ID   VA0D1_MOUSE             Reviewed;         351 AA.
AC   P51863; Q54A57; Q9QWJ2;
DT   01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT   11-JAN-2001, sequence version 2.
DT   24-JAN-2024, entry version 186.
DE   RecName: Full=V-type proton ATPase subunit d 1;
DE            Short=V-ATPase subunit d 1;
DE   AltName: Full=P39;
DE   AltName: Full=Physophilin;
DE   AltName: Full=V-ATPase 40 kDa accessory protein;
DE   AltName: Full=V-ATPase AC39 subunit;
DE   AltName: Full=Vacuolar proton pump subunit d 1;
GN   Name=Atp6v0d1 {ECO:0000312|MGI:MGI:1201778}; Synonyms=Atp6d;
OS   Mus musculus (Mouse).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC   Murinae; Mus; Mus.
OX   NCBI_TaxID=10090;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [MRNA].
RA   Howell M.L., Dean G.E.;
RT   "cDNA sequences for mouse vacuolar ATPase subunits.";
RL   Submitted (AUG-1994) to the EMBL/GenBank/DDBJ databases.
RN   [2]
RP   NUCLEOTIDE SEQUENCE [MRNA].
RC   STRAIN=BALB/cJ; TISSUE=Brain;
RX   PubMed=9753184; DOI=10.1046/j.1460-9568.1998.00130.x;
RA   Carrion-Vazquez M., Fernandez A.M., Chowen J., Nieto-Sampedro M.;
RT   "Brain Ac39/physophilin: cloning, coexpression and colocalization with
RT   synaptophysin.";
RL   Eur. J. Neurosci. 10:1153-1166(1998).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [MRNA], AND TISSUE SPECIFICITY.
RX   PubMed=12527205; DOI=10.1016/s0378-1119(02)01099-5;
RA   Sun-Wada G.-H., Yoshimizu T., Imai-Senga Y., Wada Y., Futai M.;
RT   "Diversity of mouse proton-translocating ATPase: presence of multiple
RT   isoforms of the C, d and G subunits.";
RL   Gene 302:147-153(2003).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   STRAIN=C57BL/6J; TISSUE=Thymus;
RX   PubMed=16141072; DOI=10.1126/science.1112014;
RA   Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N.,
RA   Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K.,
RA   Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.,
RA   Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R.,
RA   Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T.,
RA   Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A.,
RA   Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B.,
RA   Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M.,
RA   Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S.,
RA   Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E.,
RA   Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D.,
RA   Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M.,
RA   Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H.,
RA   Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V.,
RA   Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S.,
RA   Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H.,
RA   Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N.,
RA   Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F.,
RA   Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G.,
RA   Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z.,
RA   Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C.,
RA   Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y.,
RA   Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S.,
RA   Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K.,
RA   Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R.,
RA   van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H.,
RA   Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M.,
RA   Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C.,
RA   Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S.,
RA   Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K.,
RA   Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M.,
RA   Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C.,
RA   Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A.,
RA   Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.;
RT   "The transcriptional landscape of the mammalian genome.";
RL   Science 309:1559-1563(2005).
RN   [5]
RP   PROTEIN SEQUENCE OF 25-73; 87-128; 188-237; 240-288; 294-300; 304-320;
RP   328-339 AND 344-351, AND IDENTIFICATION BY MASS SPECTROMETRY.
RC   STRAIN=C57BL/6J; TISSUE=Brain;
RA   Lubec G., Kang S.U.;
RL   Submitted (APR-2007) to UniProtKB.
RN   [6]
RP   FUNCTION, TISSUE SPECIFICITY, AND DEVELOPMENTAL STAGE.
RX   PubMed=12963731; DOI=10.1074/jbc.m303924200;
RA   Nishi T., Kawasaki-Nishi S., Forgac M.;
RT   "Expression and function of the mouse V-ATPase d subunit isoforms.";
RL   J. Biol. Chem. 278:46396-46402(2003).
RN   [7]
RP   PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-270, AND IDENTIFICATION BY
RP   MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC   TISSUE=Brain;
RX   PubMed=18034455; DOI=10.1021/pr0701254;
RA   Ballif B.A., Carey G.R., Sunyaev S.R., Gygi S.P.;
RT   "Large-scale identification and evolution indexing of tyrosine
RT   phosphorylation sites from murine brain.";
RL   J. Proteome Res. 7:311-318(2008).
RN   [8]
RP   PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-283, AND IDENTIFICATION BY
RP   MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC   TISSUE=Brain, Brown adipose tissue, Heart, Kidney, Liver, Lung,
RC   Pancreas, Spleen, and Testis;
RX   PubMed=21183079; DOI=10.1016/j.cell.2010.12.001;
RA   Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R.,
RA   Beausoleil S.A., Villen J., Haas W., Sowa M.E., Gygi S.P.;
RT   "A tissue-specific atlas of mouse protein phosphorylation and expression.";
RL   Cell 143:1174-1189(2010).
RN   [9]
RP   INTERACTION WITH PIP4P1.
RX   PubMed=29644770; DOI=10.1111/gtc.12583;
RA   Hashimoto Y., Shirane M., Nakayama K.I.;
RT   "TMEM55B contributes to lysosomal homeostasis and amino acid-induced mTORC1
RT   activation.";
RL   Genes Cells 23:418-434(2018).
CC   -!- FUNCTION: Subunit of the V0 complex of vacuolar(H+)-ATPase (V-ATPase),
CC       a multisubunit enzyme composed of a peripheral complex (V1) that
CC       hydrolyzes ATP and a membrane integral complex (V0) that translocates
CC       protons (PubMed:12963731). V-ATPase is responsible for acidifying a
CC       variety of intracellular compartments in eukaryotic cells, thus
CC       providing most of the energy required for transport processes in the
CC       vacuolar system (By similarity). May play a role in coupling of proton
CC       transport and ATP hydrolysis (PubMed:12963731). In aerobic conditions,
CC       involved in intracellular iron homeostasis, thus triggering the
CC       activity of Fe(2+) prolyl hydroxylase (PHD) enzymes, and leading to
CC       HIF1A hydroxylation and subsequent proteasomal degradation (By
CC       similarity). May play a role in cilium biogenesis through regulation of
CC       the transport and the localization of proteins to the cilium (By
CC       similarity). {ECO:0000250|UniProtKB:P61421,
CC       ECO:0000250|UniProtKB:Q6PGV1, ECO:0000269|PubMed:12963731}.
CC   -!- SUBUNIT: V-ATPase is a heteromultimeric enzyme made up of two
CC       complexes: the ATP-hydrolytic V1 complex and the proton translocation
CC       V0 complex (By similarity). The V1 complex consists of three catalytic
CC       AB heterodimers that form a heterohexamer, three peripheral stalks each
CC       consisting of EG heterodimers, one central rotor including subunits D
CC       and F, and the regulatory subunits C and H (By similarity). The proton
CC       translocation complex V0 consists of the proton transport subunit a, a
CC       ring of proteolipid subunits c9c'', rotary subunit d, subunits e and f,
CC       and the accessory subunits ATP6AP1/Ac45 and ATP6AP2/PRR (By
CC       similarity). Interacts with ATP6AP2; ATP6AP2 is a V-ATPase accessory
CC       protein and the interaction promotes v-ATPase complex assembly (By
CC       similarity). Interacts with TMEM9; TMEM9 is a v-ATPase assembly
CC       regulator and the interaction induces the interaction with ATP6AP2 (By
CC       similarity). Interacts with PIP4P1 (PubMed:29644770).
CC       {ECO:0000250|UniProtKB:P61421, ECO:0000269|PubMed:29644770}.
CC   -!- SUBCELLULAR LOCATION: Membrane {ECO:0000250|UniProtKB:P61421};
CC       Peripheral membrane protein {ECO:0000250|UniProtKB:P61421}; Cytoplasmic
CC       side {ECO:0000250|UniProtKB:P61421}. Lysosome membrane
CC       {ECO:0000250|UniProtKB:P61421}; Peripheral membrane protein
CC       {ECO:0000305}. Cytoplasmic vesicle, clathrin-coated vesicle membrane
CC       {ECO:0000250|UniProtKB:P61420}; Peripheral membrane protein
CC       {ECO:0000305}. Note=Localizes to centrosome and the base of the cilium.
CC       {ECO:0000250|UniProtKB:Q6PGV1}.
CC   -!- TISSUE SPECIFICITY: Ubiquitous. {ECO:0000269|PubMed:12527205,
CC       ECO:0000269|PubMed:12963731}.
CC   -!- DEVELOPMENTAL STAGE: Expressed throughout early development.
CC       {ECO:0000269|PubMed:12963731}.
CC   -!- SIMILARITY: Belongs to the V-ATPase V0D/AC39 subunit family.
CC       {ECO:0000305}.
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DR   EMBL; U13840; AAC83085.1; -; mRNA.
DR   EMBL; U21549; AAA92288.1; -; mRNA.
DR   EMBL; AB088408; BAC57954.1; -; mRNA.
DR   EMBL; AK083372; BAC38889.1; -; mRNA.
DR   EMBL; AK171515; BAE42500.1; -; mRNA.
DR   CCDS; CCDS22604.1; -.
DR   RefSeq; NP_038505.2; NM_013477.3.
DR   AlphaFoldDB; P51863; -.
DR   SMR; P51863; -.
DR   BioGRID; 198264; 16.
DR   IntAct; P51863; 10.
DR   MINT; P51863; -.
DR   STRING; 10090.ENSMUSP00000013304; -.
DR   TCDB; 3.A.2.2.6; the h+- or na+-translocating f-type, v-type and a-type atpase (f-atpase) superfamily.
DR   GlyGen; P51863; 1 site, 1 O-linked glycan (1 site).
DR   iPTMnet; P51863; -.
DR   PhosphoSitePlus; P51863; -.
DR   SwissPalm; P51863; -.
DR   EPD; P51863; -.
DR   jPOST; P51863; -.
DR   MaxQB; P51863; -.
DR   PaxDb; 10090-ENSMUSP00000013304; -.
DR   PeptideAtlas; P51863; -.
DR   ProteomicsDB; 297905; -.
DR   Pumba; P51863; -.
DR   Antibodypedia; 2185; 219 antibodies from 26 providers.
DR   DNASU; 11972; -.
DR   Ensembl; ENSMUST00000013304.8; ENSMUSP00000013304.7; ENSMUSG00000013160.8.
DR   GeneID; 11972; -.
DR   KEGG; mmu:11972; -.
DR   UCSC; uc009ndg.1; mouse.
DR   AGR; MGI:1201778; -.
DR   CTD; 9114; -.
DR   MGI; MGI:1201778; Atp6v0d1.
DR   VEuPathDB; HostDB:ENSMUSG00000013160; -.
DR   eggNOG; KOG2957; Eukaryota.
DR   GeneTree; ENSGT00390000002200; -.
DR   HOGENOM; CLU_051277_0_0_1; -.
DR   InParanoid; P51863; -.
DR   OMA; MTYGYMI; -.
DR   OrthoDB; 1211584at2759; -.
DR   PhylomeDB; P51863; -.
DR   TreeFam; TF300857; -.
DR   Reactome; R-MMU-1222556; ROS and RNS production in phagocytes.
DR   Reactome; R-MMU-77387; Insulin receptor recycling.
DR   Reactome; R-MMU-917977; Transferrin endocytosis and recycling.
DR   Reactome; R-MMU-9639288; Amino acids regulate mTORC1.
DR   Reactome; R-MMU-983712; Ion channel transport.
DR   BioGRID-ORCS; 11972; 27 hits in 80 CRISPR screens.
DR   ChiTaRS; Atp6v0d1; mouse.
DR   PRO; PR:P51863; -.
DR   Proteomes; UP000000589; Chromosome 8.
DR   RNAct; P51863; Protein.
DR   Bgee; ENSMUSG00000013160; Expressed in facial nucleus and 272 other cell types or tissues.
DR   GO; GO:0016324; C:apical plasma membrane; ISO:MGI.
DR   GO; GO:0043679; C:axon terminus; ISO:MGI.
DR   GO; GO:0005813; C:centrosome; IEA:Ensembl.
DR   GO; GO:0030665; C:clathrin-coated vesicle membrane; IEA:UniProtKB-SubCell.
DR   GO; GO:0005769; C:early endosome; IDA:MGI.
DR   GO; GO:0005765; C:lysosomal membrane; IEA:UniProtKB-SubCell.
DR   GO; GO:0016020; C:membrane; ISO:MGI.
DR   GO; GO:0033181; C:plasma membrane proton-transporting V-type ATPase complex; IBA:GO_Central.
DR   GO; GO:0032991; C:protein-containing complex; ISO:MGI.
DR   GO; GO:0033176; C:proton-transporting V-type ATPase complex; IDA:MGI.
DR   GO; GO:0033179; C:proton-transporting V-type ATPase, V0 domain; IDA:MGI.
DR   GO; GO:0008021; C:synaptic vesicle; ISO:MGI.
DR   GO; GO:0030672; C:synaptic vesicle membrane; ISO:MGI.
DR   GO; GO:1902495; C:transmembrane transporter complex; IDA:MGI.
DR   GO; GO:0016471; C:vacuolar proton-transporting V-type ATPase complex; ISO:MGI.
DR   GO; GO:0000220; C:vacuolar proton-transporting V-type ATPase, V0 domain; ISS:UniProtKB.
DR   GO; GO:0044877; F:protein-containing complex binding; ISO:MGI.
DR   GO; GO:0046961; F:proton-transporting ATPase activity, rotational mechanism; IEA:InterPro.
DR   GO; GO:0036295; P:cellular response to increased oxygen levels; ISS:UniProtKB.
DR   GO; GO:0060271; P:cilium assembly; ISS:UniProtKB.
DR   GO; GO:0006879; P:intracellular iron ion homeostasis; ISS:UniProtKB.
DR   GO; GO:0097401; P:synaptic vesicle lumen acidification; IDA:SynGO.
DR   GO; GO:0007035; P:vacuolar acidification; IBA:GO_Central.
DR   GO; GO:0007034; P:vacuolar transport; IBA:GO_Central.
DR   Gene3D; 1.10.132.50; ATP synthase (C/AC39) subunit, domain 3; 1.
DR   Gene3D; 1.20.1690.10; V-type ATP synthase subunit C domain; 2.
DR   InterPro; IPR036079; ATPase_su_c/d_sf.
DR   InterPro; IPR002843; ATPase_V0-cplx_csu/dsu.
DR   InterPro; IPR016727; ATPase_V0-cplx_dsu.
DR   InterPro; IPR044911; V-type_ATPase_su_c/d_dom_3.
DR   InterPro; IPR035067; V-type_ATPase_suC/d.
DR   PANTHER; PTHR11028:SF3; V-TYPE PROTON ATPASE SUBUNIT D 1; 1.
DR   PANTHER; PTHR11028; VACUOLAR ATP SYNTHASE SUBUNIT AC39; 1.
DR   Pfam; PF01992; vATP-synt_AC39; 1.
DR   PIRSF; PIRSF018497; V-ATP_synth_D; 1.
DR   SUPFAM; SSF103486; V-type ATP synthase subunit C; 1.
DR   Genevisible; P51863; MM.
PE   1: Evidence at protein level;
KW   Cilium biogenesis/degradation; Cytoplasmic vesicle;
KW   Direct protein sequencing; Hydrogen ion transport; Ion transport; Lysosome;
KW   Membrane; Phosphoprotein; Reference proteome; Transport.
FT   CHAIN           1..351
FT                   /note="V-type proton ATPase subunit d 1"
FT                   /id="PRO_0000119351"
FT   MOD_RES         270
FT                   /note="Phosphotyrosine"
FT                   /evidence="ECO:0007744|PubMed:18034455"
FT   MOD_RES         283
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:21183079"
FT   CONFLICT        23
FT                   /note="L -> M (in Ref. 1; AAC83085)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   351 AA;  40301 MW;  62CDF67B982124C9 CRC64;
     MSFFPELYFN VDNGYLEGLV RGLKAGVLSQ ADYLNLVQCE TLEDLKLHLQ STDYGNFLAN
     EASPLTVSVI DDKLKEKMVV EFRHMRNHAY EPLASFLDFI TYSYMIDNVI LLITGTLHQR
     SIAELVPKCH PLGSFEQMEA VNIAQTPAEL YNAILVDTPL AAFFQDCISE QDLDEMNIEI
     IRNTLYKAYL ESFYKFCTLL GGTTADAMCP ILEFEADRRA FIITINSFGT ELSKEDRAKL
     FPHCGRLYPE GLAQLARADD YEQVKNVADY YPEYKLLFEG AGSNPGDKTL EDRFFEHEVK
     LNKLAFLNQF HFGVFYAFVK LKEQECRNIV WIAECIAQRH RAKIDNYIPI F
//