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Q9LT31 (VPS9A_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 78. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Vacuolar protein sorting-associated protein 9A

Short name=AtVSP9a
Gene names
Name:VPS9A
Synonyms:VPS9
Ordered Locus Names:At3g19770
ORF Names:MMB12.26
OrganismArabidopsis thaliana (Mouse-ear cress) [Reference proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis

Protein attributes

Sequence length520 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.5 Ref.9

Subunit structure

Homodimer. The homodimer interacts with RABF2B. Interacts with RABF1 and RABF2A. Ref.5 Ref.9

Tissue specificity

Widely expressed. Ref.5

Disruption phenotype

Embryonic lethality when homozygous. Embryogenesis arrested at the torpedo stage. Ref.5

Sequence similarities

Contains 1 VPS9 domain.

Alternative products

This entry describes 1 isoform produced by alternative splicing. [Select]

Note: A number of isoforms are produced. According to EST sequences.
Isoform 1 (identifier: Q9LT31-1)

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.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 520520Vacuolar protein sorting-associated protein 9A
PRO_0000406607

Regions

Domain102 – 246145VPS9

Sites

Binding site1801GTP
Binding site1851GTP

Amino acid modifications

Modified residue3301Phosphoserine Ref.6 Ref.8

Experimental info

Mutagenesis1841A → K: Loss of interaction with RABF2B. Ref.9
Mutagenesis1851D → A: Loss of interaction with RABF2B. Decreases GEF activity 12-fold. Ref.9
Mutagenesis1851D → E: Loss of interaction with RABF2B. Ref.9
Mutagenesis1851D → N: Weakens interaction with RABF2B. Increases GEF activity. Ref.9
Mutagenesis2251Y → A: Loss of interaction with RABF2B. Decreases GEF activity 25-fold. Ref.9

Secondary structure

................................... 520
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified October 1, 2000. Version 1.
Checksum: 59CEDA430B4C1C0E

FASTA52057,898
        10         20         30         40         50         60 
MENTDVFLGL HDFLERMRKP SAGDFVKSIK SFIVSFSNNA PDPEKDCAMV QEFFSKMEAA 

        70         80         90        100        110        120 
FRAHPLWSGC SEEELDSAGD GLEKYVMTKL FTRVFASNTE EVIADEKLFQ KMSLVQQFIS 

       130        140        150        160        170        180 
PENLDIQPTF QNESSWLLAQ KELQKINMYK APRDKLVCIL NCCKVINNLL LNASIASNEN 

       190        200        210        220        230        240 
APGADEFLPV LIYVTIKANP PQLHSNLLYI QRYRRESKLV GEAAYFFTNI LSAESFISNI 

       250        260        270        280        290        300 
DAKSISLDEA EFEKNMESAR ARISGLDSQT YQTGHGSAPP PRDESTLQKT QSLNPKRENT 

       310        320        330        340        350        360 
LFQSKSSDSL SGTNELLNIN SETPMKKAES ISDLENKGAT LLKDTEPSKV FQEYPYIFAS 

       370        380        390        400        410        420 
AGDLRIGDVE GLLNSYKQLV FKYVCLTKGL GDGTSLAPSS SPLQASSGFN TSKESEDHRR 

       430        440        450        460        470        480 
SSSDVQMTKE TDRSVDDLIR ALHGEGEDVN NLSDVKHEEY GAMLVEGKDE ERDSKVQGEV 

       490        500        510        520 
DAKDIELMKQ IPKREGDNSS SRPAEDEDVG SKQPVTEASE 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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]"Site-specific phosphorylation profiling of Arabidopsis proteins by mass spectrometry and peptide chip analysis."
de la Fuente van Bentem S., Anrather D., Dohnal I., Roitinger E., Csaszar E., Joore J., Buijnink J., Carreri A., Forzani C., Lorkovic Z.J., Barta A., Lecourieux D., Verhounig A., Jonak C., Hirt H.
J. Proteome Res. 7:2458-2470(2008) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AB025631, AP000417 Genomic DNA. Translation: BAB01291.1.
CP002686 Genomic DNA. Translation: AEE76284.1.
AY045810 mRNA. Translation: AAK76484.1.
AY079338 mRNA. Translation: AAL85069.1.
RefSeqNP_566645.1. NM_112867.4.
UniGeneAt.22893.

3D structure databases

PDBe
RCSB PDB
PDBj
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[»]
ProteinModelPortalQ9LT31.
SMRQ9LT31. Positions 17-262.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid6846. 1 interaction.

Proteomic databases

PaxDbQ9LT31.
PRIDEQ9LT31.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsAT3G19770.1; AT3G19770.1; AT3G19770. [Q9LT31-1]
GeneID821514.
KEGGath:AT3G19770.

Organism-specific databases

TAIRAT3G19770.

Phylogenomic databases

eggNOGNOG301606.
HOGENOMHOG000029999.
InParanoidQ9LT31.
OMAIKPEYQN.
PhylomeDBQ9LT31.
ProtClustDBCLSN2688573.

Gene expression databases

GenevestigatorQ9LT31.

Family and domain databases

InterProIPR003123. VPS9.
IPR013995. VPS9_subgr.
[Graphical view]
PfamPF02204. VPS9. 1 hit.
[Graphical view]
SMARTSM00167. VPS9. 1 hit.
[Graphical view]
PROSITEPS51205. VPS9. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ9LT31.

Entry information

Entry nameVPS9A_ARATH
AccessionPrimary (citable) accession number: Q9LT31
Entry history
Integrated into UniProtKB/Swiss-Prot: April 5, 2011
Last sequence update: October 1, 2000
Last modified: April 16, 2014
This is version 78 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names