VCIP1_RAT
ID VCIP1_RAT Reviewed; 1221 AA.
AC Q8CF97; Q7TNK5;
DT 16-FEB-2004, integrated into UniProtKB/Swiss-Prot.
DT 23-NOV-2004, sequence version 2.
DT 03-AUG-2022, entry version 121.
DE RecName: Full=Deubiquitinating protein VCPIP1 {ECO:0000305};
DE EC=3.4.19.12 {ECO:0000269|PubMed:15037600};
DE AltName: Full=Valosin-containing protein p97/p47 complex-interacting protein 1 {ECO:0000305};
DE AltName: Full=Valosin-containing protein p97/p47 complex-interacting protein p135 {ECO:0000303|PubMed:12473691};
DE Short=VCP/p47 complex-interacting 135-kDa protein {ECO:0000303|PubMed:12473691};
GN Name=Vcpip1 {ECO:0000312|RGD:708520};
GN Synonyms=Vcip135 {ECO:0000303|PubMed:12473691};
OS Rattus norvegicus (Rat).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Rattus.
OX NCBI_TaxID=10116;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], PROTEIN SEQUENCE OF 870-878 AND 1095-1105,
RP FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH VCP, AND IDENTIFICATION BY
RP MASS SPECTROMETRY.
RX PubMed=12473691; DOI=10.1083/jcb.200208112;
RA Uchiyama K., Jokitalo E., Kano F., Murata M., Zhang X., Canas B.,
RA Newman R., Rabouille C., Pappin D., Freemont P., Kondo H.;
RT "VCIP135, a novel essential factor for p97/p47-mediated membrane fusion, is
RT required for Golgi and ER assembly in vivo.";
RL J. Cell Biol. 159:855-866(2002).
RN [2]
RP SEQUENCE REVISION TO 7.
RA Kondo H., Uchiyama K., Kondo H.;
RL Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, CATALYTIC ACTIVITY, AND MUTAGENESIS
RP OF CYS-218.
RC TISSUE=Liver;
RX PubMed=15037600; DOI=10.1083/jcb.200401010;
RA Wang Y., Satoh A., Warren G., Meyer H.H.;
RT "VCIP135 acts as a deubiquitinating enzyme during p97-p47-mediated
RT reassembly of mitotic Golgi fragments.";
RL J. Cell Biol. 164:973-978(2004).
RN [4]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-746 AND SER-1197, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22673903; DOI=10.1038/ncomms1871;
RA Lundby A., Secher A., Lage K., Nordsborg N.B., Dmytriyev A., Lundby C.,
RA Olsen J.V.;
RT "Quantitative maps of protein phosphorylation sites across 14 different rat
RT organs and tissues.";
RL Nat. Commun. 3:876-876(2012).
CC -!- FUNCTION: Deubiquitinating enzyme involved in DNA repair and reassembly
CC of the Golgi apparatus and the endoplasmic reticulum following mitosis
CC (PubMed:12473691, PubMed:15037600). Necessary for VCP-mediated
CC reassembly of Golgi stacks after mitosis (PubMed:12473691,
CC PubMed:15037600). Plays a role in VCP-mediated formation of
CC transitional endoplasmic reticulum (tER) (PubMed:12473691,
CC PubMed:15037600). Mediates dissociation of the ternary complex
CC containing STX5A, NSFL1C and VCP (PubMed:12473691, PubMed:15037600).
CC Also involved in DNA repair following phosphorylation by ATM or ATR:
CC acts by catalyzing deubiquitination of SPRTN, thereby promoting SPRTN
CC recruitment to chromatin and subsequent proteolytic cleavage of
CC covalent DNA-protein cross-links (DPCs) (By similarity). Hydrolyzes
CC 'Lys-11'- and 'Lys-48'-linked polyubiquitin chains (By similarity).
CC {ECO:0000250|UniProtKB:Q96JH7, ECO:0000269|PubMed:12473691,
CC ECO:0000269|PubMed:15037600}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Thiol-dependent hydrolysis of ester, thioester, amide, peptide
CC and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-
CC residue protein attached to proteins as an intracellular targeting
CC signal).; EC=3.4.19.12; Evidence={ECO:0000269|PubMed:15037600};
CC -!- SUBUNIT: Binds VCP and the ternary complex containing STX5A, NSFL1C and
CC VCP. {ECO:0000269|PubMed:12473691}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:Q96JH7}. Cytoplasm
CC {ECO:0000250|UniProtKB:Q96JH7}. Endoplasmic reticulum
CC {ECO:0000269|PubMed:12473691}. Golgi apparatus, Golgi stack
CC {ECO:0000269|PubMed:12473691}. Note=Associated with Golgi stacks and
CC endoplasmic reticulum (PubMed:12473691). Displays cytoplasmic to
CC nuclear translocation in response to DNA-protein cross-links (DPCs)-
CC inducing agents (By similarity). {ECO:0000250|UniProtKB:Q96JH7,
CC ECO:0000269|PubMed:12473691}.
CC -!- TISSUE SPECIFICITY: Widely expressed. {ECO:0000269|PubMed:12473691}.
CC -!- PTM: Phosphorylated at Ser-1206 by ATM or ATR following induction of
CC covalent DNA-protein cross-links (DPCs).
CC {ECO:0000250|UniProtKB:Q96JH7}.
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DR EMBL; AB045378; BAC44841.2; -; mRNA.
DR EMBL; AF289091; AAQ14350.1; -; mRNA.
DR RefSeq; NP_789827.3; NM_176857.3.
DR PDB; 2MX2; NMR; -; A=772-852.
DR PDBsum; 2MX2; -.
DR AlphaFoldDB; Q8CF97; -.
DR SMR; Q8CF97; -.
DR STRING; 10116.ENSRNOP00000009136; -.
DR MEROPS; C64.006; -.
DR iPTMnet; Q8CF97; -.
DR PhosphoSitePlus; Q8CF97; -.
DR jPOST; Q8CF97; -.
DR PaxDb; Q8CF97; -.
DR PRIDE; Q8CF97; -.
DR Ensembl; ENSRNOT00000009136; ENSRNOP00000009136; ENSRNOG00000006980.
DR GeneID; 286761; -.
DR KEGG; rno:286761; -.
DR UCSC; RGD:708520; rat.
DR CTD; 80124; -.
DR RGD; 708520; Vcpip1.
DR eggNOG; KOG4345; Eukaryota.
DR GeneTree; ENSGT00390000002854; -.
DR HOGENOM; CLU_009674_0_0_1; -.
DR InParanoid; Q8CF97; -.
DR OMA; VPMGLRN; -.
DR OrthoDB; 222681at2759; -.
DR PhylomeDB; Q8CF97; -.
DR TreeFam; TF329469; -.
DR Reactome; R-RNO-5689896; Ovarian tumor domain proteases.
DR PRO; PR:Q8CF97; -.
DR Proteomes; UP000002494; Chromosome 5.
DR Bgee; ENSRNOG00000006980; Expressed in testis and 18 other tissues.
DR Genevisible; Q8CF97; RN.
DR GO; GO:0005783; C:endoplasmic reticulum; IEA:UniProtKB-SubCell.
DR GO; GO:0005795; C:Golgi stack; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; ISS:UniProtKB.
DR GO; GO:0045202; C:synapse; ISO:RGD.
DR GO; GO:0004843; F:cysteine-type deubiquitinase activity; IDA:UniProtKB.
DR GO; GO:0006974; P:cellular response to DNA damage stimulus; ISS:UniProtKB.
DR GO; GO:0016320; P:endoplasmic reticulum membrane fusion; IDA:RGD.
DR GO; GO:0007030; P:Golgi organization; IMP:RGD.
DR GO; GO:0090168; P:Golgi reassembly; IDA:RGD.
DR GO; GO:0000278; P:mitotic cell cycle; IMP:RGD.
DR GO; GO:0016579; P:protein deubiquitination; ISS:UniProtKB.
DR GO; GO:0035871; P:protein K11-linked deubiquitination; ISS:UniProtKB.
DR GO; GO:0071108; P:protein K48-linked deubiquitination; ISS:UniProtKB.
DR GO; GO:0016567; P:protein ubiquitination; IDA:UniProtKB.
DR GO; GO:0106300; P:protein-DNA covalent cross-linking repair; ISS:UniProtKB.
DR GO; GO:1905634; P:regulation of protein localization to chromatin; ISS:UniProtKB.
DR InterPro; IPR003323; OTU_dom.
DR InterPro; IPR029071; Ubiquitin-like_domsf.
DR InterPro; IPR039087; VCPIP1.
DR InterPro; IPR045827; VCPIP1_N.
DR PANTHER; PTHR14843; PTHR14843; 1.
DR Pfam; PF02338; OTU; 1.
DR Pfam; PF19437; VCIP135_N; 1.
DR SUPFAM; SSF54236; SSF54236; 1.
DR PROSITE; PS50802; OTU; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Cytoplasm; Direct protein sequencing;
KW DNA damage; DNA repair; Endoplasmic reticulum; Golgi apparatus; Hydrolase;
KW Nucleus; Phosphoprotein; Protease; Reference proteome; Thiol protease;
KW Ubl conjugation pathway.
FT CHAIN 1..1221
FT /note="Deubiquitinating protein VCPIP1"
FT /id="PRO_0000065771"
FT DOMAIN 207..360
FT /note="OTU"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00139"
FT REGION 1..40
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 724..778
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 988..1009
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1117..1177
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1189..1221
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..21
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 740..774
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1129..1177
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 215
FT /evidence="ECO:0000250|UniProtKB:Q96FW1"
FT ACT_SITE 218
FT /note="Nucleophile"
FT /evidence="ECO:0000305|PubMed:15037600"
FT ACT_SITE 353
FT /evidence="ECO:0000250|UniProtKB:Q96FW1"
FT MOD_RES 407
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:Q96JH7"
FT MOD_RES 746
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:22673903"
FT MOD_RES 756
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q96JH7"
FT MOD_RES 762
FT /note="Phosphothreonine"
FT /evidence="ECO:0000250|UniProtKB:Q96JH7"
FT MOD_RES 767
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q96JH7"
FT MOD_RES 993
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q96JH7"
FT MOD_RES 997
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q96JH7"
FT MOD_RES 1076
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q96JH7"
FT MOD_RES 1197
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:22673903"
FT MOD_RES 1206
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q96JH7"
FT MUTAGEN 218
FT /note="C->A,S: Loss of deubiquitinating activity and
FT ability to promote VCP-mediated Golgi membrane fusion."
FT /evidence="ECO:0000269|PubMed:15037600"
FT CONFLICT 7
FT /note="P -> L (in Ref. 3; AAQ14350)"
FT /evidence="ECO:0000305"
FT CONFLICT 158
FT /note="D -> N (in Ref. 3; AAQ14350)"
FT /evidence="ECO:0000305"
FT CONFLICT 603
FT /note="R -> K (in Ref. 3; AAQ14350)"
FT /evidence="ECO:0000305"
FT CONFLICT 652
FT /note="H -> L (in Ref. 3; AAQ14350)"
FT /evidence="ECO:0000305"
FT CONFLICT 675
FT /note="I -> V (in Ref. 3; AAQ14350)"
FT /evidence="ECO:0000305"
FT STRAND 776..780
FT /evidence="ECO:0007829|PDB:2MX2"
FT TURN 781..783
FT /evidence="ECO:0007829|PDB:2MX2"
FT STRAND 784..788
FT /evidence="ECO:0007829|PDB:2MX2"
FT HELIX 796..806
FT /evidence="ECO:0007829|PDB:2MX2"
FT TURN 819..822
FT /evidence="ECO:0007829|PDB:2MX2"
FT TURN 830..834
FT /evidence="ECO:0007829|PDB:2MX2"
SQ SEQUENCE 1221 AA; 134566 MW; 23487E853AD9FD4B CRC64;
MSQPPPPPPL PPPPPPPEAP QTSSSLAAAA TPGGLSKRRD RRILSGSCPD PKCQARLFFP
ASGSVSIECT ECGQRHEQQQ LLGVEEVTDP DVVLHNLLRN ALLGVTGAPK KNTELVKVMG
LSNYHCKLLS PILARYGMDK QTGRAKLLRD MNQGELFDCA LLGDRAFLIE PEHVNTVGYG
KDRSGSLLYL HDTLEDIKRA NKSQECLIPV HVDGDGHCLV HAVSRALVGR ELFWHALREN
LKQHFQQHLA RYQALFHDFI DAAEWEDIIN ECDPLFVPPE GVPLGLRNIH IFGLANVLHR
PIILLDSLSG MRSSGDYSAT FLPGLIPAEK CTGRDGHLNK PICIAWSSSG RNHYIPLVGI
KGAALPKLPM NLLPKAWGVP QDLIKKYIKL EEDGGCVIGG DRSLQDKYLL RLVAAMEEVF
MDKHGIHPSL VADVHQYFYR RTGVIGVQPE EVTAAAKKAV MDNRLHKCLL CGALSELHVP
PEWLAPGGKL YNLAKSTHGQ LRPDKNYSFP LNNLVCSYDP VKDVLLPDYG LSNLTACNWC
HGTSVRRVRG DGSIVYLDGD RTNSRSTGGK CGCGFKHFWE GKEYDNLPEA FPITLEWGGR
VVRETVYWFQ YESDPSLNSN VYDVAMKLVT KHFPGEFGSE ILVQKVVHTI LHQTAKKNPD
DYTPVNIDGA HAQRIGDVQG QELESQLPTK IILTGQKTKT LHKEELNMSK TERTIQQNIT
EQASVMQKRK TEKLKQEQKG QPRTVSPSTI RDGPSSAPAT PTKAPYSPTT SKEKKIRITT
NDGRQSMVTL KSSTTFFELQ ESIAREFNIP PYLQCIRYGF PPKELMPPQA GMEKEPVPLQ
HGDRITIEIL KGKAEGGPST AAHSAHTVRQ EEIAVTGKLS SKELQEQADK EMYSLCLLAT
LMGEDVWSYA KGLPHMFQQG GVFYNIMKKT MGMADGKHCT FPHLPGKTFV YNASEDRLEL
CVDAAGHFPI GPDVEDLVKE AVSQVRAEAT TRSRESSPSH GLLKLGSGGV VKKKSEQLHN
VTAFQGKGHS LGTASSNPHM DPRARETLAV RKHNTGTDFS NSSIKTEPPV FTAASSNSEL
IRIAPGVVTM RDGRQIDPDV VEAQRKKLQE MVSSIQASMD KHLRDQSTEQ TPSDLSQRKV
EAVSSSVRPG NLQTGLPESF SLTGGTENLN TETTDSRVAD VLGAAFATRS KAQKENSMEE
PEEMDSQDAE TTNTTEPMDH S
