VPS9A_ARATH
ID VPS9A_ARATH Reviewed; 520 AA.
AC Q9LT31;
DT 05-APR-2011, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 126.
DE RecName: Full=Vacuolar protein sorting-associated protein 9A {ECO:0000305};
DE Short=AtVPS9a {ECO:0000303|PubMed:18055610};
GN Name=VPS9A {ECO:0000303|PubMed:18055610}; Synonyms=VPS9 {ECO:0000305};
GN OrderedLocusNames=At3g19770 {ECO:0000312|Araport:AT3G19770};
GN ORFNames=MMB12.26 {ECO:0000312|EMBL:BAB01291.1};
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=10819329; DOI=10.1093/dnares/7.2.131;
RA Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 3. I. Sequence
RT features of the regions of 4,504,864 bp covered by sixty P1 and TAC
RT clones.";
RL DNA Res. 7:131-135(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10907853; DOI=10.1093/dnares/7.3.217;
RA Kaneko T., Katoh T., Sato S., Nakamura Y., Asamizu E., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 3. II. Sequence
RT features of the 4,251,695 bp regions covered by 90 P1, TAC and BAC
RT clones.";
RL DNA Res. 7:217-221(2000).
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].
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 FUNCTION, INTERACTION WITH RABF1; RABF2A AND RABF2B, TISSUE SPECIFICITY,
RP AND DISRUPTION PHENOTYPE.
RX PubMed=18055610; DOI=10.1105/tpc.107.053876;
RA Goh T., Uchida W., Arakawa S., Ito E., Dainobu T., Ebine K., Takeuchi M.,
RA Sato K., Ueda T., Nakano A.;
RT "VPS9a, the common activator for two distinct types of Rab5 GTPases, is
RT essential for the development of Arabidopsis thaliana.";
RL Plant Cell 19:3504-3515(2007).
RN [6]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-330, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Root;
RX PubMed=18433157; DOI=10.1021/pr8000173;
RA de la Fuente van Bentem S., Anrather D., Dohnal I., Roitinger E.,
RA Csaszar E., Joore J., Buijnink J., Carreri A., Forzani C., Lorkovic Z.J.,
RA Barta A., Lecourieux D., Verhounig A., Jonak C., Hirt H.;
RT "Site-specific phosphorylation profiling of Arabidopsis proteins by mass
RT spectrometry and peptide chip analysis.";
RL J. Proteome Res. 7:2458-2470(2008).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=cv. Columbia;
RX PubMed=19245862; DOI=10.1016/j.jprot.2009.02.004;
RA Jones A.M.E., MacLean D., Studholme D.J., Serna-Sanz A., Andreasson E.,
RA Rathjen J.P., Peck S.C.;
RT "Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis
RT thaliana.";
RL J. Proteomics 72:439-451(2009).
RN [8]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-330, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19376835; DOI=10.1104/pp.109.138677;
RA Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A.,
RA Grossmann J., Gruissem W., Baginsky S.;
RT "Large-scale Arabidopsis phosphoproteome profiling reveals novel
RT chloroplast kinase substrates and phosphorylation networks.";
RL Plant Physiol. 150:889-903(2009).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (2.08 ANGSTROMS) OF 1-265 IN COMPLEX WITH GDP,
RP FUNCTION, SUBUNIT, INTERACTION WITH RABF2B, AND MUTAGENESIS OF ALA-184;
RP ASP-185 AND TYR-225.
RX PubMed=20833725; DOI=10.1074/jbc.m110.152132;
RA Uejima T., Ihara K., Goh T., Ito E., Sunada M., Ueda T., Nakano A.,
RA Wakatsuki S.;
RT "GDP-bound and nucleotide-free intermediates of the guanine nucleotide
RT exchange in the Rab5.Vps9 system.";
RL J. Biol. Chem. 285:36689-36697(2010).
CC -!- FUNCTION: Functions as guanine nucleotide exchange factor (GEF) for Rab
CC small GTPases. Activates specifically RABF1, RABF2A and RABF2B
CC proteins. Required for early stages of embryogenesis, cytokinesis,
CC embryogenesis, and organ development. Is essential for the
CC establishment or maintenance of the polar localization of the auxin
CC efflux carrier PIN1. {ECO:0000269|PubMed:18055610,
CC ECO:0000269|PubMed:20833725}.
CC -!- SUBUNIT: Homodimer. The homodimer interacts with RABF2B. Interacts with
CC RABF1 and RABF2A. {ECO:0000269|PubMed:18055610,
CC ECO:0000269|PubMed:20833725}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=1;
CC Comment=A number of isoforms are produced. According to EST
CC sequences.;
CC Name=1;
CC IsoId=Q9LT31-1; Sequence=Displayed;
CC -!- TISSUE SPECIFICITY: Widely expressed. {ECO:0000269|PubMed:18055610}.
CC -!- DISRUPTION PHENOTYPE: Embryonic lethality when homozygous.
CC Embryogenesis arrested at the torpedo stage.
CC {ECO:0000269|PubMed:18055610}.
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DR EMBL; AB025631; BAB01291.1; -; Genomic_DNA.
DR EMBL; AP000417; BAB01291.1; JOINED; Genomic_DNA.
DR EMBL; CP002686; AEE76284.1; -; Genomic_DNA.
DR EMBL; AY045810; AAK76484.1; -; mRNA.
DR EMBL; AY079338; AAL85069.1; -; mRNA.
DR RefSeq; NP_566645.1; NM_112867.5. [Q9LT31-1]
DR PDB; 2EFC; X-ray; 2.09 A; A/C=1-265.
DR PDB; 2EFD; X-ray; 3.00 A; A/C=1-265.
DR PDB; 2EFE; X-ray; 2.08 A; A/C=1-265.
DR PDB; 2EFH; X-ray; 2.10 A; A/C=1-265.
DR PDB; 4G01; X-ray; 2.20 A; A=1-265.
DR PDBsum; 2EFC; -.
DR PDBsum; 2EFD; -.
DR PDBsum; 2EFE; -.
DR PDBsum; 2EFH; -.
DR PDBsum; 4G01; -.
DR AlphaFoldDB; Q9LT31; -.
DR SMR; Q9LT31; -.
DR BioGRID; 6846; 1.
DR STRING; 3702.AT3G19770.1; -.
DR iPTMnet; Q9LT31; -.
DR PaxDb; Q9LT31; -.
DR PRIDE; Q9LT31; -.
DR ProteomicsDB; 242780; -. [Q9LT31-1]
DR EnsemblPlants; AT3G19770.1; AT3G19770.1; AT3G19770. [Q9LT31-1]
DR GeneID; 821514; -.
DR Gramene; AT3G19770.1; AT3G19770.1; AT3G19770. [Q9LT31-1]
DR KEGG; ath:AT3G19770; -.
DR Araport; AT3G19770; -.
DR TAIR; locus:2092211; AT3G19770.
DR eggNOG; KOG2319; Eukaryota.
DR HOGENOM; CLU_036671_1_0_1; -.
DR InParanoid; Q9LT31; -.
DR OMA; KIQEYPF; -.
DR PhylomeDB; Q9LT31; -.
DR EvolutionaryTrace; Q9LT31; -.
DR PRO; PR:Q9LT31; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9LT31; baseline and differential.
DR Genevisible; Q9LT31; AT.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0030139; C:endocytic vesicle; IBA:GO_Central.
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; IDA:TAIR.
DR GO; GO:0031267; F:small GTPase binding; IBA:GO_Central.
DR GO; GO:0000919; P:cell plate assembly; IMP:TAIR.
DR GO; GO:0042546; P:cell wall biogenesis; IMP:TAIR.
DR GO; GO:0009793; P:embryo development ending in seed dormancy; IMP:TAIR.
DR GO; GO:0045324; P:late endosome to vacuole transport; IGI:TAIR.
DR GO; GO:0048528; P:post-embryonic root development; IMP:TAIR.
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 3D-structure; Alternative splicing; GTP-binding; GTPase activation;
KW Nucleotide-binding; Phosphoprotein; Reference proteome.
FT CHAIN 1..520
FT /note="Vacuolar protein sorting-associated protein 9A"
FT /id="PRO_0000406607"
FT DOMAIN 102..246
FT /note="VPS9"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00550"
FT REGION 267..331
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 396..433
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 464..520
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 283..327
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 396..411
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 412..433
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 464..513
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 180
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000269|PubMed:20833725,
FT ECO:0007744|PDB:2EFC"
FT BINDING 185
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000269|PubMed:20833725,
FT ECO:0007744|PDB:2EFC"
FT MOD_RES 330
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18433157,
FT ECO:0007744|PubMed:19376835"
FT MUTAGEN 184
FT /note="A->K: Loss of interaction with RABF2B."
FT /evidence="ECO:0000269|PubMed:20833725"
FT MUTAGEN 185
FT /note="D->A: Loss of interaction with RABF2B. Decreases GEF
FT activity 12-fold."
FT /evidence="ECO:0000269|PubMed:20833725"
FT MUTAGEN 185
FT /note="D->E: Loss of interaction with RABF2B."
FT /evidence="ECO:0000269|PubMed:20833725"
FT MUTAGEN 185
FT /note="D->N: Weakens interaction with RABF2B. Increases GEF
FT activity."
FT /evidence="ECO:0000269|PubMed:20833725"
FT MUTAGEN 225
FT /note="Y->A: Loss of interaction with RABF2B. Decreases GEF
FT activity 25-fold."
FT /evidence="ECO:0000269|PubMed:20833725"
FT HELIX 20..22
FT /evidence="ECO:0007829|PDB:2EFE"
FT HELIX 23..34
FT /evidence="ECO:0007829|PDB:2EFE"
FT TURN 35..38
FT /evidence="ECO:0007829|PDB:2EFE"
FT HELIX 43..62
FT /evidence="ECO:0007829|PDB:2EFE"
FT HELIX 65..67
FT /evidence="ECO:0007829|PDB:2EFE"
FT HELIX 72..94
FT /evidence="ECO:0007829|PDB:2EFE"
FT HELIX 99..115
FT /evidence="ECO:0007829|PDB:2EFE"
FT TURN 116..118
FT /evidence="ECO:0007829|PDB:2EFE"
FT HELIX 121..124
FT /evidence="ECO:0007829|PDB:2EFE"
FT HELIX 128..130
FT /evidence="ECO:0007829|PDB:2EFE"
FT HELIX 137..144
FT /evidence="ECO:0007829|PDB:2EFE"
FT HELIX 145..148
FT /evidence="ECO:0007829|PDB:2EFE"
FT HELIX 152..176
FT /evidence="ECO:0007829|PDB:2EFE"
FT HELIX 184..198
FT /evidence="ECO:0007829|PDB:2EFE"
FT HELIX 203..213
FT /evidence="ECO:0007829|PDB:2EFE"
FT TURN 216..218
FT /evidence="ECO:0007829|PDB:2EFE"
FT HELIX 221..238
FT /evidence="ECO:0007829|PDB:2EFE"
FT TURN 242..246
FT /evidence="ECO:0007829|PDB:2EFE"
FT HELIX 249..261
FT /evidence="ECO:0007829|PDB:2EFE"
SQ SEQUENCE 520 AA; 57898 MW; 59CEDA430B4C1C0E CRC64;
MENTDVFLGL HDFLERMRKP SAGDFVKSIK SFIVSFSNNA PDPEKDCAMV QEFFSKMEAA
FRAHPLWSGC SEEELDSAGD GLEKYVMTKL FTRVFASNTE EVIADEKLFQ KMSLVQQFIS
PENLDIQPTF QNESSWLLAQ KELQKINMYK APRDKLVCIL NCCKVINNLL LNASIASNEN
APGADEFLPV LIYVTIKANP PQLHSNLLYI QRYRRESKLV GEAAYFFTNI LSAESFISNI
DAKSISLDEA EFEKNMESAR ARISGLDSQT YQTGHGSAPP PRDESTLQKT QSLNPKRENT
LFQSKSSDSL SGTNELLNIN SETPMKKAES ISDLENKGAT LLKDTEPSKV FQEYPYIFAS
AGDLRIGDVE GLLNSYKQLV FKYVCLTKGL GDGTSLAPSS SPLQASSGFN TSKESEDHRR
SSSDVQMTKE TDRSVDDLIR ALHGEGEDVN NLSDVKHEEY GAMLVEGKDE ERDSKVQGEV
DAKDIELMKQ IPKREGDNSS SRPAEDEDVG SKQPVTEASE
