VPS54_ARATH
ID VPS54_ARATH Reviewed; 1034 AA.
AC F4JT76; O49467; Q0WUR3;
DT 22-JAN-2014, integrated into UniProtKB/Swiss-Prot.
DT 28-JUN-2011, sequence version 1.
DT 25-MAY-2022, entry version 69.
DE RecName: Full=Vacuolar protein sorting-associated protein 54, chloroplastic;
DE Short=AtVPS54;
DE Flags: Precursor;
GN Name=VPS54; OrderedLocusNames=At4g19490; ORFNames=F24J7.50;
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=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 [2]
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 [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP TISSUE SPECIFICITY, GENE FAMILY, AND NOMENCLATURE.
RX PubMed=15235115; DOI=10.1104/pp.103.037747;
RA Lobstein E., Guyon A., Ferault M., Twell D., Pelletier G., Bonhomme S.;
RT "The putative Arabidopsis homolog of yeast vps52p is required for pollen
RT tube elongation, localizes to Golgi, and might be involved in vesicle
RT trafficking.";
RL Plant Physiol. 135:1480-1490(2004).
RN [5]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=18583349; DOI=10.1093/jxb/ern162;
RA Guermonprez H., Smertenko A., Crosnier M.-T., Durandet M., Vrielynck N.,
RA Guerche P., Hussey P.J., Satiat-Jeunemaitre B., Bonhomme S.;
RT "The POK/AtVPS52 protein localizes to several distinct post-Golgi
RT compartments in sporophytic and gametophytic cells.";
RL J. Exp. Bot. 59:3087-3098(2008).
RN [6]
RP SUBCELLULAR LOCATION, SUBUNIT, AND INTERACTION WITH VPS53.
RX PubMed=21398432; DOI=10.1093/jxb/err060;
RA Wang L.-C., Tsai M.-C., Chang K.-Y., Fan Y.-S., Yeh C.-H., Wu S.-J.;
RT "Involvement of the Arabidopsis HIT1/AtVPS53 tethering protein homologue in
RT the acclimation of the plasma membrane to heat stress.";
RL J. Exp. Bot. 62:3609-3620(2011).
CC -!- FUNCTION: Acts as component of the GARP complex that is involved in
CC retrograde transport from early and late endosomes to the trans-Golgi
CC network (TGN). The GARP complex facilitates tethering as well as SNARE
CC complex assembly at the Golgi (By similarity). Probably involved in
CC pollen tube elongation and other polar growth. {ECO:0000250,
CC ECO:0000269|PubMed:18583349}.
CC -!- SUBUNIT: Component of the Golgi-associated retrograde protein (GARP)
CC complex, composed by VPS52, VPS53 and VPS54. Interacts directly with
CC VPS53. {ECO:0000269|PubMed:21398432}.
CC -!- SUBCELLULAR LOCATION: Golgi apparatus membrane; Peripheral membrane
CC protein. Golgi apparatus, trans-Golgi network membrane; Peripheral
CC membrane protein. Plastid, chloroplast. Note=Localized in the GARP
CC complex in the Golgi and post-Golgi compartments.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=F4JT76-1; Sequence=Displayed;
CC Name=2;
CC IsoId=F4JT76-2; Sequence=VSP_053517;
CC -!- TISSUE SPECIFICITY: Present in pollen. Mostly expressed in roots and
CC flower buds, and, at lower levels, in vegetative tissues and mature
CC flowers. {ECO:0000269|PubMed:15235115}.
CC -!- DISRUPTION PHENOTYPE: Lethal when homozygous. In hemizygous plants,
CC male-specific transmission defect. {ECO:0000269|PubMed:18583349}.
CC -!- SIMILARITY: Belongs to the VPS54 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAA16926.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB78951.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AL021768; CAA16926.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161551; CAB78951.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE84188.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE84189.1; -; Genomic_DNA.
DR EMBL; AK227083; BAE99135.1; -; mRNA.
DR PIR; T05209; T05209.
DR RefSeq; NP_193684.4; NM_118069.5. [F4JT76-1]
DR RefSeq; NP_849409.2; NM_179078.3. [F4JT76-1]
DR AlphaFoldDB; F4JT76; -.
DR SMR; F4JT76; -.
DR BioGRID; 12983; 1.
DR IntAct; F4JT76; 1.
DR STRING; 3702.AT4G19490.2; -.
DR iPTMnet; F4JT76; -.
DR PaxDb; F4JT76; -.
DR PRIDE; F4JT76; -.
DR ProteomicsDB; 242741; -. [F4JT76-1]
DR EnsemblPlants; AT4G19490.1; AT4G19490.1; AT4G19490. [F4JT76-1]
DR EnsemblPlants; AT4G19490.2; AT4G19490.2; AT4G19490. [F4JT76-1]
DR GeneID; 827690; -.
DR Gramene; AT4G19490.1; AT4G19490.1; AT4G19490. [F4JT76-1]
DR Gramene; AT4G19490.2; AT4G19490.2; AT4G19490. [F4JT76-1]
DR KEGG; ath:AT4G19490; -.
DR Araport; AT4G19490; -.
DR TAIR; locus:2122945; AT4G19490.
DR eggNOG; KOG2115; Eukaryota.
DR HOGENOM; CLU_005185_2_0_1; -.
DR InParanoid; F4JT76; -.
DR OMA; SQKQAVM; -.
DR OrthoDB; 449680at2759; -.
DR PRO; PR:F4JT76; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; F4JT76; baseline and differential.
DR Genevisible; F4JT76; AT.
DR GO; GO:0009507; C:chloroplast; IEA:UniProtKB-SubCell.
DR GO; GO:0005829; C:cytosol; IEA:GOC.
DR GO; GO:0000938; C:GARP complex; IDA:UniProtKB.
DR GO; GO:0000139; C:Golgi membrane; IDA:UniProtKB.
DR GO; GO:0019905; F:syntaxin binding; IBA:GO_Central.
DR GO; GO:0006896; P:Golgi to vacuole transport; IBA:GO_Central.
DR GO; GO:0015031; P:protein transport; IEA:UniProtKB-KW.
DR GO; GO:0042147; P:retrograde transport, endosome to Golgi; IBA:GO_Central.
DR InterPro; IPR039745; Vps54.
DR InterPro; IPR012501; Vps54_C.
DR PANTHER; PTHR12965; PTHR12965; 1.
DR Pfam; PF07928; Vps54; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Chloroplast; Coiled coil; Golgi apparatus; Membrane;
KW Plastid; Protein transport; Reference proteome; Transit peptide; Transport.
FT TRANSIT 1..87
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 88..1034
FT /note="Vacuolar protein sorting-associated protein 54,
FT chloroplastic"
FT /id="PRO_0000424847"
FT REGION 1..42
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 529..548
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 694..758
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 224..264
FT /evidence="ECO:0000255"
FT COMPBIAS 694..711
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 722..758
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT VAR_SEQ 1..471
FT /note="MDSHPSLMGRSITNSNRSSLDLGRPSSSSSSSPSPLTKSISDASSQSLSSIL
FT NNPHGGKSGVYGSDASWVGWWSSSTFVAPAEFAPVASTKLPGSELTRSDFHGYVSSISE
FT SHGRFEDIRKHTREESCGFDQESHVSGLAACLREVPSLYFKEDFALEDGATFRSACPFS
FT SLNENLALQEKLSQYLDVVELHLVKEISVRSDSFFEAQGQLQDLNVKIVEGCSRIRELK
FT ETIRLLDRNLVDSARQIQELSSTRINMLELQRKLRLILYVNQALSALKLLVASADCAGA
FT LDITDDLQNLLAGDELTGLYCFRHLRDHVTSSIDSINSILTSEFMRISIHDTGEIDVLI
FT LSAANIRGSISSNGNTGEEVKLEEEDTSTLCDRLLPLVIGLLRTAKFPSILRMYRDTLT
FT SEMKNAIKKAVADLLPILVARSLESDFSHGERSVDDGGGLSLASKLRTLSSEAFVNLLT
FT AIFKIV -> M (in isoform 2)"
FT /evidence="ECO:0000303|Ref.3"
FT /id="VSP_053517"
SQ SEQUENCE 1034 AA; 113865 MW; 0CA834634FB10D18 CRC64;
MDSHPSLMGR SITNSNRSSL DLGRPSSSSS SSPSPLTKSI SDASSQSLSS ILNNPHGGKS
GVYGSDASWV GWWSSSTFVA PAEFAPVAST KLPGSELTRS DFHGYVSSIS ESHGRFEDIR
KHTREESCGF DQESHVSGLA ACLREVPSLY FKEDFALEDG ATFRSACPFS SLNENLALQE
KLSQYLDVVE LHLVKEISVR SDSFFEAQGQ LQDLNVKIVE GCSRIRELKE TIRLLDRNLV
DSARQIQELS STRINMLELQ RKLRLILYVN QALSALKLLV ASADCAGALD ITDDLQNLLA
GDELTGLYCF RHLRDHVTSS IDSINSILTS EFMRISIHDT GEIDVLILSA ANIRGSISSN
GNTGEEVKLE EEDTSTLCDR LLPLVIGLLR TAKFPSILRM YRDTLTSEMK NAIKKAVADL
LPILVARSLE SDFSHGERSV DDGGGLSLAS KLRTLSSEAF VNLLTAIFKI VQAHLVRASE
VKKAIEWILC NIDGHYAADS VAAAIAVGAV AAETAQEIGF QGGSLVSSPL GKATSKAPPL
QGKSSDASSL MNMSRNFRAD VLRENTEAVF AACEVTHGRW AKLLGVRALL HPKLKLQEFM
SIYDLTQEFI TSTEKIGGRL GSSIRGTLQS QAKAFVDSQH ESRMTKLKAV LDQETWDEID
VPEEFQSIIS SLFASQRLIS GKVDDADLNS YHSNRLPLNG SLTSGSGDQN SELRNEKSES
SEGSVVSDAQ VKPTVSPESL ERSKAGVSSA TNNQSNQKAH GKSNLFYQGV GYHMVNCGLI
LLKMLSEYID MNNSLPALSS EIVLRVVEVL RFFNTRTCQL VLGAGAMQVS GLKSIKAKHL
ALASQVIDFT YTIIPETRRI LFSKVPETRK PLLSVEIDKV AQDFRIHRDE IYTKLVQIMR
ERLLAHLHGL PKVVEGWNRP PDTNKQTKEF AWPLTREVGY LHRVLSETLH EADVQAIFRQ
VISIIHTQTS QTLTNLEISS TEAKKRLKLH VELILKCIRS LPSDNANQSD IPNWGQLDEF
FAEHFREEEA GEAE
