VA0D1_BOVIN
ID VA0D1_BOVIN Reviewed; 351 AA.
AC P61420; P12953; Q02547; Q3T0P9;
DT 24-MAY-2004, integrated into UniProtKB/Swiss-Prot.
DT 24-MAY-2004, sequence version 1.
DT 03-AUG-2022, entry version 125.
DE RecName: Full=V-type proton ATPase subunit d 1;
DE Short=V-ATPase subunit d 1;
DE AltName: Full=32 kDa accessory protein;
DE AltName: Full=P39;
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; Synonyms=ATP6D, VPATPD;
OS Bos taurus (Bovine).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Laurasiatheria; Artiodactyla; Ruminantia; Pecora; Bovidae;
OC Bovinae; Bos.
OX NCBI_TaxID=9913;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], AND PARTIAL PROTEIN SEQUENCE.
RC TISSUE=Adrenal medulla;
RX PubMed=2903164; DOI=10.1016/s0021-9258(19)77884-3;
RA Wang S.-Y., Moriyama Y., Mandel M., Hulmes J.D., Pan Y.-C.E., Danho W.,
RA Nelson H., Nelson N.;
RT "Cloning of cDNA encoding a 32-kDa protein. An accessory polypeptide of the
RT H+-ATPase from chromaffin granules.";
RL J. Biol. Chem. 263:17638-17642(1988).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=Crossbred X Angus; TISSUE=Ileum;
RG NIH - Mammalian Gene Collection (MGC) project;
RL Submitted (AUG-2005) to the EMBL/GenBank/DDBJ databases.
RN [3] {ECO:0007744|PDB:6XBW, ECO:0007744|PDB:6XBY}
RP STRUCTURE BY ELECTRON MICROSCOPY (3.37 ANGSTROMS), FUNCTION, IDENTIFICATION
RP IN THE V-ATPASE COMPLEX, SUBCELLULAR LOCATION, IDENTIFICATION BY MASS
RP SPECTROMETRY, AND TISSUE SPECIFICITY.
RX PubMed=32764564; DOI=10.1038/s41467-020-17762-9;
RA Wang R., Long T., Hassan A., Wang J., Sun Y., Xie X.S., Li X.;
RT "Cryo-EM structures of intact V-ATPase from bovine brain.";
RL Nat. Commun. 11:3921-3921(2020).
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:32764564). 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 (PubMed:32764564). May play a
CC role in coupling of proton transport and ATP hydrolysis (By
CC similarity). In aerobic conditions, involved in intracellular iron
CC homeostasis, thus triggering the activity of Fe(2+) prolyl hydroxylase
CC (PHD) enzymes, and leading to HIF1A hydroxylation and subsequent
CC proteasomal degradation (By similarity). May play a role in cilium
CC biogenesis through regulation of the transport and the localization of
CC proteins to the cilium (By similarity). {ECO:0000250|UniProtKB:P51863,
CC ECO:0000250|UniProtKB:P61421, ECO:0000250|UniProtKB:Q6PGV1,
CC ECO:0000269|PubMed:32764564}.
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:32764564). 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:32764564). 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:32764564). Interacts with ATP6AP2;
CC ATP6AP2 is a V-ATPase accessory protein and the interaction promotes v-
CC ATPase complex assembly (PubMed:32764564). Interacts with TMEM9; TMEM9
CC is a v-ATPase assembly regulator and the interaction induces the
CC interaction with ATP6AP2 (By similarity). Interacts with PIP4P1 (By
CC similarity). {ECO:0000250|UniProtKB:P61421,
CC ECO:0000269|PubMed:32764564}.
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:0000269|PubMed:32764564}; Peripheral membrane protein
CC {ECO:0000305}. Note=Localizes to centrosome and the base of the cilium.
CC {ECO:0000250|UniProtKB:Q6PGV1}.
CC -!- TISSUE SPECIFICITY: Expressed in brain (at protein level).
CC {ECO:0000269|PubMed:32764564}.
CC -!- PTM: The N-terminus is blocked.
CC -!- SIMILARITY: Belongs to the V-ATPase V0D/AC39 subunit family.
CC {ECO:0000305}.
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DR EMBL; J04204; AAA64520.1; -; mRNA.
DR EMBL; BC102305; AAI02306.1; -; mRNA.
DR PIR; A32123; A32123.
DR RefSeq; NP_776930.1; NM_174505.3.
DR PDB; 6XBW; EM; 3.37 A; d=1-351.
DR PDB; 6XBY; EM; 3.79 A; d=1-351.
DR PDB; 7KHR; EM; 3.62 A; d=1-351.
DR PDBsum; 6XBW; -.
DR PDBsum; 6XBY; -.
DR PDBsum; 7KHR; -.
DR AlphaFoldDB; P61420; -.
DR SMR; P61420; -.
DR CORUM; P61420; -.
DR STRING; 9913.ENSBTAP00000019346; -.
DR PaxDb; P61420; -.
DR PRIDE; P61420; -.
DR Ensembl; ENSBTAT00000019346; ENSBTAP00000019346; ENSBTAG00000014553.
DR GeneID; 282148; -.
DR KEGG; bta:282148; -.
DR CTD; 9114; -.
DR VEuPathDB; HostDB:ENSBTAG00000014553; -.
DR VGNC; VGNC:26312; ATP6V0D1.
DR eggNOG; KOG2957; Eukaryota.
DR GeneTree; ENSGT00390000002200; -.
DR HOGENOM; CLU_051277_0_0_1; -.
DR InParanoid; P61420; -.
DR OMA; MLSRAED; -.
DR OrthoDB; 910004at2759; -.
DR TreeFam; TF300857; -.
DR Proteomes; UP000009136; Chromosome 18.
DR Bgee; ENSBTAG00000014553; Expressed in Ammon's horn and 105 other tissues.
DR ExpressionAtlas; P61420; baseline and differential.
DR GO; GO:0030665; C:clathrin-coated vesicle membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0005769; C:early endosome; IBA:GO_Central.
DR GO; GO:0005765; C:lysosomal membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0033181; C:plasma membrane proton-transporting V-type ATPase complex; IBA:GO_Central.
DR GO; GO:0016471; C:vacuolar proton-transporting V-type ATPase complex; IBA:GO_Central.
DR GO; GO:0000220; C:vacuolar proton-transporting V-type ATPase, V0 domain; IDA:UniProtKB.
DR GO; GO:0046961; F:proton-transporting ATPase activity, rotational mechanism; IEA:InterPro.
DR GO; GO:0006879; P:cellular iron ion homeostasis; ISS:UniProtKB.
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:0045851; P:pH reduction; IC:UniProtKB.
DR GO; GO:1902600; P:proton transmembrane transport; IC:UniProtKB.
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; -; 1.
DR Gene3D; 1.20.1690.10; -; 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; PTHR11028; 1.
DR Pfam; PF01992; vATP-synt_AC39; 1.
DR PIRSF; PIRSF018497; V-ATP_synth_D; 1.
DR SUPFAM; SSF103486; SSF103486; 1.
PE 1: Evidence at protein level;
KW 3D-structure; 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_0000119349"
FT MOD_RES 270
FT /note="Phosphotyrosine"
FT /evidence="ECO:0000250|UniProtKB:P51863"
FT MOD_RES 283
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P51863"
FT STRAND 7..13
FT /evidence="ECO:0007829|PDB:6XBW"
FT HELIX 14..22
FT /evidence="ECO:0007829|PDB:6XBW"
FT HELIX 24..26
FT /evidence="ECO:0007829|PDB:6XBW"
FT HELIX 30..37
FT /evidence="ECO:0007829|PDB:6XBW"
FT HELIX 42..48
FT /evidence="ECO:0007829|PDB:6XBW"
FT HELIX 49..51
FT /evidence="ECO:0007829|PDB:6XBW"
FT STRAND 56..61
FT /evidence="ECO:0007829|PDB:6XBW"
FT HELIX 67..86
FT /evidence="ECO:0007829|PDB:6XBW"
FT TURN 91..93
FT /evidence="ECO:0007829|PDB:6XBW"
FT HELIX 94..100
FT /evidence="ECO:0007829|PDB:6XBW"
FT HELIX 102..117
FT /evidence="ECO:0007829|PDB:6XBW"
FT HELIX 122..124
FT /evidence="ECO:0007829|PDB:6XBW"
FT TURN 125..128
FT /evidence="ECO:0007829|PDB:6XBW"
FT STRAND 131..133
FT /evidence="ECO:0007829|PDB:6XBW"
FT TURN 139..142
FT /evidence="ECO:0007829|PDB:6XBW"
FT HELIX 152..155
FT /evidence="ECO:0007829|PDB:6XBW"
FT TURN 159..163
FT /evidence="ECO:0007829|PDB:6XBW"
FT HELIX 164..166
FT /evidence="ECO:0007829|PDB:6XBW"
FT TURN 169..175
FT /evidence="ECO:0007829|PDB:6XBW"
FT HELIX 180..199
FT /evidence="ECO:0007829|PDB:6XBW"
FT HELIX 203..206
FT /evidence="ECO:0007829|PDB:6XBW"
FT HELIX 209..226
FT /evidence="ECO:0007829|PDB:6XBW"
FT STRAND 227..230
FT /evidence="ECO:0007829|PDB:6XBW"
FT HELIX 234..239
FT /evidence="ECO:0007829|PDB:6XBW"
FT TURN 246..250
FT /evidence="ECO:0007829|PDB:6XBW"
FT HELIX 251..255
FT /evidence="ECO:0007829|PDB:6XBW"
FT HELIX 261..266
FT /evidence="ECO:0007829|PDB:6XBW"
FT TURN 267..270
FT /evidence="ECO:0007829|PDB:6XBW"
FT TURN 272..276
FT /evidence="ECO:0007829|PDB:6XBW"
FT STRAND 284..287
FT /evidence="ECO:0007829|PDB:6XBW"
FT HELIX 290..303
FT /evidence="ECO:0007829|PDB:6XBW"
FT HELIX 304..306
FT /evidence="ECO:0007829|PDB:6XBW"
FT HELIX 313..337
FT /evidence="ECO:0007829|PDB:6XBW"
SQ SEQUENCE 351 AA; 40329 MW; A720F8A87511203C CRC64;
MSFFPELYFN VDNGYLEGLV RGLKAGVLSQ ADYLNLVQCE TLEDLKLHLQ STDYGNFLAN
EASPLTVSVI DDRLKEKMVV 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
