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Serine/threonine-protein kinase VPS15 (EC 2.7.11.1) (Vacuolar protein sorting-associated protein 15) (AtVPS15)

 VPS15_ARATH             Reviewed;        1494 AA.
Q9M0E5;
25-OCT-2017, integrated into UniProtKB/Swiss-Prot.
01-OCT-2000, sequence version 1.
07-NOV-2018, entry version 155.
RecName: Full=Serine/threonine-protein kinase VPS15 {ECO:0000303|PubMed:21833541};
EC=2.7.11.1 {ECO:0000255|PROSITE-ProRule:PRU00159};
AltName: Full=Vacuolar protein sorting-associated protein 15 {ECO:0000303|PubMed:21833541};
Short=AtVPS15 {ECO:0000303|PubMed:21833541};
Name=VPS15 {ECO:0000303|PubMed:21833541};
OrderedLocusNames=At4g29380 {ECO:0000312|Araport:AT4G29380};
ORFNames=F17A13.200 {ECO:0000312|EMBL:CAB79696.1};
Arabidopsis thaliana (Mouse-ear cress).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
Arabidopsis.
NCBI_TaxID=3702;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=10617198; DOI=10.1038/47134;
Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G.,
Pohl T., Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N.,
Harris B., Ansorge W., Brandt P., Grivell L.A., Rieger M.,
Weichselgartner M., de Simone V., Obermaier B., Mache R., Mueller M.,
Kreis M., Delseny M., Puigdomenech P., Watson M., Schmidtheini T.,
Reichert B., Portetelle D., Perez-Alonso M., Boutry M., Bancroft I.,
Vos P., Hoheisel J., Zimmermann W., Wedler H., Ridley P.,
Langham S.-A., McCullagh B., Bilham L., Robben J.,
van der Schueren J., Grymonprez B., Chuang Y.-J., Vandenbussche F.,
Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R., Defoor E.,
Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W.,
Mooijman P., Klein Lankhorst R., Rose M., Hauf J., Koetter P.,
Berneiser S., Hempel S., Feldpausch M., Lamberth S., Van den Daele H.,
De Keyser A., Buysshaert C., Gielen J., Villarroel R., De Clercq R.,
van Montagu M., Rogers J., Cronin A., Quail M.A., Bray-Allen S.,
Clark L., Doggett J., Hall S., Kay M., Lennard N., McLay K., Mayes R.,
Pettett A., Rajandream M.A., Lyne M., Benes V., Rechmann S.,
Borkova D., Bloecker H., Scharfe M., Grimm M., Loehnert T.-H.,
Dose S., de Haan M., Maarse A.C., Schaefer M., Mueller-Auer S.,
Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D., Herzl A.,
Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R.,
Schnabl S., Hiller R., Schmidt W., Lecharny A., Aubourg S.,
Chefdor F., Cooke R., Berger C., Monfort A., Casacuberta E.,
Gibbons T., Weber N., Vandenbol M., Bargues M., Terol J., Torres A.,
Perez-Perez A., Purnelle B., Bent E., Johnson S., Tacon D., Jesse T.,
Heijnen L., Schwarz S., Scholler P., Heber S., Francs P., Bielke C.,
Frishman D., Haase D., Lemcke K., Mewes H.-W., Stocker S.,
Zaccaria P., Bevan M., Wilson R.K., de la Bastide M., Habermann K.,
Parnell L., Dedhia N., Gnoj L., Schutz K., Huang E., Spiegel L.,
Sekhon M., Murray J., Sheet P., Cordes M., Abu-Threideh J.,
Stoneking T., Kalicki J., Graves T., Harmon G., Edwards J.,
Latreille P., Courtney L., Cloud J., Abbott A., Scott K., Johnson D.,
Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D.,
Du H., Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C.,
Antonoiu B., Zidanic M., Strong C., Sun H., Lamar B., Yordan C.,
Ma P., Zhong J., Preston R., Vil D., Shekher M., Matero A., Shah R.,
Swaby I.K., O'Shaughnessy A., Rodriguez M., Hoffman J., Till S.,
Granat S., Shohdy N., Hasegawa A., Hameed A., Lodhi M., Johnson A.,
Chen E., Marra M.A., Martienssen R., McCombie W.R.;
"Sequence and analysis of chromosome 4 of the plant Arabidopsis
thaliana.";
Nature 402:769-777(1999).
[2]
GENOME REANNOTATION.
STRAIN=cv. Columbia;
PubMed=27862469; DOI=10.1111/tpj.13415;
Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
Town C.D.;
"Araport11: a complete reannotation of the Arabidopsis thaliana
reference genome.";
Plant J. 89:789-804(2017).
[3]
FUNCTION, DISRUPTION PHENOTYPE, TISSUE SPECIFICITY, SUBCELLULAR
LOCATION, AND DEVELOPMENTAL STAGE.
STRAIN=cv. Columbia;
PubMed=21833541; DOI=10.1007/s11103-011-9806-9;
Xu N., Gao X.-Q., Zhao X.Y., Zhu D.Z., Zhou L.Z., Zhang X.S.;
"Arabidopsis AtVPS15 is essential for pollen development and
germination through modulating phosphatidylinositol 3-phosphate
formation.";
Plant Mol. Biol. 77:251-260(2011).
[4]
FUNCTION, DISRUPTION PHENOTYPE, TISSUE SPECIFICITY, INTERACTION WITH
VPS34, DEVELOPMENTAL STAGE, AND SUBCELLULAR LOCATION.
STRAIN=cv. Columbia;
PubMed=22361507; DOI=10.1016/j.jgg.2012.01.002;
Wang W.-Y., Zhang L., Xing S., Ma Z., Liu J., Gu H., Qin G., Qu L.-J.;
"Arabidopsis AtVPS15 plays essential roles in pollen germination
possibly by interacting with AtVPS34.";
J. Genet. Genomics 39:81-92(2012).
-!- FUNCTION: Serine/threonine-protein kinase required for cytoplasm
to vacuole transport (Cvt) and autophagy as a part of the
autophagy-specific VPS34 PI3-kinase complex I (By similarity).
Required for pollen development and germination, probably via the
modulation of phosphatidylinositol 3-phosphate (PI3P) formation
and vacuolar organization (PubMed:21833541, PubMed:22361507).
{ECO:0000250|UniProtKB:P22219, ECO:0000269|PubMed:21833541,
ECO:0000269|PubMed:22361507}.
-!- CATALYTIC ACTIVITY: ATP + a protein = ADP + a phosphoprotein.
{ECO:0000255|PROSITE-ProRule:PRU00159}.
-!- SUBUNIT: Interacts with VPS34. {ECO:0000269|PubMed:22361507}.
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:21833541}.
Golgi apparatus, trans-Golgi network membrane
{ECO:0000250|UniProtKB:P22219}; Lipid-anchor
{ECO:0000250|UniProtKB:P22219}. Endosome membrane
{ECO:0000269|PubMed:22361507}; Lipid-anchor
{ECO:0000250|UniProtKB:P22219}.
-!- TISSUE SPECIFICITY: Mainly expressed in anthers, pollen grains and
pollen tubes, and, to a lower extent, in other tissues and organs
including seedlings, roots, stems, leaves, flowers, pitils and
siliques. {ECO:0000269|PubMed:21833541,
ECO:0000269|PubMed:22361507}.
-!- DEVELOPMENTAL STAGE: In anthers, barely detected in
microsporocytes at stage 6, but accumulates strongly in tetrads at
stage 7, microspores, mature pollen grains, and tapetum cells.
Also detectable in the growing pollen tubes on the stigma.
{ECO:0000269|PubMed:21833541, ECO:0000269|PubMed:22361507}.
-!- PTM: Autophosphorylated. {ECO:0000250|UniProtKB:P22219}.
-!- DISRUPTION PHENOTYPE: Reduced male gametophyte transmission.
Abnormal pollen grains with unusual large vacuoles. Reduced pollen
germination rescued by phosphatidylinositol 3-phosphate (PI3P)
treatment. {ECO:0000269|PubMed:21833541,
ECO:0000269|PubMed:22361507}.
-!- SIMILARITY: Belongs to the protein kinase superfamily. Ser/Thr
protein kinase family. {ECO:0000255|PROSITE-ProRule:PRU00159}.
-----------------------------------------------------------------------
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EMBL; AL161574; CAB79696.1; -; Genomic_DNA.
EMBL; CP002687; AEE85624.1; -; Genomic_DNA.
RefSeq; NP_194667.1; NM_119083.3.
UniGene; At.27874; -.
ProteinModelPortal; Q9M0E5; -.
STRING; 3702.AT4G29380.1; -.
iPTMnet; Q9M0E5; -.
PaxDb; Q9M0E5; -.
PRIDE; Q9M0E5; -.
EnsemblPlants; AT4G29380.1; AT4G29380.1; AT4G29380.
GeneID; 829059; -.
Gramene; AT4G29380.1; AT4G29380.1; AT4G29380.
KEGG; ath:AT4G29380; -.
Araport; AT4G29380; -.
TAIR; locus:2118234; AT4G29380.
eggNOG; KOG1240; Eukaryota.
eggNOG; ENOG410XPDN; LUCA.
HOGENOM; HOG000030331; -.
InParanoid; Q9M0E5; -.
KO; K08333; -.
OMA; WCILYPS; -.
OrthoDB; EOG09360091; -.
PhylomeDB; Q9M0E5; -.
Reactome; R-ATH-1632852; Macroautophagy.
Reactome; R-ATH-1660514; Synthesis of PIPs at the Golgi membrane.
Reactome; R-ATH-1660516; Synthesis of PIPs at the early endosome membrane.
Reactome; R-ATH-1660517; Synthesis of PIPs at the late endosome membrane.
Reactome; R-ATH-5668599; RHO GTPases Activate NADPH Oxidases.
PRO; PR:Q9M0E5; -.
Proteomes; UP000006548; Chromosome 4.
ExpressionAtlas; Q9M0E5; baseline and differential.
GO; GO:0080008; C:Cul4-RING E3 ubiquitin ligase complex; ISS:TAIR.
GO; GO:0005737; C:cytoplasm; IDA:TAIR.
GO; GO:0010008; C:endosome membrane; IDA:UniProtKB.
GO; GO:0005794; C:Golgi apparatus; IEA:UniProtKB-SubCell.
GO; GO:0005770; C:late endosome; IBA:GO_Central.
GO; GO:0005643; C:nuclear pore; IBA:GO_Central.
GO; GO:0071561; C:nucleus-vacuole junction; IBA:GO_Central.
GO; GO:0034271; C:phosphatidylinositol 3-kinase complex, class III, type I; IBA:GO_Central.
GO; GO:0034272; C:phosphatidylinositol 3-kinase complex, class III, type II; IBA:GO_Central.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0004674; F:protein serine/threonine kinase activity; IBA:GO_Central.
GO; GO:0030242; P:autophagy of peroxisome; IBA:GO_Central.
GO; GO:0045324; P:late endosome to vacuole transport; IBA:GO_Central.
GO; GO:0016236; P:macroautophagy; IBA:GO_Central.
GO; GO:0048015; P:phosphatidylinositol-mediated signaling; IMP:UniProtKB.
GO; GO:0009555; P:pollen development; IMP:TAIR.
GO; GO:0009846; P:pollen germination; IMP:UniProtKB.
GO; GO:0006468; P:protein phosphorylation; IBA:GO_Central.
GO; GO:0006623; P:protein targeting to vacuole; IBA:GO_Central.
Gene3D; 1.25.10.10; -; 1.
Gene3D; 2.130.10.10; -; 1.
InterPro; IPR011989; ARM-like.
InterPro; IPR016024; ARM-type_fold.
InterPro; IPR000357; HEAT.
InterPro; IPR021133; HEAT_type_2.
InterPro; IPR011009; Kinase-like_dom_sf.
InterPro; IPR000719; Prot_kinase_dom.
InterPro; IPR008271; Ser/Thr_kinase_AS.
InterPro; IPR015943; WD40/YVTN_repeat-like_dom_sf.
InterPro; IPR001680; WD40_repeat.
InterPro; IPR017986; WD40_repeat_dom.
InterPro; IPR036322; WD40_repeat_dom_sf.
Pfam; PF02985; HEAT; 1.
Pfam; PF00069; Pkinase; 1.
Pfam; PF00400; WD40; 1.
SMART; SM00220; S_TKc; 1.
SMART; SM00320; WD40; 5.
SUPFAM; SSF48371; SSF48371; 1.
SUPFAM; SSF50978; SSF50978; 1.
SUPFAM; SSF56112; SSF56112; 1.
PROSITE; PS50077; HEAT_REPEAT; 2.
PROSITE; PS50011; PROTEIN_KINASE_DOM; 1.
PROSITE; PS00108; PROTEIN_KINASE_ST; 1.
PROSITE; PS50082; WD_REPEATS_2; 4.
PROSITE; PS50294; WD_REPEATS_REGION; 3.
1: Evidence at protein level;
ATP-binding; Autophagy; Complete proteome; Cytoplasm; Endosome;
Golgi apparatus; Kinase; Lipoprotein; Membrane; Myristate;
Nucleotide-binding; Phosphoprotein; Protein transport;
Reference proteome; Repeat; Serine/threonine-protein kinase;
Transferase; Transport; WD repeat.
INIT_MET 1 1 Removed. {ECO:0000255}.
CHAIN 2 1494 Serine/threonine-protein kinase VPS15.
/FTId=PRO_0000441931.
DOMAIN 27 307 Protein kinase. {ECO:0000255|PROSITE-
ProRule:PRU00159}.
REPEAT 383 421 HEAT 1. {ECO:0000255}.
REPEAT 480 517 HEAT 2. {ECO:0000255}.
REPEAT 524 562 HEAT 3. {ECO:0000255}.
REPEAT 610 646 HEAT 4. {ECO:0000255}.
REPEAT 648 685 HEAT 5. {ECO:0000255}.
REPEAT 687 724 HEAT 6. {ECO:0000255}.
REPEAT 727 764 HEAT 7. {ECO:0000255}.
REPEAT 1079 1118 WD 1. {ECO:0000255}.
REPEAT 1127 1166 WD 2. {ECO:0000255}.
REPEAT 1184 1226 WD 3. {ECO:0000255}.
REPEAT 1231 1270 WD 4. {ECO:0000255}.
REPEAT 1276 1323 WD 5. {ECO:0000255}.
REPEAT 1371 1409 WD 6. {ECO:0000255}.
REPEAT 1466 1494 WD 7. {ECO:0000255}.
NP_BIND 33 41 ATP. {ECO:0000255|PROSITE-
ProRule:PRU00159}.
COMPBIAS 953 1065 Ser-rich. {ECO:0000255|PROSITE-
ProRule:PRU00016}.
ACT_SITE 149 149 Proton acceptor. {ECO:0000255|PROSITE-
ProRule:PRU00159}.
BINDING 54 54 ATP. {ECO:0000255|PROSITE-
ProRule:PRU00159}.
LIPID 2 2 N-myristoyl glycine. {ECO:0000255}.
SEQUENCE 1494 AA; 168124 MW; 78D71855073E8BFD CRC64;
MGNKIARTTQ VSATEYYLHD LPSSYNLVLK EVLGRGRFLK SIQCKHDEGL VVVKVYFKRG
DSIDLREYER RLVKIKDVFL SLEHPHVWPF QFWQETDKAA YLVRQYFYSN LHDRLSTRPF
LSLVEKKWLA FQLLLAVKQC HEKDICHGDI KCENVLLTSW NWLYLADFAS FKPTYIPYDD
PSDFSFFFDT RGQRLCYLAP ERFYEHGGET QVAQDAPLKP SMDIFAVGCV IAELFLEGQP
LFELAQLLAY RRGQHDPSQH LEKIPDPGIR KMILHMIQLE PEARLSAEDY LQNYVGVVFP
NYFSPFLHTL YCCWNPLPSD MRVATCQGIF QEILKKMMEN KSGDEIGVDS PVTSNPMNAS
TVQETFANHK LNSSKDLIRN TVNSKDEIFY SISDALKKNR HPFLKKITMD DLGTLMSLYD
SRSDTYGTPF LPVEGNMRCE GMVLIASMLC SCIRNIKLPH LRREAILLLR SCSLYIDDDD
RLQRVLPYVV ALLSDPTAIV RCAAMETLCD ILPLVRDFPP SDAKIFPEYI FPMLSMLPED
TEESVRICYA SNIAKLALTA YGFLIHSFQL SDVGVLNELN SQQISTTPAS ETPSHLQKAN
GNAQLQQLRK TIAEVVQELV MGPKQTPNVR RALLQDIGEL CFFFGQRQSN DFLLPILPAF
LNDRDEQLRS VFFEKIVYVC FFVGQRSVEE YLLPYIDQAL SDQTEAVIVN ALECLSTLCK
SSFLRKRALL QMIECVYPLL CYPSQWVRRA VVTFIAASSE CLGAVDSYAF IAPVIRSYLS
RLPASIASEE GLLSCLKPPV TREVVYRIFE KTRNPEFMAK QRKMWYSSSP QSKDWESVDL
FDKDAGELNS VECRAEQKQS VEGKKQIKSA SKQPEVQGKY AEKDAKLRIP RNPRPNASNT
VELRDPVYPE KLQFSGFMAP YVSGANSFIE PENIPLYSFS MDKRAATNPP VASESSLQMN
SLGMGSLSVP WMDSMSKSFN LASSVPVPKL ISGSFHVGTN PKQFYRVVHE PESRENDQIS
SAISKFQDLG VSSSSKSASV TSEDASSPAD LVGEPSLSRT SVPDSGWKPR GVLVAHLQEH
RSAVNDIATS SDHSFFVSAS DDSTVKVWDS RKLEKDISFR SRLTYHLEGS RGMCTTMLRN
STQVVVGASD GVIHMFSIDH ISRGLGNVVE KYSGIVDIKK KDVKEGALVS LLNYTADSLS
GPMVMYSTQN CGIHLWDTRS DLDAWTLKAN PEEGYVSSLV TSPCGNWFVS GSSRGVLTLW
DLRFRVPVNS WQYPIICPIE KMCLCFLPPS VSVSTTMKPL IYVAAGCNEV SLWNAEGGSC
HQVLRVANYE NETDVSEFQW KLPSNKVNPK PNHRQNMSSK YRIEELNEPP PRLPGIRSLL
PLPGGDLLTG GTDLKIRRWD YSSPERSYCI CGPSLKGVGN DDFYELKTNT GVQFVQETKR
RPLATKLTAK AVLAAAATDT AGCHRDSVQS LASVKLNQRL LISSSRDGAI KVWK


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