Vacuolar protein sorting-associated protein 9A - Arabidopsis thaliana (Mouse-ear cress)

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Q9LT31 (VPS9A_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 72. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Vacuolar protein sorting-associated protein 9A
Short name=AtVSP9a

Gene names

Name:	VPS9A
Synonyms:	VPS9
Ordered Locus Names:	At3g19770
ORF Names:	MMB12.26

Organism

Arabidopsis thaliana (Mouse-ear cress) [Reference proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	520 AA.
Sequence status	Complete.
Protein existence	Evidence 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.

Ontologies

Keywords
Coding sequence diversity	Alternative splicing
Ligand	GTP-binding Nucleotide-binding
Molecular function	GTPase activation
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	cell plate assembly Inferred from mutant phenotype Ref.5. Source: TAIR cell wall biogenesis Inferred from mutant phenotype Ref.5. Source: TAIR embryo development Inferred from mutant phenotype Ref.5. Source: TAIR positive regulation of GTPase activity Inferred from electronic annotation. Source: GOC post-embryonic root development Inferred from mutant phenotype Ref.5. Source: TAIR
Cellular_component	cytosol Inferred from direct assay Ref.6. Source: TAIR membrane Inferred from direct assay PubMed 17432890. Source: TAIR nucleus Inferred from direct assay Ref.6. Source: TAIR
Molecular_function	GTP binding Inferred from electronic annotation. Source: UniProtKB-KW GTPase activator activity Inferred from electronic annotation. Source: UniProtKB-KW Rho guanyl-nucleotide exchange factor activity Inferred from direct assay Ref.5. Source: TAIR
Complete GO annotation...

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 key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 520

520

Vacuolar protein sorting-associated protein 9A

PRO_0000406607

Regions

Domain

102 – 246

145

VPS9

Sites

Binding site

180

GTP

Binding site

185

GTP

Amino acid modifications

Modified residue

330

Phosphoserine Ref.6 Ref.8

Modified residue

332

Phosphoserine Ref.7

Experimental info

Mutagenesis

184

A → K: Loss of interaction with RABF2B. Ref.9

Mutagenesis

185

D → A: Loss of interaction with RABF2B. Decreases GEF activity 12-fold. Ref.9

Mutagenesis

185

D → E: Loss of interaction with RABF2B. Ref.9

Mutagenesis

185

D → N: Weakens interaction with RABF2B. Increases GEF activity. Ref.9

Mutagenesis

225

Y → A: Loss of interaction with RABF2B. Decreases GEF activity 25-fold. Ref.9

Secondary structure

520

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

Isoform 1 [UniParc].

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

520

57,898

        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' referencesShow '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. 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, MASS SPECTROMETRY.
[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: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-332, MASS SPECTROMETRY.
[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, MASS SPECTROMETRY.
[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.

IPI

IPI00543757.

RefSeq

NP_566645.1. NM_112867.4.

UniGene

At.22893.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

Q9LT31.

SMR

Q9LT31. Positions 17-262.

ModBase

Search...

Proteomic databases

PaxDb

Q9LT31.

PRIDE

Q9LT31.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblPlants

AT3G19770.1; AT3G19770.1; AT3G19770.

GeneID

821514.

KEGG

ath:AT3G19770.

Organism-specific databases

TAIR

At3g19770.

Phylogenomic databases

eggNOG

NOG301606.

HOGENOM

HOG000029999.

InParanoid

Q9LT31.

OMA

MEESEFE.

PhylomeDB

Q9LT31.

ProtClustDB

CLSN2688573.

Gene expression databases

ArrayExpress

Q9LT31.

Genevestigator

Q9LT31.

Family and domain databases

InterPro

IPR003123. VPS9.
IPR013995. VPS9_subgr.
[Graphical view]

Pfam

PF02204. VPS9. 1 hit.
[Graphical view]

SMART

SM00167. VPS9. 1 hit.
[Graphical view]

PROSITE

PS51205. VPS9. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

Q9LT31.

Entry information

Entry name

VPS9A_ARATH

Accession

Primary (citable) accession number: Q9LT31

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 5, 2011
Last sequence update:	October 1, 2000
Last modified:	May 1, 2013
This is version 72 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program

Relevant documents

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Alternative products

Sequence annotation (Features)

Molecule processing

Regions

Sites

Amino acid modifications

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents