VTC4_YEAST
ID VTC4_YEAST Reviewed; 721 AA.
AC P47075; D6VWG5; Q7Z872; Q86ZR4;
DT 01-FEB-1996, integrated into UniProtKB/Swiss-Prot.
DT 31-AUG-2004, sequence version 2.
DT 03-AUG-2022, entry version 176.
DE RecName: Full=Vacuolar transporter chaperone 4;
DE AltName: Full=Phosphate metabolism protein 3;
GN Name=VTC4; Synonyms=PHM3; OrderedLocusNames=YJL012C; ORFNames=J1345;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, TOPOLOGY, AND SUBCELLULAR
RP LOCATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=12584253; DOI=10.1242/jcs.00328;
RA Mueller O., Neumann H., Bayer M.J., Mayer A.;
RT "Role of the Vtc proteins in V-ATPase stability and membrane trafficking.";
RL J. Cell Sci. 116:1107-1115(2003).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=8641269; DOI=10.1002/j.1460-2075.1996.tb00557.x;
RA Galibert F., Alexandraki D., Baur A., Boles E., Chalwatzis N., Chuat J.-C.,
RA Coster F., Cziepluch C., de Haan M., Domdey H., Durand P., Entian K.-D.,
RA Gatius M., Goffeau A., Grivell L.A., Hennemann A., Herbert C.J.,
RA Heumann K., Hilger F., Hollenberg C.P., Huang M.-E., Jacq C.,
RA Jauniaux J.-C., Katsoulou C., Kirchrath L., Kleine K., Kordes E.,
RA Koetter P., Liebl S., Louis E.J., Manus V., Mewes H.-W., Miosga T.,
RA Obermaier B., Perea J., Pohl T.M., Portetelle D., Pujol A., Purnelle B.,
RA Ramezani Rad M., Rasmussen S.W., Rose M., Rossau R.,
RA Schaaff-Gerstenschlaeger I., Smits P.H.M., Scarcez T., Soriano N.,
RA To Van D., Tzermia M., Van Broekhoven A., Vandenbol M., Wedler H.,
RA von Wettstein D., Wambutt R., Zagulski M., Zollner A., Karpfinger-Hartl L.;
RT "Complete nucleotide sequence of Saccharomyces cerevisiae chromosome X.";
RL EMBO J. 15:2031-2049(1996).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [4]
RP PROTEIN SEQUENCE OF 1-9; 74-86; 122-129; 138-149; 158-175; 201-212;
RP 267-280; 310-320; 362-371; 374-384; 401-410; 429-455; 598-606 AND 612-622,
RP AND IDENTIFICATION BY MASS SPECTROMETRY.
RA Bienvenut W.V., Peters C.;
RL Submitted (JUN-2005) to UniProtKB.
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 577-642.
RC STRAIN=ATCC 204511 / S288c / AB972;
RX PubMed=12844361; DOI=10.1186/gb-2003-4-7-r45;
RA Brachat S., Dietrich F.S., Voegeli S., Zhang Z., Stuart L., Lerch A.,
RA Gates K., Gaffney T.D., Philippsen P.;
RT "Reinvestigation of the Saccharomyces cerevisiae genome annotation by
RT comparison to the genome of a related fungus: Ashbya gossypii.";
RL Genome Biol. 4:R45.1-R45.13(2003).
RN [6]
RP FUNCTION, AND INDUCTION.
RX PubMed=11102525; DOI=10.1091/mbc.11.12.4309;
RA Ogawa N., DeRisi J.L., Brown P.O.;
RT "New components of a system for phosphate accumulation and polyphosphate
RT metabolism in Saccharomyces cerevisiae revealed by genomic expression
RT analysis.";
RL Mol. Biol. Cell 11:4309-4321(2000).
RN [7]
RP FUNCTION, IDENTIFICATION IN VTC COMPLEX, SUBUNIT, AND INTERACTION WITH NYV1
RP AND VPH1.
RX PubMed=11823419; DOI=10.1093/emboj/21.3.259;
RA Mueller O., Bayer M.J., Peters C., Andersen J.S., Mann M., Mayer A.;
RT "The Vtc proteins in vacuole fusion: coupling NSF activity to V(0) trans-
RT complex formation.";
RL EMBO J. 21:259-269(2002).
RN [8]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [9]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
RN [10]
RP UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-75, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22106047; DOI=10.1002/pmic.201100166;
RA Starita L.M., Lo R.S., Eng J.K., von Haller P.D., Fields S.;
RT "Sites of ubiquitin attachment in Saccharomyces cerevisiae.";
RL Proteomics 12:236-240(2012).
RN [11] {ECO:0007744|PDB:5IIG, ECO:0007744|PDB:5IIQ, ECO:0007744|PDB:5IIT}
RP X-RAY CRYSTALLOGRAPHY (2.13 ANGSTROMS) OF 1-178, FUNCTION, AND DOMAIN.
RX PubMed=27080106; DOI=10.1126/science.aad9858;
RA Wild R., Gerasimaite R., Jung J.Y., Truffault V., Pavlovic I., Schmidt A.,
RA Saiardi A., Jessen H.J., Poirier Y., Hothorn M., Mayer A.;
RT "Control of eukaryotic phosphate homeostasis by inositol polyphosphate
RT sensor domains.";
RL Science 352:986-990(2016).
CC -!- FUNCTION: Component of the vacuolar transporter chaperone (VTC)
CC complex, which plays a role in vacuolar membrane fusion
CC (PubMed:12584253, PubMed:11102525, PubMed:11823419). Required for
CC SEC18/NSF activity in SNARE priming, membrane binding of LMA1 and V(0)
CC trans-complex formation (PubMed:11823419). Binds inositol
CC hexakisphosphate (Ins6P) and similar inositol polyphosphates, such as
CC 5-diphospho-inositol pentakisphosphate (5-InsP7); these are important
CC intracellular signaling molecules (PubMed:27080106). Inositol
CC polyphosphate binding promotes vacuolar polyphosphate synthesis
CC (PubMed:27080106). {ECO:0000269|PubMed:11102525,
CC ECO:0000269|PubMed:11823419, ECO:0000269|PubMed:12584253,
CC ECO:0000269|PubMed:27080106}.
CC -!- SUBUNIT: The VTC complex is an integral membrane heterooligomer
CC composed of VTC1, VTC2, VTC3 and VTC4. The complex interacts with the
CC v-SNARE NYV1 and with the V(0) subunit of V-ATPase VPH1.
CC {ECO:0000269|PubMed:11823419}.
CC -!- INTERACTION:
CC P47075; Q06449: PIN3; NbExp=2; IntAct=EBI-25789, EBI-35523;
CC -!- SUBCELLULAR LOCATION: Vacuole membrane {ECO:0000269|PubMed:12584253};
CC Multi-pass membrane protein {ECO:0000269|PubMed:12584253}.
CC -!- INDUCTION: By low phosphate. {ECO:0000269|PubMed:11102525}.
CC -!- DOMAIN: The SPX domain has very high affinity for inositol
CC polyphosphates, such as myo-inositol hexakisphosphate and 5-diphospho-
CC myo-inositol pentakisphosphate (5-InsP7), and moderate affinity for
CC inorganic pyrophosphate. Its affinity for inorganic phosphate is tow to
CC three orders of magnitude lower. {ECO:0000305|PubMed:27080106}.
CC -!- MISCELLANEOUS: Present with 8710 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the VTC4 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAA89303.1; Type=Frameshift; Evidence={ECO:0000305};
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AY264259; AAP21767.1; -; Genomic_DNA.
DR EMBL; Z49287; CAA89303.1; ALT_FRAME; Genomic_DNA.
DR EMBL; AY227894; AAQ17203.1; -; Genomic_DNA.
DR EMBL; BK006943; DAA08781.1; -; Genomic_DNA.
DR PIR; S56783; S56783.
DR RefSeq; NP_012522.2; NM_001181446.1.
DR PDB; 3G3Q; X-ray; 2.64 A; A/B=189-480.
DR PDB; 3G3R; X-ray; 2.00 A; A/B=189-480.
DR PDB; 3G3T; X-ray; 1.85 A; A=189-480.
DR PDB; 3G3U; X-ray; 2.07 A; A/B=189-480.
DR PDB; 5IIG; X-ray; 2.99 A; A=2-480.
DR PDB; 5IIQ; X-ray; 3.03 A; A=2-480.
DR PDB; 5IIT; X-ray; 2.13 A; A/B/C/D=1-178.
DR PDB; 5LNC; X-ray; 3.29 A; A/B=1-178.
DR PDBsum; 3G3Q; -.
DR PDBsum; 3G3R; -.
DR PDBsum; 3G3T; -.
DR PDBsum; 3G3U; -.
DR PDBsum; 5IIG; -.
DR PDBsum; 5IIQ; -.
DR PDBsum; 5IIT; -.
DR PDBsum; 5LNC; -.
DR AlphaFoldDB; P47075; -.
DR SMR; P47075; -.
DR BioGRID; 33743; 99.
DR ComplexPortal; CPX-784; Vacuolar transporter chaperone complex.
DR DIP; DIP-5608N; -.
DR IntAct; P47075; 7.
DR MINT; P47075; -.
DR STRING; 4932.YJL012C; -.
DR TCDB; 4.E.1.1.3; the vacuolar (acidocalcisome) polyphosphate polymerase (v-ppp) family.
DR iPTMnet; P47075; -.
DR MaxQB; P47075; -.
DR PaxDb; P47075; -.
DR PRIDE; P47075; -.
DR TopDownProteomics; P47075; -.
DR EnsemblFungi; YJL012C_mRNA; YJL012C; YJL012C.
DR GeneID; 853441; -.
DR KEGG; sce:YJL012C; -.
DR SGD; S000003549; VTC4.
DR VEuPathDB; FungiDB:YJL012C; -.
DR eggNOG; KOG1161; Eukaryota.
DR GeneTree; ENSGT00940000176488; -.
DR HOGENOM; CLU_009308_0_0_1; -.
DR InParanoid; P47075; -.
DR OMA; AGGKQQN; -.
DR BioCyc; YEAST:YJL012C-MON; -.
DR EvolutionaryTrace; P47075; -.
DR PRO; PR:P47075; -.
DR Proteomes; UP000002311; Chromosome X.
DR RNAct; P47075; protein.
DR GO; GO:0000421; C:autophagosome membrane; IC:ComplexPortal.
DR GO; GO:0071944; C:cell periphery; HDA:SGD.
DR GO; GO:0005783; C:endoplasmic reticulum; IDA:SGD.
DR GO; GO:0000329; C:fungal-type vacuole membrane; HDA:SGD.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0031310; C:intrinsic component of vacuolar membrane; IDA:SGD.
DR GO; GO:0016020; C:membrane; IC:ComplexPortal.
DR GO; GO:0033254; C:vacuolar transporter chaperone complex; IPI:SGD.
DR GO; GO:0005516; F:calmodulin binding; IDA:SGD.
DR GO; GO:0000822; F:inositol hexakisphosphate binding; IDA:SGD.
DR GO; GO:0008976; F:polyphosphate kinase activity; IDA:SGD.
DR GO; GO:0061736; P:engulfment of target by autophagosome; IC:ComplexPortal.
DR GO; GO:0048016; P:inositol phosphate-mediated signaling; IMP:SGD.
DR GO; GO:0016237; P:lysosomal microautophagy; IDA:SGD.
DR GO; GO:0006799; P:polyphosphate biosynthetic process; IMP:SGD.
DR GO; GO:0006797; P:polyphosphate metabolic process; IMP:SGD.
DR GO; GO:0007034; P:vacuolar transport; IDA:SGD.
DR GO; GO:0042144; P:vacuole fusion, non-autophagic; IMP:SGD.
DR Gene3D; 3.20.100.30; -; 1.
DR InterPro; IPR003807; DUF202.
DR InterPro; IPR004331; SPX_dom.
DR InterPro; IPR018966; VTC_domain.
DR InterPro; IPR042267; VTC_sf.
DR Pfam; PF02656; DUF202; 1.
DR Pfam; PF09359; VTC; 1.
DR PROSITE; PS51382; SPX; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Isopeptide bond; Membrane;
KW Reference proteome; Transmembrane; Transmembrane helix; Ubl conjugation;
KW Vacuole.
FT CHAIN 1..721
FT /note="Vacuolar transporter chaperone 4"
FT /id="PRO_0000065937"
FT TOPO_DOM 1..630
FT /note="Cytoplasmic"
FT /evidence="ECO:0000269|PubMed:12584253"
FT TRANSMEM 631..651
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 652..672
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 673..699
FT /note="Cytoplasmic"
FT /evidence="ECO:0000269|PubMed:12584253"
FT TRANSMEM 700..720
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 721
FT /note="Vacuolar"
FT /evidence="ECO:0000269|PubMed:12584253"
FT DOMAIN 1..148
FT /note="SPX"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00714"
FT REGION 126..133
FT /note="Important for inositol polyphosphate binding"
FT /evidence="ECO:0000305|PubMed:27080106"
FT REGION 489..512
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT SITE 22
FT /note="Important for inositol polyphosphate binding"
FT /evidence="ECO:0000250|UniProtKB:P43585"
FT SITE 26
FT /note="Important for inositol polyphosphate binding"
FT /evidence="ECO:0000250|UniProtKB:P43585"
FT CROSSLNK 75
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT /evidence="ECO:0007744|PubMed:22106047"
FT HELIX 2..8
FT /evidence="ECO:0007829|PDB:5IIG"
FT HELIX 15..18
FT /evidence="ECO:0007829|PDB:5IIT"
FT HELIX 22..35
FT /evidence="ECO:0007829|PDB:5IIT"
FT TURN 36..38
FT /evidence="ECO:0007829|PDB:5IIT"
FT HELIX 42..89
FT /evidence="ECO:0007829|PDB:5IIT"
FT STRAND 90..92
FT /evidence="ECO:0007829|PDB:5IIQ"
FT HELIX 96..138
FT /evidence="ECO:0007829|PDB:5IIT"
FT HELIX 143..152
FT /evidence="ECO:0007829|PDB:5IIT"
FT HELIX 160..175
FT /evidence="ECO:0007829|PDB:5IIT"
FT TURN 176..178
FT /evidence="ECO:0007829|PDB:5IIT"
FT STRAND 195..203
FT /evidence="ECO:0007829|PDB:3G3T"
FT HELIX 205..207
FT /evidence="ECO:0007829|PDB:3G3T"
FT HELIX 208..216
FT /evidence="ECO:0007829|PDB:3G3T"
FT STRAND 221..223
FT /evidence="ECO:0007829|PDB:3G3R"
FT HELIX 232..235
FT /evidence="ECO:0007829|PDB:3G3T"
FT STRAND 236..243
FT /evidence="ECO:0007829|PDB:3G3T"
FT HELIX 248..254
FT /evidence="ECO:0007829|PDB:3G3T"
FT STRAND 261..270
FT /evidence="ECO:0007829|PDB:3G3T"
FT STRAND 275..282
FT /evidence="ECO:0007829|PDB:3G3T"
FT HELIX 286..288
FT /evidence="ECO:0007829|PDB:3G3T"
FT STRAND 293..300
FT /evidence="ECO:0007829|PDB:3G3T"
FT HELIX 301..303
FT /evidence="ECO:0007829|PDB:3G3T"
FT HELIX 304..308
FT /evidence="ECO:0007829|PDB:3G3T"
FT STRAND 310..312
FT /evidence="ECO:0007829|PDB:5IIG"
FT HELIX 314..323
FT /evidence="ECO:0007829|PDB:3G3T"
FT HELIX 329..348
FT /evidence="ECO:0007829|PDB:3G3T"
FT STRAND 352..366
FT /evidence="ECO:0007829|PDB:3G3T"
FT STRAND 369..384
FT /evidence="ECO:0007829|PDB:3G3T"
FT TURN 393..396
FT /evidence="ECO:0007829|PDB:3G3R"
FT STRAND 397..399
FT /evidence="ECO:0007829|PDB:3G3T"
FT HELIX 414..416
FT /evidence="ECO:0007829|PDB:3G3T"
FT STRAND 417..419
FT /evidence="ECO:0007829|PDB:3G3T"
FT STRAND 423..431
FT /evidence="ECO:0007829|PDB:3G3T"
FT HELIX 439..445
FT /evidence="ECO:0007829|PDB:3G3T"
FT STRAND 447..449
FT /evidence="ECO:0007829|PDB:3G3Q"
FT STRAND 450..452
FT /evidence="ECO:0007829|PDB:5IIG"
FT HELIX 458..466
FT /evidence="ECO:0007829|PDB:3G3T"
FT TURN 467..470
FT /evidence="ECO:0007829|PDB:3G3T"
SQ SEQUENCE 721 AA; 83155 MW; C05234576347CC98 CRC64;
MKFGEHLSKS LIRQYSYYYI SYDDLKTELE DNLSKNNGQW TQELETDFLE SLEIELDKVY
TFCKVKHSEV FRRVKEVQEQ VQHTVRLLDS NNPPTQLDFE ILEEELSDII ADVHDLAKFS
RLNYTGFQKI IKKHDKKTGF ILKPVFQVRL DSKPFFKENY DELVVKISQL YDIARTSGRP
IKGDSSAGGK QQNFVRQTTK YWVHPDNITE LKLIILKHLP VLVFNTNKEF EREDSAITSI
YFDNENLDLY YGRLRKDEGA EAHRLRWYGG MSTDTIFVER KTHREDWTGE KSVKARFALK
ERHVNDFLKG KYTVDQVFAK MRKEGKKPMN EIENLEALAS EIQYVMLKKK LRPVVRSFYN
RTAFQLPGDA RVRISLDTEL TMVREDNFDG VDRTHKNWRR TDIGVDWPFK QLDDKDICRF
PYAVLEVKLQ TQLGQEPPEW VRELVGSHLV EPVPKFSKFI HGVATLLNDK VDSIPFWLPQ
MDVDIRKPPL PTNIEITRPG RSDNEDNDFD EDDEDDAALV AAMTNAPGNS LDIEESVGYG
ATSAPTSNTN HVVESANAAY YQRKIRNAEN PISKKYYEIV AFFDHYFNGD QISKIPKGTT
FDTQIRAPPG KTICVPVRVE PKVYFATERT YLSWLSISIL LGGVSTTLLT YGSPTAMIGS
IGFFITSLAV LIRTVMVYAK RVVNIRLKRA VDYEDKIGPG MVSVFLILSI LFSFFCNLVA
K
