(data stored in SCRATCH zone)

SWISSPROT: LIP5_ARATH

ID   LIP5_ARATH              Reviewed;         421 AA.
AC   Q9SZ15;
DT   07-JAN-2015, integrated into UniProtKB/Swiss-Prot.
DT   01-MAY-2000, sequence version 1.
DT   11-DEC-2019, entry version 123.
DE   RecName: Full=Protein HOMOLOG OF MAMMALIAN LYST-INTERACTING PROTEIN 5 {ECO:0000303|PubMed:17468262};
DE   AltName: Full=Protein EXTENSIN-LIKE;
DE            Short=EXT-LIKE;
GN   Name=LIP5 {ECO:0000303|PubMed:17468262};
GN   Synonyms=VTA1 {ECO:0000303|PubMed:24385429};
GN   OrderedLocusNames=At4g26750 {ECO:0000312|Araport:AT4G26750};
GN   ORFNames=F10M23.90 {ECO:0000312|EMBL:CAB36521.1};
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 {ECO:0000312|Proteomes:UP000006548};
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].
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   [4]
RP   FUNCTION, DISRUPTION PHENOTYPE, AND INTERACTION WITH SKD1/VPS4.
RC   STRAIN=cv. Columbia;
RX   PubMed=17468262; DOI=10.1105/tpc.106.049346;
RA   Haas T.J., Sliwinski M.K., Martinez D.E., Preuss M., Ebine K., Ueda T.,
RA   Nielsen E., Odorizzi G., Otegui M.S.;
RT   "The Arabidopsis AAA ATPase SKD1 is involved in multivesicular endosome
RT   function and interacts with its positive regulator LYST-INTERACTING
RT   PROTEIN5.";
RL   Plant Cell 19:1295-1312(2007).
RN   [5]
RP   INTERACTION WITH CHMP1A.
RX   PubMed=19304934; DOI=10.1105/tpc.108.064865;
RA   Spitzer C., Reyes F.C., Buono R., Sliwinski M.K., Haas T.J., Otegui M.S.;
RT   "The ESCRT-related CHMP1A and B proteins mediate multivesicular body
RT   sorting of auxin carriers in Arabidopsis and are required for plant
RT   development.";
RL   Plant Cell 21:749-766(2009).
RN   [6]
RP   HOMODIMER, AND INTERACTION WITH SKD1; CHMP1A; CHMP1B AND VPS60-1.
RC   STRAIN=cv. Columbia;
RX   PubMed=20663085; DOI=10.1111/j.1365-313x.2010.04310.x;
RA   Shahriari M., Keshavaiah C., Scheuring D., Sabovljevic A., Pimpl P.,
RA   Haeusler R.E., Huelskamp M., Schellmann S.;
RT   "The AAA-type ATPase AtSKD1 contributes to vacuolar maintenance of
RT   Arabidopsis thaliana.";
RL   Plant J. 64:71-85(2010).
RN   [7]
RP   ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, CLEAVAGE OF INITIATOR
RP   METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS SPECTROMETRY
RP   [LARGE SCALE ANALYSIS].
RX   PubMed=22223895; DOI=10.1074/mcp.m111.015131;
RA   Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T.,
RA   Giglione C.;
RT   "Comparative large-scale characterisation of plant vs. mammal proteins
RT   reveals similar and idiosyncratic N-alpha acetylation features.";
RL   Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012).
RN   [8]
RP   INTERACTION WITH PROS/AT4G24370.
RX   PubMed=24385429; DOI=10.1074/jbc.m113.529685;
RA   Reyes F.C., Buono R.A., Roschzttardtz H., Di Rubbo S., Yeun L.H.,
RA   Russinova E., Otegui M.S.;
RT   "A novel endosomal sorting complex required for transport (ESCRT) component
RT   in Arabidopsis thaliana controls cell expansion and development.";
RL   J. Biol. Chem. 289:4980-4988(2014).
RN   [9]
RP   FUNCTION, DISRUPTION PHENOTYPE, MUTAGENESIS OF SER-73; THR-153; SER-254;
RP   SER-285; SER-307; SER-323; PHE-388 AND PHE-395, INTERACTION WITH SKD1; MPK6
RP   AND MPK3, HOMODIMERIZATION, PHOSPHORYLATION BY MPK6 AND MPK3, INDUCTION BY
RP   PSEUDOMONAS SYRINGAE, AND SUBCELLULAR LOCATION.
RC   STRAIN=cv. Columbia;
RX   PubMed=25010425; DOI=10.1371/journal.ppat.1004243;
RA   Wang F., Shang Y., Fan B., Yu J.-Q., Chen Z.;
RT   "Arabidopsis LIP5, a positive regulator of multivesicular body biogenesis,
RT   is a critical target of pathogen-responsive MAPK cascade in plant basal
RT   defense.";
RL   PLoS Pathog. 10:E1004243-E1004243(2014).
CC   -!- FUNCTION: Involved in the endosomal multivesicular bodies (MVB)
CC       pathway. MVBs contain intraluminal vesicles (ILVs) that are generated
CC       by invagination and scission from the limiting membrane of the endosome
CC       and are delivered to lysosomes enabling degradation of membrane
CC       proteins (By similarity). Thought to be a cofactor of SKD1/VPS4, which
CC       catalyzes the disassembly of membrane-associated ESCRT-III
CC       (PubMed:17468262). Target of pathogen-responsive mitogen-activated
CC       protein kinases (MPKs) that plays a critical role in plant basal
CC       resistance to Pseudomonas syringae in a SKD1-dependent manner by
CC       promoting multivesicular bodies (MVBs) trafficking upon plant infection
CC       (PubMed:25010425). {ECO:0000250, ECO:0000269|PubMed:17468262,
CC       ECO:0000269|PubMed:25010425}.
CC   -!- SUBUNIT: Homodimer (PubMed:20663085, PubMed:25010425). Interacts with
CC       SKD1/VPS4, VPS60-1, CHMP1A and CHMP1B (PubMed:17468262,
CC       PubMed:19304934, PubMed:20663085). Binds to PROS/At4g24370
CC       (PubMed:24385429, PubMed:25010425). Interacts with MPK6 and MPK3
CC       (PubMed:25010425). {ECO:0000269|PubMed:17468262,
CC       ECO:0000269|PubMed:19304934, ECO:0000269|PubMed:20663085,
CC       ECO:0000269|PubMed:24385429, ECO:0000269|PubMed:25010425}.
CC   -!- INTERACTION:
CC       Q9ZNT0:SKD1; NbExp=2; IntAct=EBI-1606558, EBI-1606459;
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:25010425}. Endosome
CC       membrane {ECO:0000250|UniProtKB:Q9NP79}; Peripheral membrane protein
CC       {ECO:0000250|UniProtKB:Q9NP79}. Nucleus {ECO:0000269|PubMed:25010425}.
CC       Endosome, multivesicular body {ECO:0000269|PubMed:25010425}.
CC       Note=Localized in multivesicular body when associated with SKD1.
CC       {ECO:0000269|PubMed:25010425}.
CC   -!- INDUCTION: By Pseudomonas syringae pv. tomato strain DC3000
CC       (PstDC3000). {ECO:0000269|PubMed:25010425}.
CC   -!- PTM: Phosphorylated by activated MPK6 and MPK3, this activation is
CC       required to trigger multivesicular bodies (MVBs) trafficking upon plant
CC       infection. {ECO:0000269|PubMed:25010425}.
CC   -!- DISRUPTION PHENOTYPE: No strong phenotypic alterations under normal
CC       growth conditions; slightly slow growth, slightly pale green and flat
CC       leaves, and reduced seed yields (PubMed:17468262, PubMed:25010425).
CC       Increased sensitivity to Pseudomonas syringae pv. tomato strain DC3000
CC       (PstDC3000)(PubMed:25010425). {ECO:0000269|PubMed:17468262,
CC       ECO:0000269|PubMed:25010425}.
CC   -!- SIMILARITY: Belongs to the VTA1 family. {ECO:0000305}.
DR   EMBL; AL035440; CAB36521.1; -; Genomic_DNA.
DR   EMBL; AL161565; CAB79530.1; -; Genomic_DNA.
DR   EMBL; CP002687; AEE85248.1; -; Genomic_DNA.
DR   EMBL; AY048219; AAK82482.1; -; mRNA.
DR   EMBL; AY094009; AAM16165.1; -; mRNA.
DR   PIR; T04798; T04798.
DR   RefSeq; NP_194405.1; NM_118809.5.
DR   SMR; Q9SZ15; -.
DR   IntAct; Q9SZ15; 3.
DR   STRING; 3702.AT4G26750.1; -.
DR   iPTMnet; Q9SZ15; -.
DR   PaxDb; Q9SZ15; -.
DR   PRIDE; Q9SZ15; -.
DR   EnsemblPlants; AT4G26750.1; AT4G26750.1; AT4G26750.
DR   GeneID; 828782; -.
DR   Gramene; AT4G26750.1; AT4G26750.1; AT4G26750.
DR   KEGG; ath:AT4G26750; -.
DR   Araport; AT4G26750; -.
DR   TAIR; locus:2116437; AT4G26750.
DR   eggNOG; KOG0917; Eukaryota.
DR   eggNOG; ENOG4111H3M; LUCA.
DR   HOGENOM; HOG000241805; -.
DR   InParanoid; Q9SZ15; -.
DR   KO; K12199; -.
DR   OMA; GHARYAY; -.
DR   OrthoDB; 1450538at2759; -.
DR   PhylomeDB; Q9SZ15; -.
DR   PRO; PR:Q9SZ15; -.
DR   Proteomes; UP000006548; Chromosome 4.
DR   ExpressionAtlas; Q9SZ15; baseline and differential.
DR   Genevisible; Q9SZ15; AT.
DR   GO; GO:0005737; C:cytoplasm; IDA:UniProtKB.
DR   GO; GO:0010008; C:endosome membrane; IEA:UniProtKB-SubCell.
DR   GO; GO:0005771; C:multivesicular body; IDA:UniProtKB.
DR   GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR   GO; GO:0042803; F:protein homodimerization activity; IDA:UniProtKB.
DR   GO; GO:0009814; P:defense response, incompatible interaction; IMP:UniProtKB.
DR   GO; GO:0080001; P:mucilage extrusion from seed coat; IMP:TAIR.
DR   GO; GO:1900426; P:positive regulation of defense response to bacterium; IMP:TAIR.
DR   GO; GO:0015031; P:protein transport; IEA:UniProtKB-KW.
DR   GO; GO:1903335; P:regulation of vacuolar transport; IGI:TAIR.
DR   GO; GO:0016192; P:vesicle-mediated transport; IPI:TAIR.
DR   Gene3D; 1.25.40.270; -; 1.
DR   InterPro; IPR023175; VPS_Vta1/CALS_N.
DR   InterPro; IPR039431; Vta1/CALS_N.
DR   InterPro; IPR041212; Vta1_C.
DR   Pfam; PF04652; Vta1; 1.
DR   Pfam; PF18097; Vta1_C; 1.
PE   1: Evidence at protein level;
DR   PRODOM; Q9SZ15.
DR   SWISS-2DPAGE; Q9SZ15.
KW   Acetylation; Cytoplasm; Endosome; Membrane; Nucleus; Phosphoprotein;
KW   Plant defense; Protein transport; Reference proteome; Transport.
FT   INIT_MET        1
FT                   /note="Removed"
FT                   /evidence="ECO:0000244|PubMed:22223895"
FT   CHAIN           2..421
FT                   /note="Protein HOMOLOG OF MAMMALIAN LYST-INTERACTING
FT                   PROTEIN 5"
FT                   /id="PRO_0000431529"
FT   COMPBIAS        208..360
FT                   /note="Pro-rich"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00015"
FT   MOD_RES         2
FT                   /note="N-acetylserine"
FT                   /evidence="ECO:0000244|PubMed:22223895"
FT   MUTAGEN         73
FT                   /note="S->A: Loss of MK3/MK6-mediated phosphorylation; when
FT                   associated with A-153; A-254; A-285; A-307 and A-323."
FT                   /evidence="ECO:0000269|PubMed:25010425"
FT   MUTAGEN         153
FT                   /note="T->A: Loss of MK3/MK6-mediated phosphorylation; when
FT                   associated with A-73; A-254; A-285; A-307 and A-323."
FT                   /evidence="ECO:0000269|PubMed:25010425"
FT   MUTAGEN         254
FT                   /note="S->A: Loss of MK3/MK6-mediated phosphorylation; when
FT                   associated with A-73; A-153; A-285; A-307 and A-323."
FT                   /evidence="ECO:0000269|PubMed:25010425"
FT   MUTAGEN         285
FT                   /note="S->A: Loss of MK3/MK6-mediated phosphorylation; when
FT                   associated with A-73; A-153; A-254; A-307 and A-323."
FT                   /evidence="ECO:0000269|PubMed:25010425"
FT   MUTAGEN         307
FT                   /note="S->A: Loss of MK3/MK6-mediated phosphorylation; when
FT                   associated with A-73; A-153; A-254; A-285 and A-323."
FT                   /evidence="ECO:0000269|PubMed:25010425"
FT   MUTAGEN         323
FT                   /note="S->A: Loss of MK3/MK6-mediated phosphorylation; when
FT                   associated with A-73; A-153; A-254; A-285 and A-307."
FT                   /evidence="ECO:0000269|PubMed:25010425"
FT   MUTAGEN         388
FT                   /note="F->A: Reduced SKD1 interaction."
FT                   /evidence="ECO:0000269|PubMed:25010425"
FT   MUTAGEN         395
FT                   /note="F->A: Loss of SKD1 interaction."
FT                   /evidence="ECO:0000269|PubMed:25010425"
SQ   SEQUENCE   421 AA;  46218 MW;  1BD515B10FA4FA77 CRC64;
     MSNPNEPARA LLPYLQRADE LQKHEPLVAY YCRLYAMERG LKIPQSERTK TTNSILMSLI
     NQLEKDKKSL TLSPDDNMHV EGFALSVFAK ADKQDRAGRA DLGTAKTFYA ASIFFEILSQ
     FGPVPPDIEQ KHKYAAWKAA DIRKAIKEGR KPTPGDPVDD DTDLSIPSSG PSGSYDHSAS
     DTNTTSHHRT ELDPPHDSND DSSHHQFPEV PQHPLPPRFY DNPTNDYPAD VPPPPPSSYP
     SNDHLPPPTG PSDSPYPHPY SHQPYHQDPP KHMPPPQNYS SHEPSPNSLP NFQSYPSFSE
     SSLPSTSPHY PSHYQNPEPY YSSPHSAPAP SSTSFSSAPP PPPYSSNGRI NIAPVLDPAP
     SSAQKYHYDS SYQPGPEKVA EALKAARFAV GALAFDEVST AVEHLKKSLE LLTNPSAGAG
     H
//

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