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Protein

Vacuolar protein sorting-associated protein 9A

Gene

VPS9A

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: 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)DescriptionActionsGraphical viewLength
Binding sitei180GTP1
Binding sitei185GTP1

GO - Molecular functioni

GO - Biological processi

  • cell plate assembly Source: TAIR
  • cell wall biogenesis Source: TAIR
  • embryo development ending in seed dormancy Source: TAIR
  • post-embryonic root development Source: TAIR
Complete GO annotation...

Keywords - Molecular functioni

GTPase activation

Keywords - Ligandi

GTP-binding, Nucleotide-binding

Enzyme and pathway databases

ReactomeiR-ATH-8876198. RAB GEFs exchange GTP for GDP on RABs.

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
Proteomesi
  • UP000006548 Componenti: Chromosome 3

Organism-specific databases

TAIRiAT3G19770.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: TAIR
  • membrane Source: TAIR
  • 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)DescriptionActionsGraphical viewLength
Mutagenesisi184A → K: Loss of interaction with RABF2B. 1 Publication1
Mutagenesisi185D → A: Loss of interaction with RABF2B. Decreases GEF activity 12-fold. 1 Publication1
Mutagenesisi185D → E: Loss of interaction with RABF2B. 1 Publication1
Mutagenesisi185D → N: Weakens interaction with RABF2B. Increases GEF activity. 1 Publication1
Mutagenesisi225Y → A: Loss of interaction with RABF2B. Decreases GEF activity 25-fold. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004066071 – 520Vacuolar protein sorting-associated protein 9AAdd BLAST520

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei330PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiQ9LT31.

PTM databases

iPTMnetiQ9LT31.

Expressioni

Tissue specificityi

Widely expressed.1 Publication

Gene expression databases

ExpressionAtlasiQ9LT31. baseline and differential.
GenevisibleiQ9LT31. AT.

Interactioni

Subunit structurei

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

Protein-protein interaction databases

BioGridi6846. 1 interactor.
STRINGi3702.AT3G19770.1.

Structurei

Secondary structure

1520
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi20 – 22Combined sources3
Helixi23 – 34Combined sources12
Turni35 – 38Combined sources4
Helixi43 – 62Combined sources20
Helixi65 – 67Combined sources3
Helixi72 – 94Combined sources23
Helixi99 – 115Combined sources17
Turni116 – 118Combined sources3
Helixi121 – 124Combined sources4
Helixi128 – 130Combined sources3
Helixi137 – 144Combined sources8
Helixi145 – 148Combined sources4
Helixi152 – 176Combined sources25
Helixi184 – 198Combined sources15
Helixi203 – 213Combined sources11
Turni216 – 218Combined sources3
Helixi221 – 238Combined sources18
Turni242 – 246Combined sources5
Helixi249 – 261Combined sources13

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9LT31.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini102 – 246VPS9PROSITE-ProRule annotationAdd BLAST145

Sequence similaritiesi

Contains 1 VPS9 domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG2319. Eukaryota.
ENOG410YGAZ. LUCA.
HOGENOMiHOG000029999.
InParanoidiQ9LT31.
KOiK20131.
OMAiTFSNREP.
OrthoDBiEOG093609TO.
PhylomeDBiQ9LT31.

Family and domain databases

InterProiIPR003123. VPS9.
[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. AlignAdd to basket

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_112867.5. [Q9LT31-1]
UniGeneiAt.22893.

Genome annotation databases

EnsemblPlantsiAT3G19770.1; AT3G19770.1; AT3G19770. [Q9LT31-1]
GeneIDi821514.
GrameneiAT3G19770.1; AT3G19770.1; AT3G19770.
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.
RefSeqiNP_566645.1. NM_112867.5. [Q9LT31-1]
UniGeneiAt.22893.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi6846. 1 interactor.
STRINGi3702.AT3G19770.1.

PTM databases

iPTMnetiQ9LT31.

Proteomic databases

PaxDbiQ9LT31.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT3G19770.1; AT3G19770.1; AT3G19770. [Q9LT31-1]
GeneIDi821514.
GrameneiAT3G19770.1; AT3G19770.1; AT3G19770.
KEGGiath:AT3G19770.

Organism-specific databases

TAIRiAT3G19770.

Phylogenomic databases

eggNOGiKOG2319. Eukaryota.
ENOG410YGAZ. LUCA.
HOGENOMiHOG000029999.
InParanoidiQ9LT31.
KOiK20131.
OMAiTFSNREP.
OrthoDBiEOG093609TO.
PhylomeDBiQ9LT31.

Enzyme and pathway databases

ReactomeiR-ATH-8876198. RAB GEFs exchange GTP for GDP on RABs.

Miscellaneous databases

EvolutionaryTraceiQ9LT31.
PROiQ9LT31.

Gene expression databases

ExpressionAtlasiQ9LT31. baseline and differential.
GenevisibleiQ9LT31. AT.

Family and domain databases

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

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 30, 2016
This is version 98 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.