPR008974. TRAF-like.
IPR001841. Znf_RING.
IPR013083. Znf_RING/FYVE/PHD.
IPR017907. Znf_RING_CS.
IPR001293. Znf_TRAF.
[Graphical view]
PfamiPF00595. PDZ. 2 hits.
[Graphical view]
SMARTiSM00228. PDZ. 2 hits.
SM00184. RING. 1 hit.
[Graphical view]
SUPFAMiSSF49599. SSF49599. 1 hit.
SSF50156. SSF50156. 2 hits.
PROSITEiPS50106. PDZ. 2 hits.
PS00518. ZF_RING_1. 1 hit.
PS50089. ZF_RING_2. 1 hit.
PS50145. ZF_TRAF. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPZRN3_HUMAN
AccessioniPrimary (citable) accession number: Q9UPQ7
Secondary accession number(s): A7MCZ6
, Q8N2N7, Q96CC2, Q9NSQ2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 2005
Last sequence update: February 1, 2005
Last modified: November 30, 2016
This is version 147 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 3
    Human chromosome 3: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  6. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  7. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.