VPS13 membrane morphogenesis protein VPS13 [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: VPS13
Official Full Name: membrane morphogenesis protein VPS13
Primary source: SGD:S000003963
Locus tag: YLL040C
See related: AllianceGenome:SGD:S000003963; FungiDB:YLL040C; VEuPathDB:YLL040C
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: SOI1; VPT2; YME3
Summary: Enables phospholipid binding activity and phospholipid transfer activity. Involved in several processes, including protein retention in Golgi apparatus; reticulophagy; and vacuolar transport. Located in several cellular components, including nucleus-vacuole junction; prospore membrane; and vacuole-mitochondrion membrane contact site. Is active in organelle membrane contact site. Used to study Cohen syndrome and neurodegenerative disease (multiple). Human ortholog(s) of this gene implicated in Parkinson's disease 23; choreaacanthocytosis; and choreatic disease. Orthologous to several human genes including VPS13C (vacuolar protein sorting 13 homolog C). [provided by Alliance of Genome Resources, Nov 2024]
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Genomic context

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See VPS13 in Genome Data Viewer

Location:: chromosome: XII

Exon count:: 1

Sequence:: Chromosome: XII; NC_001144.5 (54211..63645, complement)

Chromosome XII - NC_001144.5 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001144.5

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

A role for Vps13-mediated lipid transfer at the ER-endosome contact site in ESCRT-mediated sorting.
Title: A role for Vps13-mediated lipid transfer at the ER-endosome contact site in ESCRT-mediated sorting.
Parallel phospholipid transfer by Vps13 and Atg2 determines autophagosome biogenesis dynamics.
Title: Parallel phospholipid transfer by Vps13 and Atg2 determines autophagosome biogenesis dynamics.
The GTPase Arf1 Is a Determinant of Yeast Vps13 Localization to the Golgi Apparatus.
Title: The GTPase Arf1 Is a Determinant of Yeast Vps13 Localization to the Golgi Apparatus.
Suppression of Vps13 adaptor protein mutants reveals a central role for PI4P in regulating prospore membrane extension.
Title: Suppression of Vps13 adaptor protein mutants reveals a central role for PI4P in regulating prospore membrane extension.
Genetic Dissection of Vps13 Regulation in Yeast Using Disease Mutations from Human Orthologs.
Title: Genetic Dissection of Vps13 Regulation in Yeast Using Disease Mutations from Human Orthologs.
The Vps13 Family of Lipid Transporters and Its Role at Membrane Contact Sites.
Title: The Vps13 Family of Lipid Transporters and Its Role at Membrane Contact Sites.
Cryo-EM reconstruction of a VPS13 fragment reveals a long groove to channel lipids between membranes.
Title: Cryo-EM reconstruction of a VPS13 fragment reveals a long groove to channel lipids between membranes.
Vps13 is required for the packaging of the ER into autophagosomes during ER-phagy.
Title: Vps13 is required for the packaging of the ER into autophagosomes during ER-phagy.
Mcp1 is a mitochondrial adaptor for Vps13, and the Vps13-Mcp1 interaction, but not Ypt35, is required when ER-mitochondria contacts are lost.
Title: Competitive organelle-specific adaptors recruit Vps13 to membrane contact sites.
findings support a model in which Mcp1 and Vps13 work as functional effectors of vacuole-mitochondria contact sites, while tethering is mediated by other factors, including Vps39.
Title: Vps13-Mcp1 interact at vacuole-mitochondria interfaces and bypass ER-mitochondria contact sites.

Submit: New GeneRIF Correction See all GeneRIFs (15)

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 lipid binding	IEA Inferred from Electronic Annotation more info
enables phospholipid binding	IDA Inferred from Direct Assay more info	PubMed
enables phospholipid transfer activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in Golgi to endosome transport	IDA Inferred from Direct Assay more info	PubMed
involved_in ascospore-type prospore membrane formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to starvation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in intermembrane lipid transfer	IDA Inferred from Direct Assay more info	PubMed
involved_in late endosome to vacuole transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in late endosome to vacuole transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in lipid transport	IEA Inferred from Electronic Annotation more info
involved_in mitochondrion organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in mitochondrion organization	IGI Inferred from Genetic Interaction more info	PubMed
involved_in phospholipid transport	IEA Inferred from Electronic Annotation more info
involved_in protein retention in Golgi apparatus	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein retention in Golgi apparatus	IMP Inferred from Mutant Phenotype 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 regulation of inclusion body assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in reticulophagy	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in Golgi apparatus	IEA Inferred from Electronic Annotation more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in endosome	IEA Inferred from Electronic Annotation more info
located_in endosome membrane	IEA Inferred from Electronic Annotation more info
located_in late endosome	IDA Inferred from Direct Assay more info	PubMed
located_in mitochondrial outer membrane	IEA Inferred from Electronic Annotation more info
located_in mitochondrion	HDA more info	PubMed
located_in mitochondrion	IEA Inferred from Electronic Annotation more info
located_in nuclear outer membrane	IEA Inferred from Electronic Annotation more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus-vacuole junction	IDA Inferred from Direct Assay more info	PubMed
is_active_in organelle membrane contact site	IDA Inferred from Direct Assay more info	PubMed
located_in peroxisome	IEA Inferred from Electronic Annotation more info
located_in prospore membrane	HDA more info	PubMed
located_in prospore membrane	IDA Inferred from Direct Assay more info	PubMed
located_in prospore membrane	IEA Inferred from Electronic Annotation more info
located_in vacuolar membrane	IEA Inferred from Electronic Annotation more info
located_in vacuole	IEA Inferred from Electronic Annotation more info
located_in vacuole-mitochondrion membrane contact site	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: membrane morphogenesis protein VPS13

NP_013060.1

Lipid transport protein; involved in vacuolar protein sorting, protein retention in the Golgi, prospore membrane formation and sporulation; required for mitochondrial integrity and ER packaging into autophagosomes during cortical reticulophagy; peripheral membrane protein found at the prospore membrane and at membrane contact sites; contains a PH-like domain; homologous to human CHAC and COH1, involved in Chorea-acanthocytosis and Cohen syndrome, respectively

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_001144.5 Reference assembly

Range

54211..63645 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001181860.1 → NP_013060.1 TPA: membrane morphogenesis protein VPS13 [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_013060.1

Status: REVIEWED

UniProtKB/Swiss-Prot

D6VXW6, O00040, Q07878

UniProtKB/TrEMBL

C7GRK1, N1P6P7

Conserved Domains (1) summary

COG5043
Location:1 → 2294

MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]