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Q9LT31

- VPS9A_ARATH

UniProt

Q9LT31 - VPS9A_ARATH

Protein

Vacuolar protein sorting-associated protein 9A

Gene

VPS9A

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 82 (01 Oct 2014)
      Sequence version 1 (01 Oct 2000)
      Previous versions | rss
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    Functioni

    Functions as guanine nucleotide exchange factor (GEF) for Rab small GTPases. Activates specifically RABF1, RABF2A and RABF2B proteins. Required for early stages of embryogenesis, cytokinesis, embryogenesis, and organ development. Is essential for the establishment or maintenance of the polar localization of the auxin efflux carrier PIN1.2 Publications

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei180 – 1801GTP
    Binding sitei185 – 1851GTP

    GO - Molecular functioni

    1. GTPase activator activity Source: UniProtKB-KW
    2. GTP binding Source: UniProtKB-KW
    3. protein binding Source: UniProtKB
    4. Rho guanyl-nucleotide exchange factor activity Source: TAIR

    GO - Biological processi

    1. cell plate assembly Source: TAIR
    2. cell wall biogenesis Source: TAIR
    3. positive regulation of Rho GTPase activity Source: GOC
    4. post-embryonic root development Source: TAIR

    Keywords - Molecular functioni

    GTPase activation

    Keywords - Ligandi

    GTP-binding, Nucleotide-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Vacuolar protein sorting-associated protein 9A
    Short name:
    AtVSP9a
    Gene namesi
    Name:VPS9A
    Synonyms:VPS9
    Ordered Locus Names:At3g19770
    ORF Names:MMB12.26
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    ProteomesiUP000006548: Chromosome 3

    Organism-specific databases

    TAIRiAT3G19770.

    Subcellular locationi

    GO - Cellular componenti

    1. cytosol Source: TAIR
    2. membrane Source: TAIR
    3. nucleus Source: TAIR

    Pathology & Biotechi

    Disruption phenotypei

    Embryonic lethality when homozygous. Embryogenesis arrested at the torpedo stage.1 Publication

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi184 – 1841A → K: Loss of interaction with RABF2B. 1 Publication
    Mutagenesisi185 – 1851D → A: Loss of interaction with RABF2B. Decreases GEF activity 12-fold. 1 Publication
    Mutagenesisi185 – 1851D → E: Loss of interaction with RABF2B. 1 Publication
    Mutagenesisi185 – 1851D → N: Weakens interaction with RABF2B. Increases GEF activity. 1 Publication
    Mutagenesisi225 – 2251Y → A: Loss of interaction with RABF2B. Decreases GEF activity 25-fold. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 520520Vacuolar protein sorting-associated protein 9APRO_0000406607Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei330 – 3301Phosphoserine2 Publications

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    PaxDbiQ9LT31.
    PRIDEiQ9LT31.

    Expressioni

    Tissue specificityi

    Widely expressed.1 Publication

    Gene expression databases

    GenevestigatoriQ9LT31.

    Interactioni

    Subunit structurei

    Homodimer. The homodimer interacts with RABF2B. Interacts with RABF1 and RABF2A.2 Publications

    Protein-protein interaction databases

    BioGridi6846. 1 interaction.

    Structurei

    Secondary structure

    1
    520
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi20 – 223
    Helixi23 – 3412
    Turni35 – 384
    Helixi43 – 6220
    Helixi65 – 673
    Helixi72 – 9423
    Helixi99 – 11517
    Turni116 – 1183
    Helixi121 – 1244
    Helixi128 – 1303
    Helixi137 – 1448
    Helixi145 – 1484
    Helixi152 – 17625
    Helixi184 – 19815
    Helixi203 – 21311
    Turni216 – 2183
    Helixi221 – 23818
    Turni242 – 2465
    Helixi249 – 26113

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2EFCX-ray2.09A/C1-265[»]
    2EFDX-ray3.00A/C1-265[»]
    2EFEX-ray2.08A/C1-265[»]
    2EFHX-ray2.10A/C1-265[»]
    4G01X-ray2.20A1-265[»]
    ProteinModelPortaliQ9LT31.
    SMRiQ9LT31. Positions 17-262.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9LT31.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini102 – 246145VPS9PROSITE-ProRule annotationAdd
    BLAST

    Sequence similaritiesi

    Contains 1 VPS9 domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiNOG301606.
    HOGENOMiHOG000029999.
    InParanoidiQ9LT31.
    OMAiIKPEYQN.
    PhylomeDBiQ9LT31.

    Family and domain databases

    InterProiIPR003123. VPS9.
    IPR013995. VPS9_subgr.
    [Graphical view]
    PfamiPF02204. VPS9. 1 hit.
    [Graphical view]
    SMARTiSM00167. VPS9. 1 hit.
    [Graphical view]
    PROSITEiPS51205. VPS9. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    This entry describes 1 isoform i produced by alternative splicing. Align

    Note: A number of isoforms are produced. According to EST sequences.

    Isoform 1 (identifier: Q9LT31-1) [UniParc]FASTAAdd to Basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

    MENTDVFLGL HDFLERMRKP SAGDFVKSIK SFIVSFSNNA PDPEKDCAMV    50
    QEFFSKMEAA FRAHPLWSGC SEEELDSAGD GLEKYVMTKL FTRVFASNTE 100
    EVIADEKLFQ KMSLVQQFIS PENLDIQPTF QNESSWLLAQ KELQKINMYK 150
    APRDKLVCIL NCCKVINNLL LNASIASNEN APGADEFLPV LIYVTIKANP 200
    PQLHSNLLYI QRYRRESKLV GEAAYFFTNI LSAESFISNI DAKSISLDEA 250
    EFEKNMESAR ARISGLDSQT YQTGHGSAPP PRDESTLQKT QSLNPKRENT 300
    LFQSKSSDSL SGTNELLNIN SETPMKKAES ISDLENKGAT LLKDTEPSKV 350
    FQEYPYIFAS AGDLRIGDVE GLLNSYKQLV FKYVCLTKGL GDGTSLAPSS 400
    SPLQASSGFN TSKESEDHRR SSSDVQMTKE TDRSVDDLIR ALHGEGEDVN 450
    NLSDVKHEEY GAMLVEGKDE ERDSKVQGEV DAKDIELMKQ IPKREGDNSS 500
    SRPAEDEDVG SKQPVTEASE 520
    Length:520
    Mass (Da):57,898
    Last modified:October 1, 2000 - v1
    Checksum:i59CEDA430B4C1C0E
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB025631, AP000417 Genomic DNA. Translation: BAB01291.1.
    CP002686 Genomic DNA. Translation: AEE76284.1.
    AY045810 mRNA. Translation: AAK76484.1.
    AY079338 mRNA. Translation: AAL85069.1.
    RefSeqiNP_566645.1. NM_112867.4. [Q9LT31-1]
    UniGeneiAt.22893.

    Genome annotation databases

    EnsemblPlantsiAT3G19770.1; AT3G19770.1; AT3G19770. [Q9LT31-1]
    GeneIDi821514.
    KEGGiath:AT3G19770.

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB025631 , AP000417 Genomic DNA. Translation: BAB01291.1 .
    CP002686 Genomic DNA. Translation: AEE76284.1 .
    AY045810 mRNA. Translation: AAK76484.1 .
    AY079338 mRNA. Translation: AAL85069.1 .
    RefSeqi NP_566645.1. NM_112867.4. [Q9LT31-1 ]
    UniGenei At.22893.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2EFC X-ray 2.09 A/C 1-265 [» ]
    2EFD X-ray 3.00 A/C 1-265 [» ]
    2EFE X-ray 2.08 A/C 1-265 [» ]
    2EFH X-ray 2.10 A/C 1-265 [» ]
    4G01 X-ray 2.20 A 1-265 [» ]
    ProteinModelPortali Q9LT31.
    SMRi Q9LT31. Positions 17-262.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 6846. 1 interaction.

    Proteomic databases

    PaxDbi Q9LT31.
    PRIDEi Q9LT31.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi AT3G19770.1 ; AT3G19770.1 ; AT3G19770 . [Q9LT31-1 ]
    GeneIDi 821514.
    KEGGi ath:AT3G19770.

    Organism-specific databases

    TAIRi AT3G19770.

    Phylogenomic databases

    eggNOGi NOG301606.
    HOGENOMi HOG000029999.
    InParanoidi Q9LT31.
    OMAi IKPEYQN.
    PhylomeDBi Q9LT31.

    Miscellaneous databases

    EvolutionaryTracei Q9LT31.

    Gene expression databases

    Genevestigatori Q9LT31.

    Family and domain databases

    InterProi IPR003123. VPS9.
    IPR013995. VPS9_subgr.
    [Graphical view ]
    Pfami PF02204. VPS9. 1 hit.
    [Graphical view ]
    SMARTi SM00167. VPS9. 1 hit.
    [Graphical view ]
    PROSITEi PS51205. VPS9. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Structural analysis of Arabidopsis thaliana chromosome 3. I. Sequence features of the regions of 4,504,864 bp covered by sixty P1 and TAC clones."
      Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Tabata S.
      DNA Res. 7:131-135(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Columbia.
    2. "Structural analysis of Arabidopsis thaliana chromosome 3. II. Sequence features of the 4,251,695 bp regions covered by 90 P1, TAC and BAC clones."
      Kaneko T., Katoh T., Sato S., Nakamura Y., Asamizu E., Tabata S.
      DNA Res. 7:217-221(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Columbia.
    3. The Arabidopsis Information Resource (TAIR)
      Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
      Cited for: GENOME REANNOTATION.
      Strain: cv. Columbia.
    4. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
      Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
      , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
      Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: cv. Columbia.
    5. "VPS9a, the common activator for two distinct types of Rab5 GTPases, is essential for the development of Arabidopsis thaliana."
      Goh T., Uchida W., Arakawa S., Ito E., Dainobu T., Ebine K., Takeuchi M., Sato K., Ueda T., Nakano A.
      Plant Cell 19:3504-3515(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, INTERACTION WITH RABF1; RABF2A AND RABF2B, TISSUE SPECIFICITY, DISRUPTION PHENOTYPE.
    6. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-330, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Root.
    7. "Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis thaliana."
      Jones A.M.E., MacLean D., Studholme D.J., Serna-Sanz A., Andreasson E., Rathjen J.P., Peck S.C.
      J. Proteomics 72:439-451(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Strain: cv. Columbia.
    8. "Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks."
      Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A., Grossmann J., Gruissem W., Baginsky S.
      Plant Physiol. 150:889-903(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-330, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    9. "GDP-bound and nucleotide-free intermediates of the guanine nucleotide exchange in the Rab5.Vps9 system."
      Uejima T., Ihara K., Goh T., Ito E., Sunada M., Ueda T., Nakano A., Wakatsuki S.
      J. Biol. Chem. 285:36689-36697(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.08 ANGSTROMS) OF 1-265 IN COMPLEX WITH GDP, FUNCTION, SUBUNIT, INTERACTION WITH RABF2B, MUTAGENESIS OF ALA-184; ASP-185 AND TYR-225.

    Entry informationi

    Entry nameiVPS9A_ARATH
    AccessioniPrimary (citable) accession number: Q9LT31
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 5, 2011
    Last sequence update: October 1, 2000
    Last modified: October 1, 2014
    This is version 82 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Arabidopsis thaliana
      Arabidopsis thaliana: entries and gene names
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3