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Protein

E3 ubiquitin-protein ligase PDZRN3

Gene

PDZRN3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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

Catalytic activityi

S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N6-ubiquitinyl-[acceptor protein]-L-lysine.

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

  • ubiquitin protein ligase activity Source: GO_Central
  • ubiquitin-protein transferase activity Source: UniProtKB
  • zinc ion binding Source: InterPro

GO - Biological processi

Keywordsi

Molecular functionTransferase
Biological processUbl conjugation pathway
LigandMetal-binding, Zinc

Enzyme and pathway databases

UniPathwayi
UPA00143

Names & Taxonomyi

Protein namesi
Recommended name:
E3 ubiquitin-protein ligase PDZRN3 (EC:2.3.2.27)
Alternative name(s):
Ligand of Numb protein X 3
PDZ domain-containing RING finger protein 3
RING-type E3 ubiquitin transferase PDZRN3Curated
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

EuPathDBiHostDB:ENSG00000121440.14
HGNCiHGNC:17704 PDZRN3
MIMi609729 gene
neXtProtiNX_Q9UPQ7

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cell junction, Cytoplasm, Synapse

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
ProteomicsDBi85416
85417 [Q9UPQ7-2]
85418 [Q9UPQ7-3]

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 Expressed in 230 organ(s), highest expression level in esophagus
CleanExiHS_PDZRN3
ExpressionAtlasiQ9UPQ7 baseline and differential
GenevisibleiQ9UPQ7 HS

Organism-specific databases

HPAiHPA038822
HPA061420

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, 15 interactors
IntActiQ9UPQ7, 2 interactors
STRINGi9606.ENSP00000263666

Structurei

Secondary structure

11066
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

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

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
OMAiMLQQKKH
OrthoDBiEOG091G0GKE
PhylomeDBiQ9UPQ7
TreeFamiTF315909

Family and domain databases

Gene3Di3.30.40.10, 2 hits
InterProiView protein in InterPro
IPR001478 PDZ
IPR036034 PDZ_sf
IPR008974 TRAF-like
IPR001841 Znf_RING
IPR013083 Znf_RING/FYVE/PHD
IPR017907 Znf_RING_CS
IPR001293 Znf_TRAF
PfamiView protein in Pfam
PF00595 PDZ, 2 hits
SMARTiView protein in SMART
SM00228 PDZ, 2 hits
SM00184 RING, 1 hit
SUPFAMiSSF49599 SSF49599, 1 hit
SSF50156 SSF50156, 2 hits
PROSITEiView protein in PROSITE
PS50106 PDZ, 2 hits
PS00518 ZF_RING_1, 1 hit
PS50089 ZF_RING_2, 1 hit
PS50145 ZF_TRAF, 1 hit

Sequences (3+)i

Sequence statusi: Complete.

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

This entry has 3 described isoforms and 4 potential isoforms that are computationally mapped.Show allAlign All

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

Computationally mapped potential isoform sequencesi

There are 4 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
B7ZAG0B7ZAG0_HUMAN
E3 ubiquitin-protein ligase PDZRN3
PDZRN3
783Annotation score:
E7ENB6E7ENB6_HUMAN
E3 ubiquitin-protein ligase PDZRN3
PDZRN3
723Annotation score:
C9JWE6C9JWE6_HUMAN
E3 ubiquitin-protein ligase PDZRN3
PDZRN3
492Annotation score:
H7C566H7C566_HUMAN
E3 ubiquitin-protein ligase PDZRN3
PDZRN3
382Annotation score:

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 → V1 PublicationCorresponds to variant dbSNP:rs3205537Ensembl.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

Similar proteinsi

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, 15 interactors
IntActiQ9UPQ7, 2 interactors
STRINGi9606.ENSP00000263666

PTM databases

iPTMnetiQ9UPQ7
PhosphoSitePlusiQ9UPQ7

Polymorphism and mutation databases

BioMutaiPDZRN3
DMDMi62288903

Proteomic databases

EPDiQ9UPQ7
PaxDbiQ9UPQ7
PeptideAtlasiQ9UPQ7
PRIDEiQ9UPQ7
ProteomicsDBi85416
85417 [Q9UPQ7-2]
85418 [Q9UPQ7-3]

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
EuPathDBiHostDB:ENSG00000121440.14
GeneCardsiPDZRN3
H-InvDBiHIX0163446
HGNCiHGNC:17704 PDZRN3
HPAiHPA038822
HPA061420
MIMi609729 gene
neXtProtiNX_Q9UPQ7
OpenTargetsiENSG00000121440
PharmGKBiPA134931098
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayi
UPA00143

Miscellaneous databases

ChiTaRSiPDZRN3 human
EvolutionaryTraceiQ9UPQ7
GeneWikiiPDZRN3
GenomeRNAii23024
PROiPR:Q9UPQ7
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000121440 Expressed in 230 organ(s), highest expression level in esophagus
CleanExiHS_PDZRN3
ExpressionAtlasiQ9UPQ7 baseline and differential
GenevisibleiQ9UPQ7 HS

Family and domain databases

Gene3Di3.30.40.10, 2 hits
InterProiView protein in InterPro
IPR001478 PDZ
IPR036034 PDZ_sf
IPR008974 TRAF-like
IPR001841 Znf_RING
IPR013083 Znf_RING/FYVE/PHD
IPR017907 Znf_RING_CS
IPR001293 Znf_TRAF
PfamiView protein in Pfam
PF00595 PDZ, 2 hits
SMARTiView protein in SMART
SM00228 PDZ, 2 hits
SM00184 RING, 1 hit
SUPFAMiSSF49599 SSF49599, 1 hit
SSF50156 SSF50156, 2 hits
PROSITEiView protein in PROSITE
PS50106 PDZ, 2 hits
PS00518 ZF_RING_1, 1 hit
PS50089 ZF_RING_2, 1 hit
PS50145 ZF_TRAF, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiPZRN3_HUMAN
AccessioniPrimary (citable) accession number: Q9UPQ7
Secondary accession number(s): A7MCZ6
, Q8N2N7, Q96CC2, Q9NSQ2
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 1, 2005
Last sequence update: February 1, 2005
Last modified: November 7, 2018
This is version 162 of the entry and version 2 of the sequence. See 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
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