VPS9A_ORYSJ
ID VPS9A_ORYSJ Reviewed; 480 AA.
AC Q10NQ3; Q0DT93;
DT 10-OCT-2018, integrated into UniProtKB/Swiss-Prot.
DT 22-AUG-2006, sequence version 1.
DT 03-AUG-2022, entry version 80.
DE RecName: Full=Vacuolar protein sorting-associated protein 9A {ECO:0000303|PubMed:23723154};
DE Short=OsVPS9A {ECO:0000303|PubMed:23723154};
DE AltName: Full=Protein GLUTELIN PRECURSOR ACCUMULATION 2 {ECO:0000303|PubMed:23723154};
GN Name=VPS9A {ECO:0000303|PubMed:23723154};
GN Synonyms=GPA2 {ECO:0000303|PubMed:23723154};
GN OrderedLocusNames=Os03g0262900 {ECO:0000312|EMBL:BAS83374.1},
GN LOC_Os03g15650 {ECO:0000312|EMBL:ABF95105.1};
GN ORFNames=OsJ_10226 {ECO:0000312|EMBL:EEE58741.1};
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16109971; DOI=10.1101/gr.3869505;
RG The rice chromosome 3 sequencing consortium;
RA Buell C.R., Yuan Q., Ouyang S., Liu J., Zhu W., Wang A., Maiti R., Haas B.,
RA Wortman J., Pertea M., Jones K.M., Kim M., Overton L., Tsitrin T.,
RA Fadrosh D., Bera J., Weaver B., Jin S., Johri S., Reardon M., Webb K.,
RA Hill J., Moffat K., Tallon L., Van Aken S., Lewis M., Utterback T.,
RA Feldblyum T., Zismann V., Iobst S., Hsiao J., de Vazeille A.R.,
RA Salzberg S.L., White O., Fraser C.M., Yu Y., Kim H., Rambo T., Currie J.,
RA Collura K., Kernodle-Thompson S., Wei F., Kudrna K., Ammiraju J.S.S.,
RA Luo M., Goicoechea J.L., Wing R.A., Henry D., Oates R., Palmer M.,
RA Pries G., Saski C., Simmons J., Soderlund C., Nelson W., de la Bastide M.,
RA Spiegel L., Nascimento L., Huang E., Preston R., Zutavern T., Palmer L.,
RA O'Shaughnessy A., Dike S., McCombie W.R., Minx P., Cordum H., Wilson R.,
RA Jin W., Lee H.R., Jiang J., Jackson S.;
RT "Sequence, annotation, and analysis of synteny between rice chromosome 3
RT and diverged grass species.";
RL Genome Res. 15:1284-1291(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
RN [6]
RP FUNCTION, INTERACTION WITH RAB5A, AND DISRUPTION PHENOTYPE.
RX PubMed=23723154; DOI=10.1093/mp/sst081;
RA Liu F., Ren Y., Wang Y., Peng C., Zhou K., Lv J., Guo X., Zhang X.,
RA Zhong M., Zhao S., Jiang L., Wang H., Bao Y., Wan J.;
RT "OsVPS9A functions cooperatively with OsRAB5A to regulate post-Golgi dense
RT vesicle-mediated storage protein trafficking to the protein storage vacuole
RT in rice endosperm cells.";
RL Mol. Plant 6:1918-1932(2013).
RN [7]
RP INTERACTION WITH GPA3 AND RAB5A, AND SUBCELLULAR LOCATION.
RX PubMed=24488962; DOI=10.1105/tpc.113.121376;
RA Ren Y., Wang Y., Liu F., Zhou K., Ding Y., Zhou F., Wang Y., Liu K.,
RA Gan L., Ma W., Han X., Zhang X., Guo X., Wu F., Cheng Z., Wang J., Lei C.,
RA Lin Q., Jiang L., Wu C., Bao Y., Wang H., Wan J.;
RT "GLUTELIN PRECURSOR ACCUMULATION3 encodes a regulator of post-Golgi
RT vesicular traffic essential for vacuolar protein sorting in rice
RT endosperm.";
RL Plant Cell 26:410-425(2014).
CC -!- FUNCTION: Functions as guanine nucleotide exchange factor (GEF) for Rab
CC small GTPases. Activates specifically RAB5A protein (Probable).
CC Functions cooperatively with RAB5A to regulate post-Golgi dense
CC vesicle-mediated transport of storage proteins to the type II protein
CC bodies (PBII) protein storage vacuoles in developing endosperm
CC (PubMed:23723154). {ECO:0000269|PubMed:23723154,
CC ECO:0000305|PubMed:23723154}.
CC -!- SUBUNIT: Interacts with RAB5A (PubMed:23723154, PubMed:24488962).
CC Interacts with GPA3 (via C-terminus) (PubMed:24488962).
CC {ECO:0000269|PubMed:23723154, ECO:0000269|PubMed:24488962}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:24488962}. Golgi
CC apparatus, trans-Golgi network {ECO:0000269|PubMed:24488962}.
CC Prevacuolar compartment {ECO:0000269|PubMed:24488962}. Note=Expressed
CC in trans-Golgi network and prevacuolar compartment when recruited by
CC GPA3. {ECO:0000269|PubMed:24488962}.
CC -!- DISRUPTION PHENOTYPE: Accumulation of proglutelins in seed endosperm
CC (PubMed:23723154). Abnormal organization of the protein storage
CC vesicles (type II protein bodies), and formation of secretory vesicle-
CC like structures (paramural bodies) charged with dense vesicles in seed
CC endosperm (PubMed:23723154). {ECO:0000269|PubMed:23723154}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAF11545.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; DP000009; ABF95105.1; -; Genomic_DNA.
DR EMBL; AP008209; BAF11545.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP014959; BAS83374.1; -; Genomic_DNA.
DR EMBL; CM000140; EEE58741.1; -; Genomic_DNA.
DR RefSeq; XP_015632668.1; XM_015777182.1.
DR AlphaFoldDB; Q10NQ3; -.
DR SMR; Q10NQ3; -.
DR STRING; 4530.OS03T0262900-01; -.
DR iPTMnet; Q10NQ3; -.
DR PaxDb; Q10NQ3; -.
DR PRIDE; Q10NQ3; -.
DR EnsemblPlants; Os03t0262900-02; Os03t0262900-02; Os03g0262900.
DR GeneID; 4332330; -.
DR Gramene; Os03t0262900-02; Os03t0262900-02; Os03g0262900.
DR KEGG; osa:4332330; -.
DR eggNOG; KOG2319; Eukaryota.
DR HOGENOM; CLU_2458549_0_0_1; -.
DR OrthoDB; 944088at2759; -.
DR PlantReactome; R-OSA-9626305; Regulatory network of nutrient accumulation.
DR Proteomes; UP000000763; Chromosome 3.
DR Proteomes; UP000007752; Chromosome 3.
DR Proteomes; UP000059680; Chromosome 3.
DR ExpressionAtlas; Q10NQ3; baseline and differential.
DR GO; GO:0005737; C:cytoplasm; IDA:UniProtKB.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0030139; C:endocytic vesicle; IBA:GO_Central.
DR GO; GO:0000325; C:plant-type vacuole; IDA:UniProtKB.
DR GO; GO:0005802; C:trans-Golgi network; IDA:UniProtKB.
DR GO; GO:0005525; F:GTP binding; IEA:UniProtKB-KW.
DR GO; GO:0005096; F:GTPase activator activity; IEA:UniProtKB-KW.
DR GO; GO:0005085; F:guanyl-nucleotide exchange factor activity; IMP:UniProtKB.
DR GO; GO:0031267; F:small GTPase binding; IBA:GO_Central.
DR GO; GO:0006886; P:intracellular protein transport; IMP:UniProtKB.
DR GO; GO:0016192; P:vesicle-mediated transport; IEA:InterPro.
DR Gene3D; 1.20.1050.80; -; 1.
DR InterPro; IPR041545; DUF5601.
DR InterPro; IPR003123; VPS9.
DR InterPro; IPR045046; Vps9-like.
DR InterPro; IPR037191; VPS9_dom_sf.
DR PANTHER; PTHR23101; PTHR23101; 1.
DR Pfam; PF18151; DUF5601; 1.
DR Pfam; PF02204; VPS9; 1.
DR SMART; SM00167; VPS9; 1.
DR SUPFAM; SSF109993; SSF109993; 1.
DR PROSITE; PS51205; VPS9; 1.
PE 1: Evidence at protein level;
KW Cytoplasm; Golgi apparatus; GTP-binding; GTPase activation;
KW Nucleotide-binding; Protein transport; Reference proteome; Transport.
FT CHAIN 1..480
FT /note="Vacuolar protein sorting-associated protein 9A"
FT /id="PRO_0000445092"
FT DOMAIN 111..255
FT /note="VPS9"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00550"
FT REGION 276..338
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 418..480
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 276..311
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 448..471
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 189
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250|UniProtKB:Q9LT31"
FT BINDING 194
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250|UniProtKB:Q9LT31"
SQ SEQUENCE 480 AA; 53841 MW; 85CDD2E9FF1D1527 CRC64;
MDGGGGGDAF GSATAPLAWH DFLERMRQPS AADFVKSIKG FIVTFSNRAP DPEHDSAAVQ
EFLENMEGAF RAHTPWAGSS EEELESAGEG LEKYVMTKLF NRVFASVPED VKSDEELFEK
MSLLQQFIRP ENLDIKPEYQ SETSWLLAQK ELQKINMYKA PRDKLACILN CCKVINNLLL
NASIVSNENP PGADEFLPVL IYVTIKANPP QLHSNLLYIQ RYRRQSRLVS EAQYFFTNIL
SAESFIWNID GESLSMDERD FQKKMDLARE RMLGLSASSE NQDNQNNLDV REQKSQTLKA
SRDSDVNLSL KDNFQGPGLE MRRDSDASSN PVERVQSISD LEKKGAAELL KDDDLNKKIQ
EYPFLFARSG DLTVADVENL LNSYKQLVLK YVALSQGMGI NLENPPVQSM QTVSDLVESE
EPKNVKNAVN FSEGSSKTSD DIKNDTLYSE VDNTGTQQTA VDPSYQKAQQ DEASDQPEHA
