TERA_DANRE
ID TERA_DANRE Reviewed; 806 AA.
AC Q7ZU99; Q76KA4;
DT 01-SEP-2009, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 154.
DE RecName: Full=Transitional endoplasmic reticulum ATPase {ECO:0000250|UniProtKB:P23787};
DE Short=TER ATPase {ECO:0000250|UniProtKB:P23787};
DE EC=3.6.4.6 {ECO:0000250|UniProtKB:P23787};
DE AltName: Full=Protein CDC48 {ECO:0000303|PubMed:12914916, ECO:0000312|EMBL:BAC87740.1};
DE AltName: Full=Valosin-containing protein {ECO:0000303|PubMed:12914916, ECO:0000312|EMBL:AAH50488.1};
DE Short=VCP {ECO:0000250|UniProtKB:P23787, ECO:0000303|PubMed:12914916};
GN Name=vcp {ECO:0000312|EMBL:AAH50488.1,
GN ECO:0000312|ZFIN:ZDB-GENE-030131-5408}; Synonyms=cdc48;
GN ORFNames=si:ch211-113n10.2;
OS Danio rerio (Zebrafish) (Brachydanio rerio).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
OC Danionidae; Danioninae; Danio.
OX NCBI_TaxID=7955;
RN [1] {ECO:0000305, ECO:0000312|EMBL:BAC87740.1}
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, INDUCTION, AND MUTAGENESIS OF
RP TYR-805.
RC TISSUE=Embryo {ECO:0000269|PubMed:12914916};
RX PubMed=12914916; DOI=10.1016/s0014-5793(03)00723-3;
RA Imamura S., Ojima N., Yamashita M.;
RT "Cold-inducible expression of the cell division cycle gene CDC48 and its
RT promotion of cell proliferation during cold acclimation in zebrafish
RT cells.";
RL FEBS Lett. 549:14-20(2003).
RN [2] {ECO:0000305, ECO:0000312|EMBL:AAS92631.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Kidney marrow {ECO:0000269|PubMed:15520368};
RX PubMed=15520368; DOI=10.1073/pnas.0407241101;
RA Song H.-D., Sun X.-J., Deng M., Zhang G.-W., Zhou Y., Wu X.-Y., Sheng Y.,
RA Chen Y., Ruan Z., Jiang C.-L., Fan H.-Y., Zon L.I., Kanki J.P., Liu T.X.,
RA Look A.T., Chen Z.;
RT "Hematopoietic gene expression profile in zebrafish kidney marrow.";
RL Proc. Natl. Acad. Sci. U.S.A. 101:16240-16245(2004).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Tuebingen;
RX PubMed=23594743; DOI=10.1038/nature12111;
RA Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M.,
RA Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I.,
RA Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.,
RA White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y.,
RA Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B.,
RA Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S.,
RA Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M.,
RA Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J.,
RA Clee C., Oliver K., Clark R., Riddle C., Elliot D., Threadgold G.,
RA Harden G., Ware D., Begum S., Mortimore B., Kerry G., Heath P.,
RA Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S.,
RA Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N.,
RA Lloyd C., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J.,
RA Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J.,
RA Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D.,
RA McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S.,
RA Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E.,
RA Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A.,
RA Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P.,
RA Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J.,
RA Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E.,
RA Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C.,
RA Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C.,
RA Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M.,
RA Oberlander M., Rudolph-Geiger S., Teucke M., Lanz C., Raddatz G.,
RA Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F.,
RA Schuster S.C., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M.,
RA Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M.,
RA de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C.,
RA Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.;
RT "The zebrafish reference genome sequence and its relationship to the human
RT genome.";
RL Nature 496:498-503(2013).
RN [4] {ECO:0000312|EMBL:CAM13143.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=AB {ECO:0000312|EMBL:AAH50488.1};
RC TISSUE=Kidney {ECO:0000312|EMBL:AAH67384.1};
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (MAR-2004) to the EMBL/GenBank/DDBJ databases.
RN [5] {ECO:0000305}
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-3, AND IDENTIFICATION BY MASS
RP SPECTROMETRY.
RC TISSUE=Embryo {ECO:0000269|PubMed:18307296};
RX PubMed=18307296; DOI=10.1021/pr700667w;
RA Lemeer S., Pinkse M.W.H., Mohammed S., van Breukelen B., den Hertog J.,
RA Slijper M., Heck A.J.R.;
RT "Online automated in vivo zebrafish phosphoproteomics: from large-scale
RT analysis down to a single embryo.";
RL J. Proteome Res. 7:1555-1564(2008).
CC -!- FUNCTION: Necessary for the fragmentation of Golgi stacks during
CC mitosis and for their reassembly after mitosis. Involved in the
CC formation of the nuclear envelope, and of the transitional endoplasmic
CC reticulum (tER). The transfer of membranes from the endoplasmic
CC reticulum to the Golgi apparatus occurs via 50-70 nm transition
CC vesicles which derive from part-rough, part-smooth transitional
CC elements of the endoplasmic reticulum (tER). Vesicle budding from the
CC tER is an ATP-dependent process. Also involved in DNA damage response:
CC recruited to double-strand breaks (DSBs) sites and promotes the
CC recruitment of tp53bp1 at DNA damage sites (By similarity). Together
CC with sprtn metalloprotease, involved in the repair of covalent DNA-
CC protein cross-links (DPCs) during DNA synthesis (By similarity).
CC Involved in interstrand cross-link repair in response to replication
CC stress by mediating unloading of the ubiquitinated CMG helicase complex
CC (By similarity). Enhances cell cycle progression and inhibits apoptosis
CC at low temperatures (PubMed:12914916). Essential for the maturation of
CC ubiquitin-containing autophagosomes and the clearance of ubiquitinated
CC protein by autophagy (By similarity). Acts as a negative regulator of
CC type I interferon production by promoting ubiquitination of ddx58/rig-i
CC (By similarity). May play a role in the ubiquitin-dependent sorting of
CC membrane proteins to lysosomes where they undergo degradation (By
CC similarity). May more particularly play a role in caveolins sorting in
CC cells (By similarity). By controlling the steady-state expression of
CC the IGF1R receptor, indirectly regulates the insulin-like growth factor
CC receptor signaling pathway (By similarity).
CC {ECO:0000250|UniProtKB:P23787, ECO:0000250|UniProtKB:P46462,
CC ECO:0000250|UniProtKB:P55072, ECO:0000269|PubMed:12914916}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.6;
CC Evidence={ECO:0000250|UniProtKB:P23787};
CC -!- SUBUNIT: Homohexamer. {ECO:0000250|UniProtKB:P23787}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm, cytosol
CC {ECO:0000250|UniProtKB:P23787}. Endoplasmic reticulum
CC {ECO:0000250|UniProtKB:P55072}. Nucleus {ECO:0000250|UniProtKB:P23787}.
CC -!- INDUCTION: By cold. {ECO:0000269|PubMed:12914916}.
CC -!- SIMILARITY: Belongs to the AAA ATPase family. {ECO:0000255}.
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DR EMBL; AB093594; BAC87740.1; -; mRNA.
DR EMBL; AY576993; AAS92631.1; -; mRNA.
DR EMBL; CR318632; CAM13143.1; -; Genomic_DNA.
DR EMBL; BC050488; AAH50488.1; -; mRNA.
DR EMBL; BC067384; AAH67384.1; -; mRNA.
DR RefSeq; NP_958889.1; NM_201481.1.
DR AlphaFoldDB; Q7ZU99; -.
DR SMR; Q7ZU99; -.
DR IntAct; Q7ZU99; 1.
DR MINT; Q7ZU99; -.
DR STRING; 7955.ENSDARP00000012048; -.
DR iPTMnet; Q7ZU99; -.
DR PaxDb; Q7ZU99; -.
DR PRIDE; Q7ZU99; -.
DR Ensembl; ENSDART00000023779; ENSDARP00000012048; ENSDARG00000020008.
DR GeneID; 327197; -.
DR KEGG; dre:327197; -.
DR CTD; 7415; -.
DR ZFIN; ZDB-GENE-030131-5408; vcp.
DR eggNOG; KOG0730; Eukaryota.
DR GeneTree; ENSGT00900000141071; -.
DR HOGENOM; CLU_000688_12_0_1; -.
DR InParanoid; Q7ZU99; -.
DR OMA; HACHDIK; -.
DR OrthoDB; 194195at2759; -.
DR PhylomeDB; Q7ZU99; -.
DR TreeFam; TF300542; -.
DR Reactome; R-DRE-110320; Translesion Synthesis by POLH.
DR Reactome; R-DRE-3371511; HSF1 activation.
DR Reactome; R-DRE-382556; ABC-family proteins mediated transport.
DR Reactome; R-DRE-532668; N-glycan trimming in the ER and Calnexin/Calreticulin cycle.
DR Reactome; R-DRE-5358346; Hedgehog ligand biogenesis.
DR Reactome; R-DRE-5689877; Josephin domain DUBs.
DR Reactome; R-DRE-5689896; Ovarian tumor domain proteases.
DR Reactome; R-DRE-6798695; Neutrophil degranulation.
DR Reactome; R-DRE-8876725; Protein methylation.
DR Reactome; R-DRE-8951664; Neddylation.
DR Reactome; R-DRE-9013407; RHOH GTPase cycle.
DR Reactome; R-DRE-9755511; KEAP1-NFE2L2 pathway.
DR PRO; PR:Q7ZU99; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Chromosome 5.
DR Bgee; ENSDARG00000020008; Expressed in testis and 24 other tissues.
DR GO; GO:0005737; C:cytoplasm; ISS:UniProtKB.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0035861; C:site of double-strand break; ISS:UniProtKB.
DR GO; GO:0034098; C:VCP-NPL4-UFD1 AAA ATPase complex; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016887; F:ATP hydrolysis activity; IBA:GO_Central.
DR GO; GO:0008289; F:lipid binding; IEA:UniProtKB-KW.
DR GO; GO:0031593; F:polyubiquitin modification-dependent protein binding; IBA:GO_Central.
DR GO; GO:0097352; P:autophagosome maturation; ISS:UniProtKB.
DR GO; GO:0006914; P:autophagy; ISS:UniProtKB.
DR GO; GO:0006974; P:cellular response to DNA damage stimulus; ISS:UniProtKB.
DR GO; GO:0043009; P:chordate embryonic development; IMP:ZFIN.
DR GO; GO:0006281; P:DNA repair; ISS:UniProtKB.
DR GO; GO:0006302; P:double-strand break repair; ISS:UniProtKB.
DR GO; GO:0032510; P:endosome to lysosome transport via multivesicular body sorting pathway; ISS:UniProtKB.
DR GO; GO:0071712; P:ER-associated misfolded protein catabolic process; IBA:GO_Central.
DR GO; GO:0036503; P:ERAD pathway; ISS:UniProtKB.
DR GO; GO:0036297; P:interstrand cross-link repair; ISS:UniProtKB.
DR GO; GO:0007626; P:locomotory behavior; IMP:ZFIN.
DR GO; GO:0016236; P:macroautophagy; ISS:UniProtKB.
DR GO; GO:0051228; P:mitotic spindle disassembly; IBA:GO_Central.
DR GO; GO:0043161; P:proteasome-mediated ubiquitin-dependent protein catabolic process; ISS:UniProtKB.
DR GO; GO:0016567; P:protein ubiquitination; ISS:UniProtKB.
DR GO; GO:0010506; P:regulation of autophagy; IMP:ZFIN.
DR GO; GO:0032434; P:regulation of proteasomal ubiquitin-dependent protein catabolic process; IMP:ZFIN.
DR GO; GO:1905634; P:regulation of protein localization to chromatin; ISS:UniProtKB.
DR GO; GO:2000058; P:regulation of ubiquitin-dependent protein catabolic process; IMP:ZFIN.
DR GO; GO:0030970; P:retrograde protein transport, ER to cytosol; IBA:GO_Central.
DR GO; GO:0019985; P:translesion synthesis; ISS:UniProtKB.
DR GO; GO:0030433; P:ubiquitin-dependent ERAD pathway; ISS:UniProtKB.
DR Gene3D; 3.40.50.300; -; 2.
DR InterPro; IPR003593; AAA+_ATPase.
DR InterPro; IPR005938; AAA_ATPase_CDC48.
DR InterPro; IPR041569; AAA_lid_3.
DR InterPro; IPR009010; Asp_de-COase-like_dom_sf.
DR InterPro; IPR003959; ATPase_AAA_core.
DR InterPro; IPR003960; ATPase_AAA_CS.
DR InterPro; IPR004201; Cdc48_dom2.
DR InterPro; IPR029067; CDC48_domain_2-like_sf.
DR InterPro; IPR003338; CDC4_N-term_subdom.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR015415; Vps4_C.
DR Pfam; PF00004; AAA; 2.
DR Pfam; PF17862; AAA_lid_3; 2.
DR Pfam; PF02933; CDC48_2; 1.
DR Pfam; PF02359; CDC48_N; 1.
DR Pfam; PF09336; Vps4_C; 1.
DR SMART; SM00382; AAA; 2.
DR SMART; SM01072; CDC48_2; 1.
DR SMART; SM01073; CDC48_N; 1.
DR SUPFAM; SSF50692; SSF50692; 1.
DR SUPFAM; SSF52540; SSF52540; 2.
DR SUPFAM; SSF54585; SSF54585; 1.
DR TIGRFAMs; TIGR01243; CDC48; 1.
DR PROSITE; PS00674; AAA; 2.
PE 1: Evidence at protein level;
KW ATP-binding; Autophagy; Cell cycle; Cytoplasm; DNA damage; DNA repair;
KW Endoplasmic reticulum; Hydrolase; Lipid-binding; Nucleotide-binding;
KW Nucleus; Phosphoprotein; Reference proteome; Transport.
FT CHAIN 1..806
FT /note="Transitional endoplasmic reticulum ATPase"
FT /id="PRO_0000382233"
FT REGION 708..727
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 768..806
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 768..794
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 247..253
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P55072"
FT BINDING 348
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P55072"
FT BINDING 384
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P55072"
FT BINDING 521..526
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q01853"
FT MOD_RES 3
FT /note="Phosphoserine"
FT /evidence="ECO:0000269|PubMed:18307296"
FT MUTAGEN 805
FT /note="Y->A: Inhibits cell-proliferation and enhances
FT apoptosis at low temperatures."
FT /evidence="ECO:0000269|PubMed:12914916"
FT CONFLICT 641..643
FT /note="QLI -> HIM (in Ref. 1; BAC87740)"
FT /evidence="ECO:0000305"
FT CONFLICT 709
FT /note="R -> L (in Ref. 1; BAC87740)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 806 AA; 89424 MW; E126C61DFD7EE174 CRC64;
MASGGESKND DLSTAILKQK NRPNRLIVDE SINEDNSVVS LSQAKMDELQ LFRGDTVLLK
GKKRRETVCI VLSDDTCSDE KVRMNRVVRN NLRVRLGDVI SIQPCPDVKY GKRIHVLPID
DTVEGITGNL FEVYLKPYFL EAYRPIRKGD IFLVRGGMRA VEFKVVETDP SPYCIVAPDT
VIHCEGEPIK REDEEESLNE VGYDDIGGVR KQLAQIKEMV ELPLRHPALF KAIGVKPPRG
ILLYGPPGTG KTLIARAVAN ETGAFFFLIN GPEIMSKLAG ESESNLRKAF EEAEKNAPAI
IFIDELDAIA PKREKTHGEV ERRIVSQLLT LMDGLKQRAH VIVMAATNRP NSIDPALRRF
GRFDREVDIG IPDATGRLEI LQIHTKNMKL ADDVDLEQVA NETHGHVGAD LAALCSEAAL
QAIRKKMDLI DLEDETIDAE VMNSLAVTMD DFRWALSQSN PSALRETVVE VPNITWEDIG
GLDDVKRELQ ELVQYPVEHP DKFLKFGMTP SKGVLFYGPP GCGKTLLAKA IANECQANFI
SIKGPELLTM WFGESEANVR EIFDKARQAA PCVLFFDELD SIAKARGGNV GDGGGAADRV
INQILTEMDG MSSKKNVFII GATNRPDIID PAILRPGRLD QLIYIPLPDE KSRIAILKAN
LRKSPISKDV DLDFLAKMTN GFSGADLTEI CQRACKLAIR ESIENEIRRE RERQTNPSAM
EVEEDDPVPE IRKDHFEEAM RFARRSVSDN DIRKYEMFAQ TLQQSRGFGS FRFPSSNQGG
SGPSQGSSGG GGGNVFNEDN DDDLYG
