VATD_HUMAN
ID VATD_HUMAN Reviewed; 247 AA.
AC Q9Y5K8; B2RE33; Q9Y688;
DT 01-DEC-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1999, sequence version 1.
DT 03-AUG-2022, entry version 187.
DE RecName: Full=V-type proton ATPase subunit D;
DE Short=V-ATPase subunit D;
DE AltName: Full=V-ATPase 28 kDa accessory protein;
DE AltName: Full=Vacuolar proton pump subunit D;
GN Name=ATP6V1D; Synonyms=ATP6M, VATD;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC TISSUE=Heart;
RA Zhao Y., Cao H.Q., Wei Y.J., Jiang Y.X., Zhao X.W., Liu D.Q., Meng X.M.,
RA Liu Y.Q., Xu Y.Y., Sheng H., Liu S., Qiao M., Hui R.T., Ding J.F.;
RL Submitted (APR-1999) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Pituitary;
RX PubMed=10931946; DOI=10.1073/pnas.160270997;
RA Hu R.-M., Han Z.-G., Song H.-D., Peng Y.-D., Huang Q.-H., Ren S.-X.,
RA Gu Y.-J., Huang C.-H., Li Y.-B., Jiang C.-L., Fu G., Zhang Q.-H., Gu B.-W.,
RA Dai M., Mao Y.-F., Gao G.-F., Rong R., Ye M., Zhou J., Xu S.-H., Gu J.,
RA Shi J.-X., Jin W.-R., Zhang C.-K., Wu T.-M., Huang G.-Y., Chen Z.,
RA Chen M.-D., Chen J.-L.;
RT "Gene expression profiling in the human hypothalamus-pituitary-adrenal axis
RT and full-length cDNA cloning.";
RL Proc. Natl. Acad. Sci. U.S.A. 97:9543-9548(2000).
RN [3]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC TISSUE=Brain;
RA Quan L., Hong W., Shizhou A.;
RT "cDNA of human vacuolar H-ATPase subunit D (VATD) interacts with Rb.";
RL Submitted (NOV-1998) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Trachea;
RX PubMed=14702039; DOI=10.1038/ng1285;
RA Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
RA Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
RA Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
RA Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
RA Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H.,
RA Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M.,
RA Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K.,
RA Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T.,
RA Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M.,
RA Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S.,
RA Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H.,
RA Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K.,
RA Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N.,
RA Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
RA Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
RA Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
RA Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
RA Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y.,
RA Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K.,
RA Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T.,
RA Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T.,
RA Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y.,
RA Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H.,
RA Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y.,
RA Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H.,
RA Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O.,
RA Isogai T., Sugano S.;
RT "Complete sequencing and characterization of 21,243 full-length human
RT cDNAs.";
RL Nat. Genet. 36:40-45(2004).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M.,
RA Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J.,
RA Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S.,
RA Turner R., Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H.,
RA Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K.,
RA Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D.,
RA Hunkapiller M.W., Myers E.W., Venter J.C.;
RL Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Placenta;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=21269460; DOI=10.1186/1752-0509-5-17;
RA Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T.,
RA Bennett K.L., Superti-Furga G., Colinge J.;
RT "Initial characterization of the human central proteome.";
RL BMC Syst. Biol. 5:17-17(2011).
RN [8]
RP FUNCTION IN CILIOGENESIS, INTERACTION WITH SNX10, AND SUBCELLULAR LOCATION.
RX PubMed=21844891; DOI=10.1038/cr.2011.134;
RA Chen Y., Wu B., Xu L., Li H., Xia J., Yin W., Li Z., Shi D., Li S., Lin S.,
RA Shu X., Pei D.;
RT "A SNX10/V-ATPase pathway regulates ciliogenesis in vitro and in vivo.";
RL Cell Res. 22:333-345(2012).
RN [9]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=25944712; DOI=10.1002/pmic.201400617;
RA Vaca Jacome A.S., Rabilloud T., Schaeffer-Reiss C., Rompais M., Ayoub D.,
RA Lane L., Bairoch A., Van Dorsselaer A., Carapito C.;
RT "N-terminome analysis of the human mitochondrial proteome.";
RL Proteomics 15:2519-2524(2015).
RN [10] {ECO:0007744|PDB:6WLZ, ECO:0007744|PDB:6WM2, ECO:0007744|PDB:6WM3, ECO:0007744|PDB:6WM4}
RP STRUCTURE BY ELECTRON MICROSCOPY (2.90 ANGSTROMS), FUNCTION, AND
RP IDENTIFICATION IN THE V-ATPASE COMPLEX.
RX PubMed=33065002; DOI=10.1016/j.molcel.2020.09.029;
RA Wang L., Wu D., Robinson C.V., Wu H., Fu T.M.;
RT "Structures of a Complete Human V-ATPase Reveal Mechanisms of Its
RT Assembly.";
RL Mol. Cell 80:501-511.e3(2020).
CC -!- FUNCTION: Subunit of the V1 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:33065002). V-ATPase is responsible for acidifying and
CC maintaining the pH of intracellular compartments and in some cell
CC types, is targeted to the plasma membrane, where it is responsible for
CC acidifying the extracellular environment (By similarity). May play a
CC role in cilium biogenesis through regulation of the transport and the
CC localization of proteins to the cilium (PubMed:21844891).
CC {ECO:0000250|UniProtKB:P39942, ECO:0000269|PubMed:21844891,
CC ECO:0000269|PubMed:33065002}.
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 (PubMed:33065002). The V1 complex consists of three
CC catalytic AB heterodimers that form a heterohexamer, three peripheral
CC stalks each consisting of EG heterodimers, one central rotor including
CC subunits D and F, and the regulatory subunits C and H
CC (PubMed:33065002). The proton translocation complex V0 consists of the
CC proton transport subunit a, a ring of proteolipid subunits c9c'',
CC rotary subunit d, subunits e and f, and the accessory subunits
CC ATP6AP1/Ac45 and ATP6AP2/PRR (PubMed:33065002). Interacts with SNX10
CC (PubMed:21844891). {ECO:0000269|PubMed:21844891,
CC ECO:0000269|PubMed:33065002}.
CC -!- INTERACTION:
CC Q9Y5K8; Q16864: ATP6V1F; NbExp=3; IntAct=EBI-2684998, EBI-714690;
CC Q9Y5K8; Q9BUW7: BBLN; NbExp=5; IntAct=EBI-2684998, EBI-752084;
CC Q9Y5K8; Q96CS2: HAUS1; NbExp=3; IntAct=EBI-2684998, EBI-2514791;
CC Q9Y5K8; Q7Z3Y8: KRT27; NbExp=3; IntAct=EBI-2684998, EBI-3044087;
CC Q9Y5K8; O14777: NDC80; NbExp=3; IntAct=EBI-2684998, EBI-715849;
CC Q9Y5K8; Q8N1B4: VPS52; NbExp=6; IntAct=EBI-2684998, EBI-2799833;
CC -!- SUBCELLULAR LOCATION: Membrane {ECO:0000305|PubMed:21844891};
CC Peripheral membrane protein {ECO:0000305|PubMed:21844891}; Cytoplasmic
CC side {ECO:0000305|PubMed:21844891}. Cytoplasmic vesicle, clathrin-
CC coated vesicle membrane {ECO:0000250|UniProtKB:P39942}; Peripheral
CC membrane protein {ECO:0000305}. Cytoplasm, cytoskeleton, microtubule
CC organizing center, centrosome {ECO:0000269|PubMed:21844891}. Cell
CC projection, cilium {ECO:0000269|PubMed:21844891}. Note=Localizes to
CC centrosome and the base of the cilium. {ECO:0000269|PubMed:21844891}.
CC -!- SIMILARITY: Belongs to the V-ATPase D subunit family. {ECO:0000305}.
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DR EMBL; AF145316; AAD33953.1; -; mRNA.
DR EMBL; AF100741; AAD40384.1; -; mRNA.
DR EMBL; AF104629; AAG30726.1; -; mRNA.
DR EMBL; AK315784; BAG38130.1; -; mRNA.
DR EMBL; CH471061; EAW80931.1; -; Genomic_DNA.
DR EMBL; BC001411; AAH01411.1; -; mRNA.
DR CCDS; CCDS9780.1; -.
DR RefSeq; NP_057078.1; NM_015994.3.
DR PDB; 6WLZ; EM; 2.90 A; G=1-247.
DR PDB; 6WM2; EM; 3.10 A; G=1-247.
DR PDB; 6WM3; EM; 3.40 A; G=1-247.
DR PDB; 6WM4; EM; 3.60 A; G=1-247.
DR PDBsum; 6WLZ; -.
DR PDBsum; 6WM2; -.
DR PDBsum; 6WM3; -.
DR PDBsum; 6WM4; -.
DR AlphaFoldDB; Q9Y5K8; -.
DR SMR; Q9Y5K8; -.
DR BioGRID; 119513; 82.
DR ComplexPortal; CPX-2470; Vacuolar proton translocating ATPase complex, ATP6V0A1 variant.
DR ComplexPortal; CPX-6904; Vacuolar proton translocating ATPase complex, ATP6V0A2 variant.
DR ComplexPortal; CPX-6905; Vacuolar proton translocating ATPase complex, ATP6V0A3 variant.
DR ComplexPortal; CPX-6912; Vacuolar proton translocating ATPase complex, ATP6V0A4 variant.
DR IntAct; Q9Y5K8; 36.
DR MINT; Q9Y5K8; -.
DR STRING; 9606.ENSP00000216442; -.
DR DrugBank; DB01133; Tiludronic acid.
DR iPTMnet; Q9Y5K8; -.
DR PhosphoSitePlus; Q9Y5K8; -.
DR SwissPalm; Q9Y5K8; -.
DR BioMuta; ATP6V1D; -.
DR DMDM; 10720351; -.
DR EPD; Q9Y5K8; -.
DR jPOST; Q9Y5K8; -.
DR MassIVE; Q9Y5K8; -.
DR MaxQB; Q9Y5K8; -.
DR PaxDb; Q9Y5K8; -.
DR PeptideAtlas; Q9Y5K8; -.
DR PRIDE; Q9Y5K8; -.
DR ProteomicsDB; 86435; -.
DR Antibodypedia; 24797; 104 antibodies from 30 providers.
DR DNASU; 51382; -.
DR Ensembl; ENST00000216442.12; ENSP00000216442.7; ENSG00000100554.12.
DR Ensembl; ENST00000554087.5; ENSP00000451167.1; ENSG00000100554.12.
DR GeneID; 51382; -.
DR KEGG; hsa:51382; -.
DR MANE-Select; ENST00000216442.12; ENSP00000216442.7; NM_015994.4; NP_057078.1.
DR UCSC; uc001xjf.4; human.
DR CTD; 51382; -.
DR DisGeNET; 51382; -.
DR GeneCards; ATP6V1D; -.
DR HGNC; HGNC:13527; ATP6V1D.
DR HPA; ENSG00000100554; Low tissue specificity.
DR MIM; 609398; gene.
DR neXtProt; NX_Q9Y5K8; -.
DR OpenTargets; ENSG00000100554; -.
DR PharmGKB; PA25157; -.
DR VEuPathDB; HostDB:ENSG00000100554; -.
DR eggNOG; KOG1647; Eukaryota.
DR GeneTree; ENSGT00390000010770; -.
DR HOGENOM; CLU_069688_0_0_1; -.
DR InParanoid; Q9Y5K8; -.
DR OMA; SKNIMGV; -.
DR OrthoDB; 1313938at2759; -.
DR PhylomeDB; Q9Y5K8; -.
DR TreeFam; TF300160; -.
DR BioCyc; MetaCyc:HS02107-MON; -.
DR PathwayCommons; Q9Y5K8; -.
DR Reactome; R-HSA-1222556; ROS and RNS production in phagocytes.
DR Reactome; R-HSA-6798695; Neutrophil degranulation.
DR Reactome; R-HSA-77387; Insulin receptor recycling.
DR Reactome; R-HSA-917977; Transferrin endocytosis and recycling.
DR Reactome; R-HSA-9639288; Amino acids regulate mTORC1.
DR Reactome; R-HSA-983712; Ion channel transport.
DR SignaLink; Q9Y5K8; -.
DR BioGRID-ORCS; 51382; 646 hits in 1081 CRISPR screens.
DR ChiTaRS; ATP6V1D; human.
DR GeneWiki; ATP6V1D; -.
DR GenomeRNAi; 51382; -.
DR Pharos; Q9Y5K8; Tbio.
DR PRO; PR:Q9Y5K8; -.
DR Proteomes; UP000005640; Chromosome 14.
DR RNAct; Q9Y5K8; protein.
DR Bgee; ENSG00000100554; Expressed in endothelial cell and 208 other tissues.
DR ExpressionAtlas; Q9Y5K8; baseline and differential.
DR Genevisible; Q9Y5K8; HS.
DR GO; GO:0005929; C:cilium; IEA:UniProtKB-SubCell.
DR GO; GO:0030665; C:clathrin-coated vesicle membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0005829; C:cytosol; TAS:Reactome.
DR GO; GO:0010008; C:endosome membrane; IC:ComplexPortal.
DR GO; GO:0070062; C:extracellular exosome; HDA:UniProtKB.
DR GO; GO:0000139; C:Golgi membrane; IC:ComplexPortal.
DR GO; GO:0005765; C:lysosomal membrane; HDA:UniProtKB.
DR GO; GO:0016020; C:membrane; IDA:UniProtKB.
DR GO; GO:0005815; C:microtubule organizing center; IEA:UniProtKB-SubCell.
DR GO; GO:0005886; C:plasma membrane; TAS:Reactome.
DR GO; GO:0033176; C:proton-transporting V-type ATPase complex; IDA:UniProtKB.
DR GO; GO:0035579; C:specific granule membrane; TAS:Reactome.
DR GO; GO:0000221; C:vacuolar proton-transporting V-type ATPase, V1 domain; ISS:UniProtKB.
DR GO; GO:0046961; F:proton-transporting ATPase activity, rotational mechanism; IEA:InterPro.
DR GO; GO:0060271; P:cilium assembly; IMP:UniProtKB.
DR GO; GO:0048388; P:endosomal lumen acidification; IC:ComplexPortal.
DR GO; GO:0061795; P:Golgi lumen acidification; IC:ComplexPortal.
DR GO; GO:0051452; P:intracellular pH reduction; IC:ComplexPortal.
DR GO; GO:0007042; P:lysosomal lumen acidification; IC:ComplexPortal.
DR GO; GO:0061512; P:protein localization to cilium; IMP:UniProtKB.
DR GO; GO:1902600; P:proton transmembrane transport; IC:ComplexPortal.
DR GO; GO:0016241; P:regulation of macroautophagy; NAS:ParkinsonsUK-UCL.
DR GO; GO:0007035; P:vacuolar acidification; IC:ComplexPortal.
DR InterPro; IPR002699; V_ATPase_D.
DR PANTHER; PTHR11671; PTHR11671; 1.
DR Pfam; PF01813; ATP-synt_D; 1.
DR TIGRFAMs; TIGR00309; V_ATPase_subD; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cell projection; Cilium biogenesis/degradation; Cytoplasm;
KW Cytoplasmic vesicle; Cytoskeleton; Hydrogen ion transport; Ion transport;
KW Membrane; Reference proteome; Transport.
FT CHAIN 1..247
FT /note="V-type proton ATPase subunit D"
FT /id="PRO_0000144231"
FT CONFLICT 228..235
FT /note="EVLEPANL -> RCWSLLIF (in Ref. 2; AAD40384)"
FT /evidence="ECO:0000305"
FT HELIX 15..73
FT /evidence="ECO:0007829|PDB:6WLZ"
FT HELIX 80..85
FT /evidence="ECO:0007829|PDB:6WLZ"
FT STRAND 94..101
FT /evidence="ECO:0007829|PDB:6WLZ"
FT STRAND 104..110
FT /evidence="ECO:0007829|PDB:6WLZ"
FT STRAND 118..126
FT /evidence="ECO:0007829|PDB:6WM2"
FT HELIX 129..174
FT /evidence="ECO:0007829|PDB:6WLZ"
FT HELIX 176..215
FT /evidence="ECO:0007829|PDB:6WLZ"
SQ SEQUENCE 247 AA; 28263 MW; 4185E5F6A74EFB1C CRC64;
MSGKDRIEIF PSRMAQTIMK ARLKGAQTGR NLLKKKSDAL TLRFRQILKK IIETKMLMGE
VMREAAFSLA EAKFTAGDFS TTVIQNVNKA QVKIRAKKDN VAGVTLPVFE HYHEGTDSYE
LTGLARGGEQ LAKLKRNYAK AVELLVELAS LQTSFVTLDE AIKITNRRVN AIEHVIIPRI
ERTLAYIITE LDEREREEFY RLKKIQEKKK ILKEKSEKDL EQRRAAGEVL EPANLLAEEK
DEDLLFE
