VPS21 Rab family GTPase VPS21 [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: VPS21
Official Full Name: Rab family GTPase VPS21
Primary source: SGD:S000005615
Locus tag: YOR089C
See related: AllianceGenome:SGD:S000005615; FungiDB:YOR089C; VEuPathDB:YOR089C
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Saccharomyces cerevisiae S288C (strain: S288C)
Lineage: Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
Also known as: VPS12; VPT12; YPT21; YPT51
Summary: Enables GTPase activity. Involved in several processes, including multivesicular body assembly; protein localization to organelle; and reticulophagy. Located in early endosome and late endosome. Orthologous to human RAB5A (RAB5A, member RAS oncogene family). [provided by Alliance of Genome Resources, Apr 2022]
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Genomic context

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Location:: chromosome: XV

Exon count:: 1

Sequence:: Chromosome: XV; NC_001147.6 (490196..490828, complement)

Chromosome XV - NC_001147.6 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001147.6

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway.
Title: Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway.
In this study, we demonstrate that activated Ypt7p localizes to the vacuolar membrane in cells lacking all yeast Rab5 genes. We also show that the vps21Delta ypt7Delta double mutant exhibits a much severer vacuolar phenotype in comparison with the vps21Delta or ypt7Delta single mutant.
Title: Rab5-independent activation and function of yeast Rab7-like protein, Ypt7p, in the AP-3 pathway.
Data indicate that efficient Vps21 recycling requires both Ypt7 and endosome-vacuole fusion, thus suggesting extended control of a GAP cascade beyond Rab interactions.
Title: Identification of a Rab GTPase-activating protein cascade that controls recycling of the Rab5 GTPase Vps21 from the vacuole.
Finally, three sequential steps of this pathway are delineated: Atg9-dependent exit from the ER en route to autophagy, Ypt1- and core Atgs-mediated pre-autophagsomal-structure organization, and Ypt51-mediated delivery of APs to the vacuole
Title: A Role for Macro-ER-Phagy in ER Quality Control.
The endocytic traffic branches into two routes to reach the vacuole: a Rab5-dependent vacuolar protein sorting pathway and a Rab5-independent AP-3-mediated pathway.
Title: Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole.
Data indicate that Cells lacking both Vps9 and Muk1 closely phenocopy double and triple knock-out strains lacking Rab5 paralogs.
Title: Vps9 family protein Muk1 is the second Rab5 guanosine nucleotide exchange factor in budding yeast.
Endosomal class E compartments accumulate chronically active Vps21, the yeast Rab5A ortholog.
Title: Class E compartments form in response to ESCRT dysfunction in yeast due to hyperactivity of the Vps21 Rab GTPase.
CORVET (class C core vacuole/endosome tethering) binds to SNAREs and Rab5/Vps21-GTP and can specifically tether Vps21-positive membranes.
Title: The CORVET complex promotes tethering and fusion of Rab5/Vps21-positive membranes.
Gyp3 spatially restricts active Vps21 to intermediate endosomes.
Title: Termination of isoform-selective Vps21/Rab5 signaling at endolysosomal organelles by Msb3/Gyp3.
Msb3 forms a specific transition complex with Vps21 and has the highest activity of all recombinant GAPs for Vps21
Title: The Msb3/Gyp3 GAP controls the activity of the Rab GTPases Vps21 and Ypt7 at endosomes and vacuoles.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Orthologs from OrthoDB

Gene Ontology Provided by SGD

Function	Evidence Code	Pubs
enables GTP binding	IEA Inferred from Electronic Annotation more info
enables GTPase activity	IBA Inferred from Biological aspect of Ancestor more info
enables GTPase activity	IDA Inferred from Direct Assay more info	PubMed
enables GTPase activity	IEA Inferred from Electronic Annotation more info
enables GTPase activity	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
involved_in Golgi to endosome transport	IGI Inferred from Genetic Interaction more info	PubMed
involved_in Golgi to endosome transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in endocytosis	IBA Inferred from Biological aspect of Ancestor more info
involved_in endocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in late endosome to vacuole transport via multivesicular body sorting pathway	IGI Inferred from Genetic Interaction more info	PubMed
involved_in multivesicular body assembly	IGI Inferred from Genetic Interaction more info	PubMed
involved_in protein localization to endosome	IGI Inferred from Genetic Interaction more info	PubMed
involved_in protein targeting to vacuole	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein targeting to vacuole	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein transport	IEA Inferred from Electronic Annotation more info
involved_in reticulophagy	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in vacuole inheritance	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in cytosol	IEA Inferred from Electronic Annotation more info
is_active_in early endosome	IBA Inferred from Biological aspect of Ancestor more info
located_in early endosome	IDA Inferred from Direct Assay more info	PubMed
is_active_in endocytic vesicle	IBA Inferred from Biological aspect of Ancestor more info
is_active_in endomembrane system	IBA Inferred from Biological aspect of Ancestor more info
located_in endosome	IEA Inferred from Electronic Annotation more info
located_in endosome membrane	IEA Inferred from Electronic Annotation more info
is_active_in late endosome	IBA Inferred from Biological aspect of Ancestor more info
located_in late endosome	IMP Inferred from Mutant Phenotype more info	PubMed
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in mitochondrial membrane	IEA Inferred from Electronic Annotation more info
located_in mitochondrial outer membrane	HDA more info	PubMed
located_in mitochondrion	HDA more info	PubMed
located_in mitochondrion	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: Rab family GTPase VPS21

NP_014732.1

Endosomal Rab family GTPase; required for endocytic transport and sorting of vacuolar hydrolases; required for endosomal localization of the CORVET complex; required with YPT52 for MVB biogenesis and sorting; involved in autophagy and ionic stress tolerance; geranylgeranylation required for membrane association; protein abundance increases in response to DNA replication stress; mammalian Rab5 homolog; VPS21 has a paralog, YPT53, that arose from the whole genome duplication

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

NC_001147.6 Reference assembly

Range

490196..490828 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001183508.1 → NP_014732.1 TPA: Rab family GTPase VPS21 [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_014732.1

Status: REVIEWED

UniProtKB/Swiss-Prot

D6W2F0, P36017

UniProtKB/TrEMBL

A6ZNT9, B3LJD5, B5VRY4, C7GMP5, C8ZI50, G2WMW6, N1P326

Conserved Domains (1) summary

cd01860
Location:7 → 172

Rab5_related; Rab-related GTPase family includes Rab5 and Rab22; regulates early endosome fusion