VPS39_ARATH
ID VPS39_ARATH Reviewed; 1000 AA.
AC Q8L5Y0; A0A1P8B4G5; C0Z240; O23218; Q304A1;
DT 23-MAY-2018, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2002, sequence version 1.
DT 25-MAY-2022, entry version 119.
DE RecName: Full=Vacuolar sorting protein 39 {ECO:0000303|PubMed:12589039};
DE AltName: Full=Protein EMBRYO DEFECTIVE 2754 {ECO:0000303|PubMed:15266054};
GN Name=VPS39 {ECO:0000303|PubMed:12589039};
GN Synonyms=EMB2754 {ECO:0000303|PubMed:15266054};
GN OrderedLocusNames=At4g36630 {ECO:0000312|Araport:AT4G36630};
GN ORFNames=AP22.59 {ECO:0000312|EMBL:CAB80329.1},
GN C7A10.730 {ECO:0000312|EMBL:CAB16830.1};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=9461215; DOI=10.1038/35140;
RA Bevan M., Bancroft I., Bent E., Love K., Goodman H.M., Dean C.,
RA Bergkamp R., Dirkse W., van Staveren M., Stiekema W., Drost L., Ridley P.,
RA Hudson S.-A., Patel K., Murphy G., Piffanelli P., Wedler H., Wedler E.,
RA Wambutt R., Weitzenegger T., Pohl T., Terryn N., Gielen J., Villarroel R.,
RA De Clercq R., van Montagu M., Lecharny A., Aubourg S., Gy I., Kreis M.,
RA Lao N., Kavanagh T., Hempel S., Kotter P., Entian K.-D., Rieger M.,
RA Schaefer M., Funk B., Mueller-Auer S., Silvey M., James R., Monfort A.,
RA Pons A., Puigdomenech P., Douka A., Voukelatou E., Milioni D.,
RA Hatzopoulos P., Piravandi E., Obermaier B., Hilbert H., Duesterhoeft A.,
RA Moores T., Jones J.D.G., Eneva T., Palme K., Benes V., Rechmann S.,
RA Ansorge W., Cooke R., Berger C., Delseny M., Voet M., Volckaert G.,
RA Mewes H.-W., Klosterman S., Schueller C., Chalwatzis N.;
RT "Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis
RT thaliana.";
RL Nature 391:485-488(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3).
RC STRAIN=cv. Columbia; TISSUE=Rosette leaf;
RX PubMed=19423640; DOI=10.1093/dnares/dsp009;
RA Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M.,
RA Shinozaki K.;
RT "Analysis of multiple occurrences of alternative splicing events in
RT Arabidopsis thaliana using novel sequenced full-length cDNAs.";
RL DNA Res. 16:155-164(2009).
RN [6]
RP IDENTIFICATION.
RX PubMed=12589039; DOI=10.1091/mbc.e02-08-0509;
RA Rojo E., Zouhar J., Kovaleva V., Hong S., Raikhel N.V.;
RT "The AtC-VPS protein complex is localized to the tonoplast and the
RT prevacuolar compartment in arabidopsis.";
RL Mol. Biol. Cell 14:361-369(2003).
RN [7]
RP FUNCTION [LARGE SCALE ANALYSIS], AND DISRUPTION PHENOTYPE [LARGE SCALE
RP ANALYSIS].
RC STRAIN=cv. Columbia;
RX PubMed=15266054; DOI=10.1104/pp.104.045179;
RA Tzafrir I., Pena-Muralla R., Dickerman A., Berg M., Rogers R., Hutchens S.,
RA Sweeney T.C., McElver J., Aux G., Patton D., Meinke D.;
RT "Identification of genes required for embryo development in Arabidopsis.";
RL Plant Physiol. 135:1206-1220(2004).
RN [8]
RP FUNCTION, DISRUPTION PHENOTYPE, INTERACTION WITH VPS11 AND RABG3B, SUBUNIT,
RP IDENTIFICATION BY MASS SPECTROMETRY, AND SUBCELLULAR LOCATION.
RX PubMed=29463724; DOI=10.1073/pnas.1717839115;
RA Takemoto K., Ebine K., Askani J.C., Krueger F., Gonzalez Z.A., Ito E.,
RA Goh T., Schumacher K., Nakano A., Ueda T.;
RT "Distinct sets of tethering complexes, SNARE complexes, and Rab GTPases
RT mediate membrane fusion at the vacuole in Arabidopsis.";
RL Proc. Natl. Acad. Sci. U.S.A. 115:E2457-E2466(2018).
CC -!- FUNCTION: Essential protein required during embryogenesis
CC (PubMed:15266054, PubMed:29463724). Believed to act in part as a
CC component of the putative HOPS endosomal tethering complex. HOPS is
CC required for the central vacuole formation (PubMed:29463724). May play
CC a role in clustering and fusion of late endosomes and lysosomes. Plays
CC a role in vesicle-mediated protein trafficking to lysosomal
CC compartments including the endocytic membrane transport and autophagic
CC pathways. Required for fusion of endosomes and autophagosomes with
CC lysosomes (By similarity). {ECO:0000250|UniProtKB:Q96JC1,
CC ECO:0000269|PubMed:15266054, ECO:0000269|PubMed:29463724}.
CC -!- SUBUNIT: Homooligomer (By similarity). Component of the homotypic
CC fusion and vacuole protein sorting (HOPS) complex composed of the class
CC C Vps core proteins VPS11, VCL1, VPS18 and VPS33, which in HOPS further
CC associates with VPS39 and VPS41 (PubMed:29463724). Interacts directly
CC with VPS11. Binds to RABG3B (PubMed:29463724).
CC {ECO:0000250|UniProtKB:Q96JC1, ECO:0000269|PubMed:29463724}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:29463724}. Vacuole
CC membrane {ECO:0000269|PubMed:29463724}; Peripheral membrane protein
CC {ECO:0000269|PubMed:29463724}; Cytoplasmic side {ECO:0000305}. Note=Co-
CC localizes with VPS18 and RABG3F at subdomains of the vacuolar membrane
CC with a small number of punctate structures in the cytoplasm. Sometimes
CC observed at the vertex zone, the ring-shaped edge of vacuole-vacuole
CC contact sites. Strong colocalization with VAMP713 at the contact sites
CC of two vacuoles. {ECO:0000269|PubMed:29463724}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=3;
CC Name=1;
CC IsoId=Q8L5Y0-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q8L5Y0-2; Sequence=VSP_059581, VSP_059582;
CC Name=3;
CC IsoId=Q8L5Y0-3; Sequence=VSP_059580, VSP_059581, VSP_059582;
CC -!- DISRUPTION PHENOTYPE: Defective embryo arrested at cotyledon stage
CC (PubMed:15266054, PubMed:29463724). Heterozygous mutants produce some
CC yellowish seeds with developmentally retarded or abnormally shaped
CC embryos. Conditional dexamethasone (DEX)-inducible mutants exhibit
CC altered vacuolar morphology showing fragmented round vacuoles
CC (PubMed:29463724). {ECO:0000269|PubMed:15266054,
CC ECO:0000269|PubMed:29463724}.
CC -!- SIMILARITY: Belongs to the VAM6/VPS39 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB16830.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB80329.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC -!- WEB RESOURCE: Name=Seed defective Arabidopsis mutants;
CC URL="http://seedgenes.org/MutantList";
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DR EMBL; Z99708; CAB16830.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161589; CAB80329.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE86679.1; -; Genomic_DNA.
DR EMBL; CP002687; ANM66487.1; -; Genomic_DNA.
DR EMBL; AY099879; AAM20730.1; -; mRNA.
DR EMBL; AK318654; BAH56769.1; -; mRNA.
DR PIR; E85432; E85432.
DR RefSeq; NP_001328378.1; NM_001342413.1. [Q8L5Y0-2]
DR RefSeq; NP_195381.6; NM_119826.8. [Q8L5Y0-1]
DR AlphaFoldDB; Q8L5Y0; -.
DR SMR; Q8L5Y0; -.
DR STRING; 3702.AT4G36630.1; -.
DR iPTMnet; Q8L5Y0; -.
DR PaxDb; Q8L5Y0; -.
DR PRIDE; Q8L5Y0; -.
DR ProteomicsDB; 242482; -. [Q8L5Y0-1]
DR EnsemblPlants; AT4G36630.1; AT4G36630.1; AT4G36630. [Q8L5Y0-1]
DR EnsemblPlants; AT4G36630.2; AT4G36630.2; AT4G36630. [Q8L5Y0-2]
DR GeneID; 829815; -.
DR Gramene; AT4G36630.1; AT4G36630.1; AT4G36630. [Q8L5Y0-1]
DR Gramene; AT4G36630.2; AT4G36630.2; AT4G36630. [Q8L5Y0-2]
DR KEGG; ath:AT4G36630; -.
DR Araport; AT4G36630; -.
DR TAIR; locus:2115355; AT4G36630.
DR eggNOG; KOG2063; Eukaryota.
DR HOGENOM; CLU_004190_0_0_1; -.
DR InParanoid; Q8L5Y0; -.
DR OMA; LFRLPNF; -.
DR OrthoDB; 291710at2759; -.
DR PhylomeDB; Q8L5Y0; -.
DR PRO; PR:Q8L5Y0; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q8L5Y0; baseline and differential.
DR GO; GO:0005737; C:cytoplasm; IDA:UniProtKB.
DR GO; GO:0030897; C:HOPS complex; IDA:UniProtKB.
DR GO; GO:0016020; C:membrane; IBA:GO_Central.
DR GO; GO:0009705; C:plant-type vacuole membrane; IDA:UniProtKB.
DR GO; GO:0005886; C:plasma membrane; HDA:TAIR.
DR GO; GO:0009506; C:plasmodesma; HDA:TAIR.
DR GO; GO:0006914; P:autophagy; IBA:GO_Central.
DR GO; GO:0034058; P:endosomal vesicle fusion; IBA:GO_Central.
DR GO; GO:0006886; P:intracellular protein transport; IEA:InterPro.
DR GO; GO:0007033; P:vacuole organization; IMP:UniProtKB.
DR InterPro; IPR000547; Clathrin_H-chain/VPS_repeat.
DR InterPro; IPR001180; CNH_dom.
DR InterPro; IPR032914; Vam6/VPS39/TRAP1.
DR InterPro; IPR019452; VPS39/TGF_beta_rcpt-assoc_1.
DR InterPro; IPR019453; VPS39/TGF_beta_rcpt-assoc_2.
DR InterPro; IPR036322; WD40_repeat_dom_sf.
DR PANTHER; PTHR12894; PTHR12894; 1.
DR Pfam; PF00637; Clathrin; 1.
DR Pfam; PF00780; CNH; 1.
DR Pfam; PF10366; Vps39_1; 1.
DR Pfam; PF10367; Vps39_2; 1.
DR SUPFAM; SSF50978; SSF50978; 1.
DR PROSITE; PS50219; CNH; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Autophagy; Cytoplasm; Membrane; Protein transport;
KW Reference proteome; Transport; Vacuole.
FT CHAIN 1..1000
FT /note="Vacuolar sorting protein 39"
FT /id="PRO_0000444307"
FT DOMAIN 16..282
FT /note="CNH"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00795"
FT REPEAT 607..796
FT /note="CHCR"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01006"
FT REGION 394..413
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 844..864
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 396..410
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT VAR_SEQ 1..353
FT /note="Missing (in isoform 3)"
FT /id="VSP_059580"
FT VAR_SEQ 902..916
FT /note="NLLPFLAPLLRNSSE -> VNVLNLTYTYPITTY (in isoform 2 and
FT isoform 3)"
FT /id="VSP_059581"
FT VAR_SEQ 917..1000
FT /note="Missing (in isoform 2 and isoform 3)"
FT /id="VSP_059582"
SQ SEQUENCE 1000 AA; 110639 MW; EB6D33933DAE99A0 CRC64;
MVHNAYDSFQ LLKDCPARID AVESYGSKLF AGCYDGSLRI YSPPESSASD PSELHQETYV
LEKTVAGFSK KPIVAMEVLA SRELLLSLSE SIAFHGLPNL ETVAVITKAK GANAYSWDDR
RGFLCFSRQK RVCVFKHDGG GGFVEVRDYG VPDTVKSISW CGENICLGIK KEYVILNTAN
GTLSEVFPSG RVAPPLVISL PSGELILGKE NIGVFVDQNG KLLQTERICW SEAPTSIVIQ
NPYAIALLPR RVEVRLLRSP YPLIQTIVLQ NIRRLVKSNN AVIVGLDNSV YVLFPVSIGA
QIVQLTASGN FEEALALCKV LPPDESSLRA AKESSIHTRF AHYLFENGSY EEAMEHFLAS
QVDITHVLSM YPSIILPKTT IIPQPDKMVD ISGDEASLSR GSSGISDDME SSSPRYFLES
EDNADLESKK MSHNTLMALI KYLLKRRPAV IEKATSEGTE EVISDAVGKT YGANDSSKSK
KSSKGRGMIP LNSGAREMAA ILDTALLQAL LHTGQSGAAI ELLKGVNYSD VKICEEILMK
SKNYSALLEL FKSNSMHHEA LKLLNQLADE SKTNQSQTDV TQIFSPELII EYLKPLCRTD
PMLVLEYSML VLESCPTQTI DLFLSGNISA DLVNSYLKQH APNMQGRYLE LMMAMNDTAV
SGNLQNEMVQ IYLSEVLDLY AAKSAQQKWD EKDHPPERKK LLSALESISG YSPQPLLKRL
PRDALYEERA VILGKMNQHE LALSIYVHKL HAPDLALAYC DRIYESVTYL PSGKPSSNIY
LTVLQIYLNP KKSAKDFAKR IVALGSFESS DTTKMMDSVL SSKAKGGRSK KIVAIEGAED
MRVGLSSSTD SGRSDVDTEE PLEEGDSTVM ISEVLDLLSQ RWERINGAQA LKLLPRETKL
HNLLPFLAPL LRNSSEAHRN FSVIKSLRQS ENLQVKEELY KHRKGVAQVT SESMCSLCNK
KIGTSVFAVY PNGKTLVHFV CFRDSQGMKA VSKTTHGRRR
