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Q9LT31

- VPS9A_ARATH

UniProt

Q9LT31 - VPS9A_ARATH

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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

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. Rho guanyl-nucleotide exchange factor activity Source: TAIR

GO - Biological processi

  1. cell plate assembly Source: TAIR
  2. cell wall biogenesis Source: TAIR
  3. embryo development ending in seed dormancy Source: TAIR
  4. positive regulation of Rho GTPase activity Source: GOC
  5. post-embryonic root development Source: TAIR
Complete GO annotation...

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
Complete GO annotation...

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

ExpressionAtlasiQ9LT31. baseline and differential.
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 – 223Combined sources
Helixi23 – 3412Combined sources
Turni35 – 384Combined sources
Helixi43 – 6220Combined sources
Helixi65 – 673Combined sources
Helixi72 – 9423Combined sources
Helixi99 – 11517Combined sources
Turni116 – 1183Combined sources
Helixi121 – 1244Combined sources
Helixi128 – 1303Combined sources
Helixi137 – 1448Combined sources
Helixi145 – 1484Combined sources
Helixi152 – 17625Combined sources
Helixi184 – 19815Combined sources
Helixi203 – 21311Combined sources
Turni216 – 2183Combined sources
Helixi221 – 23818Combined sources
Turni242 – 2465Combined sources
Helixi249 – 26113Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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

        10         20         30         40         50
MENTDVFLGL HDFLERMRKP SAGDFVKSIK SFIVSFSNNA PDPEKDCAMV
60 70 80 90 100
QEFFSKMEAA FRAHPLWSGC SEEELDSAGD GLEKYVMTKL FTRVFASNTE
110 120 130 140 150
EVIADEKLFQ KMSLVQQFIS PENLDIQPTF QNESSWLLAQ KELQKINMYK
160 170 180 190 200
APRDKLVCIL NCCKVINNLL LNASIASNEN APGADEFLPV LIYVTIKANP
210 220 230 240 250
PQLHSNLLYI QRYRRESKLV GEAAYFFTNI LSAESFISNI DAKSISLDEA
260 270 280 290 300
EFEKNMESAR ARISGLDSQT YQTGHGSAPP PRDESTLQKT QSLNPKRENT
310 320 330 340 350
LFQSKSSDSL SGTNELLNIN SETPMKKAES ISDLENKGAT LLKDTEPSKV
360 370 380 390 400
FQEYPYIFAS AGDLRIGDVE GLLNSYKQLV FKYVCLTKGL GDGTSLAPSS
410 420 430 440 450
SPLQASSGFN TSKESEDHRR SSSDVQMTKE TDRSVDDLIR ALHGEGEDVN
460 470 480 490 500
NLSDVKHEEY GAMLVEGKDE ERDSKVQGEV DAKDIELMKQ IPKREGDNSS
510 520
SRPAEDEDVG SKQPVTEASE
Length:520
Mass (Da):57,898
Last modified:October 1, 2000 - v1
Checksum:i59CEDA430B4C1C0E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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:
PDBei
RCSB PDBi
PDBji
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

ExpressionAtlasi Q9LT31. baseline and differential.
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

« Hide 'large scale' publications
  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: November 26, 2014
This is version 84 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