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Protein

Deubiquitinating protein VCIP135

Gene

Vcpip1

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Acts as a deubiquitinating enzyme. Necessary for VCP-mediated reassembly of Golgi stacks after mitosis. May play a role in VCP-mediated formation of transitional endoplasmic reticulum (tER). Mediates dissociation of the ternary complex containing STX5A, NSFL1C and VCP. Hydrolyzes 'Lys-11'- and 'Lys-48'-linked polyubiquitin chains.2 Publications

Catalytic activityi

Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei215By similarity1
Active sitei218NucleophileBy similarity1
Active sitei353By similarity1

GO - Molecular functioni

  • thiol-dependent ubiquitin-specific protease activity Source: UniProtKB

GO - Biological processi

  • endoplasmic reticulum membrane fusion Source: RGD
  • Golgi organization Source: RGD
  • Golgi reassembly Source: RGD
  • mitotic nuclear division Source: RGD
  • protein K11-linked deubiquitination Source: UniProtKB
  • protein K48-linked deubiquitination Source: UniProtKB
  • protein ubiquitination Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protease, Thiol protease

Keywords - Biological processi

Ubl conjugation pathway

Protein family/group databases

MEROPSiC64.006.

Names & Taxonomyi

Protein namesi
Recommended name:
Deubiquitinating protein VCIP135 (EC:3.4.19.12)
Alternative name(s):
Valosin-containing protein p97/p47 complex-interacting protein 1
Valosin-containing protein p97/p47 complex-interacting protein p135
Gene namesi
Name:Vcpip1
Synonyms:Vcip135
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 5

Organism-specific databases

RGDi708520. Vcpip1.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Endoplasmic reticulum, Golgi apparatus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi218C → A or S: Loss of deubiquitinating activity and ability to promote VCP-mediated Golgi membrane fusion. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000657711 – 1221Deubiquitinating protein VCIP135Add BLAST1221

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei407N6-acetyllysineBy similarity1
Modified residuei746PhosphoserineCombined sources1
Modified residuei756PhosphoserineBy similarity1
Modified residuei762PhosphothreonineBy similarity1
Modified residuei767PhosphoserineBy similarity1
Modified residuei993PhosphoserineBy similarity1
Modified residuei997PhosphoserineBy similarity1
Modified residuei1076PhosphoserineBy similarity1
Modified residuei1197PhosphoserineCombined sources1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

PaxDbiQ8CF97.
PRIDEiQ8CF97.

PTM databases

iPTMnetiQ8CF97.
PhosphoSitePlusiQ8CF97.

Expressioni

Tissue specificityi

Widely expressed.

Gene expression databases

BgeeiENSRNOG00000006980.
GenevisibleiQ8CF97. RN.

Interactioni

Subunit structurei

Binds VCP and the ternary complex containing STX5A, NSFL1C and VCP.

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000009136.

Structurei

Secondary structure

11221
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi776 – 780Combined sources5
Turni781 – 783Combined sources3
Beta strandi784 – 788Combined sources5
Helixi796 – 806Combined sources11
Turni819 – 822Combined sources4
Turni830 – 834Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2MX2NMR-A772-852[»]
ProteinModelPortaliQ8CF97.
SMRiQ8CF97.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini207 – 360OTUPROSITE-ProRule annotationAdd BLAST154

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi4 – 20Pro-richAdd BLAST17

Sequence similaritiesi

Contains 1 OTU domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiENOG410IQZJ. Eukaryota.
ENOG410ZMR9. LUCA.
GeneTreeiENSGT00390000002854.
HOGENOMiHOG000154813.
HOVERGENiHBG059748.
InParanoidiQ8CF97.
KOiK11861.
OMAiGCGFKHY.
OrthoDBiEOG091G03HK.
PhylomeDBiQ8CF97.
TreeFamiTF329469.

Family and domain databases

InterProiIPR003323. OTU_dom.
IPR029071. Ubiquitin-rel_dom.
[Graphical view]
PfamiPF02338. OTU. 1 hit.
[Graphical view]
SUPFAMiSSF54236. SSF54236. 1 hit.
PROSITEiPS50802. OTU. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q8CF97-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSQPPPPPPL PPPPPPPEAP QTSSSLAAAA TPGGLSKRRD RRILSGSCPD
60 70 80 90 100
PKCQARLFFP ASGSVSIECT ECGQRHEQQQ LLGVEEVTDP DVVLHNLLRN
110 120 130 140 150
ALLGVTGAPK KNTELVKVMG LSNYHCKLLS PILARYGMDK QTGRAKLLRD
160 170 180 190 200
MNQGELFDCA LLGDRAFLIE PEHVNTVGYG KDRSGSLLYL HDTLEDIKRA
210 220 230 240 250
NKSQECLIPV HVDGDGHCLV HAVSRALVGR ELFWHALREN LKQHFQQHLA
260 270 280 290 300
RYQALFHDFI DAAEWEDIIN ECDPLFVPPE GVPLGLRNIH IFGLANVLHR
310 320 330 340 350
PIILLDSLSG MRSSGDYSAT FLPGLIPAEK CTGRDGHLNK PICIAWSSSG
360 370 380 390 400
RNHYIPLVGI KGAALPKLPM NLLPKAWGVP QDLIKKYIKL EEDGGCVIGG
410 420 430 440 450
DRSLQDKYLL RLVAAMEEVF MDKHGIHPSL VADVHQYFYR RTGVIGVQPE
460 470 480 490 500
EVTAAAKKAV MDNRLHKCLL CGALSELHVP PEWLAPGGKL YNLAKSTHGQ
510 520 530 540 550
LRPDKNYSFP LNNLVCSYDP VKDVLLPDYG LSNLTACNWC HGTSVRRVRG
560 570 580 590 600
DGSIVYLDGD RTNSRSTGGK CGCGFKHFWE GKEYDNLPEA FPITLEWGGR
610 620 630 640 650
VVRETVYWFQ YESDPSLNSN VYDVAMKLVT KHFPGEFGSE ILVQKVVHTI
660 670 680 690 700
LHQTAKKNPD DYTPVNIDGA HAQRIGDVQG QELESQLPTK IILTGQKTKT
710 720 730 740 750
LHKEELNMSK TERTIQQNIT EQASVMQKRK TEKLKQEQKG QPRTVSPSTI
760 770 780 790 800
RDGPSSAPAT PTKAPYSPTT SKEKKIRITT NDGRQSMVTL KSSTTFFELQ
810 820 830 840 850
ESIAREFNIP PYLQCIRYGF PPKELMPPQA GMEKEPVPLQ HGDRITIEIL
860 870 880 890 900
KGKAEGGPST AAHSAHTVRQ EEIAVTGKLS SKELQEQADK EMYSLCLLAT
910 920 930 940 950
LMGEDVWSYA KGLPHMFQQG GVFYNIMKKT MGMADGKHCT FPHLPGKTFV
960 970 980 990 1000
YNASEDRLEL CVDAAGHFPI GPDVEDLVKE AVSQVRAEAT TRSRESSPSH
1010 1020 1030 1040 1050
GLLKLGSGGV VKKKSEQLHN VTAFQGKGHS LGTASSNPHM DPRARETLAV
1060 1070 1080 1090 1100
RKHNTGTDFS NSSIKTEPPV FTAASSNSEL IRIAPGVVTM RDGRQIDPDV
1110 1120 1130 1140 1150
VEAQRKKLQE MVSSIQASMD KHLRDQSTEQ TPSDLSQRKV EAVSSSVRPG
1160 1170 1180 1190 1200
NLQTGLPESF SLTGGTENLN TETTDSRVAD VLGAAFATRS KAQKENSMEE
1210 1220
PEEMDSQDAE TTNTTEPMDH S
Length:1,221
Mass (Da):134,566
Last modified:November 23, 2004 - v2
Checksum:i23487E853AD9FD4B
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti7P → L in AAQ14350 (PubMed:15037600).Curated1
Sequence conflicti158D → N in AAQ14350 (PubMed:15037600).Curated1
Sequence conflicti603R → K in AAQ14350 (PubMed:15037600).Curated1
Sequence conflicti652H → L in AAQ14350 (PubMed:15037600).Curated1
Sequence conflicti675I → V in AAQ14350 (PubMed:15037600).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB045378 mRNA. Translation: BAC44841.2.
AF289091 mRNA. Translation: AAQ14350.1.
RefSeqiNP_789827.3. NM_176857.3.
UniGeneiRn.204326.

Genome annotation databases

EnsembliENSRNOT00000009136; ENSRNOP00000009136; ENSRNOG00000006980.
GeneIDi286761.
KEGGirno:286761.
UCSCiRGD:708520. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB045378 mRNA. Translation: BAC44841.2.
AF289091 mRNA. Translation: AAQ14350.1.
RefSeqiNP_789827.3. NM_176857.3.
UniGeneiRn.204326.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2MX2NMR-A772-852[»]
ProteinModelPortaliQ8CF97.
SMRiQ8CF97.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000009136.

Protein family/group databases

MEROPSiC64.006.

PTM databases

iPTMnetiQ8CF97.
PhosphoSitePlusiQ8CF97.

Proteomic databases

PaxDbiQ8CF97.
PRIDEiQ8CF97.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000009136; ENSRNOP00000009136; ENSRNOG00000006980.
GeneIDi286761.
KEGGirno:286761.
UCSCiRGD:708520. rat.

Organism-specific databases

CTDi80124.
RGDi708520. Vcpip1.

Phylogenomic databases

eggNOGiENOG410IQZJ. Eukaryota.
ENOG410ZMR9. LUCA.
GeneTreeiENSGT00390000002854.
HOGENOMiHOG000154813.
HOVERGENiHBG059748.
InParanoidiQ8CF97.
KOiK11861.
OMAiGCGFKHY.
OrthoDBiEOG091G03HK.
PhylomeDBiQ8CF97.
TreeFamiTF329469.

Miscellaneous databases

PROiQ8CF97.

Gene expression databases

BgeeiENSRNOG00000006980.
GenevisibleiQ8CF97. RN.

Family and domain databases

InterProiIPR003323. OTU_dom.
IPR029071. Ubiquitin-rel_dom.
[Graphical view]
PfamiPF02338. OTU. 1 hit.
[Graphical view]
SUPFAMiSSF54236. SSF54236. 1 hit.
PROSITEiPS50802. OTU. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiVCIP1_RAT
AccessioniPrimary (citable) accession number: Q8CF97
Secondary accession number(s): Q7TNK5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 16, 2004
Last sequence update: November 23, 2004
Last modified: November 2, 2016
This is version 99 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. 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.