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Protein

E3 ubiquitin-protein ligase synoviolin

Gene

Syvn1

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Acts as an E3 ubiquitin-protein ligase which accepts ubiquitin specifically from endoplasmic reticulum-associated UBC7 E2 ligase and transfers it to substrates, promoting their degradation. Component of the endoplasmic reticulum quality control (ERQC) system also called ER-associated degradation (ERAD) involved in ubiquitin-dependent degradation of misfolded endoplasmic reticulum proteins. Also promotes the degradation of normal but naturally short-lived proteins such as SGK. Protects cells from ER stress-induced apoptosis. Sequesters p53/TP53 in the cytoplasm and promotes its degradation, thereby negatively regulating its biological function in transcription, cell cycle regulation and apoptosis. Required for embryogenesis.3 Publications

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)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri291 – 33040RING-type; atypicalPROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Developmental protein, 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 synoviolin (EC:6.3.2.-)
Alternative name(s):
Synovial apoptosis inhibitor 1
Gene namesi
Name:Syvn1
Synonyms:Hrd1, Kiaa1810
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Unplaced

Organism-specific databases

MGIiMGI:1921376. Syvn1.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini23 – 4119LumenalSequence analysisAdd
BLAST
Transmembranei42 – 6221HelicalSequence analysisAdd
BLAST
Topological domaini63 – 9836CytoplasmicSequence analysisAdd
BLAST
Transmembranei99 – 11921HelicalSequence analysisAdd
BLAST
Topological domaini120 – 14021LumenalSequence analysisAdd
BLAST
Transmembranei141 – 16121HelicalSequence analysisAdd
BLAST
Topological domaini162 – 1698CytoplasmicSequence analysis
Transmembranei170 – 19021HelicalSequence analysisAdd
BLAST
Topological domaini191 – 22434LumenalSequence analysisAdd
BLAST
Transmembranei225 – 24521HelicalSequence analysisAdd
BLAST
Topological domaini246 – 612367CytoplasmicSequence analysisAdd
BLAST

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Endoplasmic reticulum, Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2222Sequence analysisAdd
BLAST
Chaini23 – 612590E3 ubiquitin-protein ligase synoviolinPRO_0000280549Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei608 – 6081PhosphoserineBy similarity

Post-translational modificationi

Auto-ubiquitinated.By similarity

Keywords - PTMi

Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiQ9DBY1.
PaxDbiQ9DBY1.
PeptideAtlasiQ9DBY1.
PRIDEiQ9DBY1.

PTM databases

iPTMnetiQ9DBY1.
PhosphoSiteiQ9DBY1.

Expressioni

Tissue specificityi

Ubiquitously expressed, with highest levels in bone, spleen, lung and testis. In the brain, present in neurons but not in glial cells. Up-regulated in synovial tissues from mice with collagen-induced arthritis (at protein level).2 Publications

Inductioni

By cerebral ischemia.1 Publication

Gene expression databases

BgeeiENSMUSG00000024807.
CleanExiMM_SYVN1.

Interactioni

Subunit structurei

Homodimer. Interacts with p53/TP53 and HTT. Interacts with VCP, HERPUD1 and DERL1. Part of a complex containing SYVN1, HERPUD1, SELS and DERL1; which probably transfer misfolded proteins from the ER to VCP. Part of a complex containing SYVN1, SEL1L and DERL2. Interacts with UBXN6. Interacts (via N-terminal loop) with SEL1L; recruits ERLEC1 and OS9. May form a complex with ERLEC1; HSPA5; OS9 AND SEL1L (By similarity).By similarity1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
NcstnP577162EBI-644384,EBI-998934

GO - Molecular functioni

Protein-protein interaction databases

BioGridi216511. 4 interactions.
IntActiQ9DBY1. 5 interactions.
MINTiMINT-1662447.
STRINGi10090.ENSMUSP00000114843.

Structurei

3D structure databases

ProteinModelPortaliQ9DBY1.
SMRiQ9DBY1. Positions 291-331.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni21 – 4222Interaction with SEL1L1 PublicationAdd
BLAST
Regioni236 – 27035Interaction with p53/TP53Add
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi339 – 472134Pro-richAdd
BLAST
Compositional biasi599 – 6024Poly-Arg

Domaini

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

Sequence similaritiesi

Belongs to the HRD1 family.Curated
Contains 1 RING-type zinc finger.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri291 – 33040RING-type; atypicalPROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Signal, Transmembrane, Transmembrane helix, Zinc-finger

Phylogenomic databases

eggNOGiKOG0802. Eukaryota.
COG5243. LUCA.
HOGENOMiHOG000294196.
HOVERGENiHBG094015.
InParanoidiQ9DBY1.
KOiK10601.
PhylomeDBiQ9DBY1.
TreeFamiTF318635.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR032832. E3_lig_synoviolin/Hrd1.
IPR001841. Znf_RING.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PANTHERiPTHR22763:SF25. PTHR22763:SF25. 1 hit.
PfamiPF13639. zf-RING_2. 1 hit.
[Graphical view]
SMARTiSM00184. RING. 1 hit.
[Graphical view]
PROSITEiPS50089. ZF_RING_2. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9DBY1-1) [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
MFRTAVMMAA SLALTGAVVA HAYYLKHQFY PTVVYLTKSS PSMAVLYIQA
60 70 80 90 100
FVLVFLLGKV MGKVFFGQLR AAEMEHLLER SWYAVTETCL AFTVFRDDFS
110 120 130 140 150
PRFVALFTLL LFLKCFHWLA EDRVDFMERS PNISWLFHCR IVSLMFLLGI
160 170 180 190 200
LDFLFVSHAY HSILTRGASV QLVFGFEYAI LMTMVLTIFI KYVLHSVDLQ
210 220 230 240 250
SENPWDNKAV YMLYTELFTG FIKVLLYMAF MTIMIKVHTF PLFAIRPMYL
260 270 280 290 300
AMRQFKKAVT DAIMSRRAIR NMNTLYPDAT PEELQAVDNV CIICREEMVT
310 320 330 340 350
GAKRLPCNHI FHTSCLRSWF QRQQTCPTCR MDVLRASLPA QSPPPPEPAD
360 370 380 390 400
QGPPPAPHPQ PLLPQPPNFP QGLLPPFPPG MFPLWPPMGP FPPVPPPPSS
410 420 430 440 450
GEAAAPPPTS TAVSRPSGAA TTTAAGTSTS APAPGSVPGP EAGPAPGFPF
460 470 480 490 500
PPPWMGMPLP PPFAFPPMPV PPAGFAGLTP EELRALEGHE RQHLEARLQS
510 520 530 540 550
LRNIHTLLDA AMLQINQYLT VLASLGPPRP ATSVNPTEET ASTVVSAAPS
560 570 580 590 600
TSAPSSEAPT PSPGASPPIP EAEKPPAPES VGIVEELPED GEPDAAELRR
610
RRLQKLESPV AH
Length:612
Mass (Da):67,296
Last modified:March 20, 2007 - v3
Checksum:i8F7620E5016DF1F2
GO
Isoform 2 (identifier: Q9DBY1-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     75-75: E → EVICWWPQRTGFRGGYPNDWFSYHPLLTPQ
     127-177: Missing.
     369-375: FPQGLLP → CKWPFIC
     577-578: AP → GK
     579-612: Missing.

Note: No experimental confirmation available.
Show »
Length:556
Mass (Da):61,254
Checksum:i1566257B166A4A97
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti287 – 2871V → M in BAB23474 (PubMed:16141072).Curated
Sequence conflicti287 – 2871V → M in AAH46829 (PubMed:15489334).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei75 – 751E → EVICWWPQRTGFRGGYPNDW FSYHPLLTPQ in isoform 2. 1 PublicationVSP_023779
Alternative sequencei127 – 17751Missing in isoform 2. 1 PublicationVSP_023780Add
BLAST
Alternative sequencei369 – 3757FPQGLLP → CKWPFIC in isoform 2. 1 PublicationVSP_023781
Alternative sequencei577 – 5782AP → GK in isoform 2. 1 PublicationVSP_023782
Alternative sequencei579 – 61234Missing in isoform 2. 1 PublicationVSP_023783Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK122558 Transcribed RNA. Translation: BAC65840.3. Sequence problems.
AK004688 mRNA. Translation: BAB23474.2.
BC042199 mRNA. Translation: AAH42199.1.
BC046829 mRNA. Translation: AAH46829.1.
BC057917 mRNA. Translation: AAH57917.1.
BC080722 mRNA. Translation: AAH80722.1.
CCDSiCCDS29487.1. [Q9DBY1-1]
RefSeqiNP_001158181.1. NM_001164709.1.
NP_083045.4. NM_028769.5.
XP_006531913.1. XM_006531850.2.
UniGeneiMm.149870.

Genome annotation databases

GeneIDi74126.
KEGGimmu:74126.
UCSCiuc008ggm.2. mouse. [Q9DBY1-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK122558 Transcribed RNA. Translation: BAC65840.3. Sequence problems.
AK004688 mRNA. Translation: BAB23474.2.
BC042199 mRNA. Translation: AAH42199.1.
BC046829 mRNA. Translation: AAH46829.1.
BC057917 mRNA. Translation: AAH57917.1.
BC080722 mRNA. Translation: AAH80722.1.
CCDSiCCDS29487.1. [Q9DBY1-1]
RefSeqiNP_001158181.1. NM_001164709.1.
NP_083045.4. NM_028769.5.
XP_006531913.1. XM_006531850.2.
UniGeneiMm.149870.

3D structure databases

ProteinModelPortaliQ9DBY1.
SMRiQ9DBY1. Positions 291-331.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi216511. 4 interactions.
IntActiQ9DBY1. 5 interactions.
MINTiMINT-1662447.
STRINGi10090.ENSMUSP00000114843.

PTM databases

iPTMnetiQ9DBY1.
PhosphoSiteiQ9DBY1.

Proteomic databases

MaxQBiQ9DBY1.
PaxDbiQ9DBY1.
PeptideAtlasiQ9DBY1.
PRIDEiQ9DBY1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi74126.
KEGGimmu:74126.
UCSCiuc008ggm.2. mouse. [Q9DBY1-1]

Organism-specific databases

CTDi84447.
MGIiMGI:1921376. Syvn1.
RougeiSearch...

Phylogenomic databases

eggNOGiKOG0802. Eukaryota.
COG5243. LUCA.
HOGENOMiHOG000294196.
HOVERGENiHBG094015.
InParanoidiQ9DBY1.
KOiK10601.
PhylomeDBiQ9DBY1.
TreeFamiTF318635.

Enzyme and pathway databases

UniPathwayiUPA00143.

Miscellaneous databases

ChiTaRSiSyvn1. mouse.
PROiQ9DBY1.
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000024807.
CleanExiMM_SYVN1.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR032832. E3_lig_synoviolin/Hrd1.
IPR001841. Znf_RING.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PANTHERiPTHR22763:SF25. PTHR22763:SF25. 1 hit.
PfamiPF13639. zf-RING_2. 1 hit.
[Graphical view]
SMARTiSM00184. RING. 1 hit.
[Graphical view]
PROSITEiPS50089. ZF_RING_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiSYVN1_MOUSE
AccessioniPrimary (citable) accession number: Q9DBY1
Secondary accession number(s): Q80T88, Q8CGB5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 20, 2007
Last sequence update: March 20, 2007
Last modified: September 7, 2016
This is version 132 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Miscellaneous

Mice overexpressing Syvn1 develop severe spontaneous arthropathy. Mice lacking Syvn1 die in utero around E13.5 due to augmented apoptotic cell death.

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. 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.