Intermembrane lipid transfer protein VPS13 - Saccharomyces cerevisiae S288C

Intermembrane lipid transfer protein VPS13 (Saccharomyces cerevisiae S288C)

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Subcellular Location Biology & Function Interactions Cross-References

General Information

Protein Information
Protein Name	Intermembrane lipid transfer protein VPS13
Accession Code	Q07878
Gene	VPS13
Organism	Saccharomyces cerevisiae S288C (Taxonomy: 559292)
Part of Reference Proteome?	Yes
Sequence (Length: 3144)
MLESLAANLLNRLLGSYVENFDPNQLNVGIWSGDVKLKNLKLRKDCLDSLNLPIDVKSGILGDLVLTVPWSSLKNKPVKIIIEDCYLLCSPRSEDHENDEEMIKRAFRLKMRKVSEWELTNQARILSTQS ENKTSSSSSEKNNAGFMQSLTTKIIDNLQVTIKNIHLRYEDMDGIFTTGPSSVGLTLNELSAVSTDSNWAPSFIDITQNITHKLLTLNSLCLYWNTDSPPLISDDDQDRSLENFVRGFKDMIASKNSTAP KHQYILKPVSGLGKLSINKLGSTEEQPHIDLQMFYDEFGLELDDTEYNDILHVLSSIQLRQITKKFKKARPSFAVSENPTEWFKYIAACVINEIHEKNKMWTWESMKEKCEQRRLYTKLWVEKLKLKNLE APLRDPIQEAQLSELHKDLTYDEIILFRSVAKRQYAQYKLGMTEDSPTPTASSNIEPQTSNKSATKNNGSWLSSWWNGKPTEEVDEDLIMTEEQRQELYDAIEFDENEDKGPVLQVPRERVELRVTSLLK KGSFTIRKKKQNLNLGSIIFENCKVDFAQRPDSFLSSFQLNKFSLEDGSPNALYKHIISVRNSSKDQSSIDNHATGEEEEEDEPLLRASFELNPLDGLADSNLNIKLLGMTVFYHVHFITEVHKFFKASN QHMETIGNIVNAAEATVEGWTTQTRMGIESLLEDHKTVNVSLDLQAPLIILPLDPHDWDTPCAIIDAGHMSILSDLVPKEKIKEIKELSPEEYDKIDGNEINRLMFDRFQILSQDTQIFVGPDIQSTIGK INTASSTNDFRILDKMKLELTVDLSILPKAYKLPTIRVFGHLPRLSLSINDIQYKTIMNLIANSIPSMIDDEENNGDYVNYSSGSEKEMKKQIQLQLKNTLKALENMQPLQIEQKFLELHFDIDQAKIAF FQCIKNDSRNSEKLVDILCQRLNFNFDKRAKEMNLDLRVHSLDVEDYIELTDNKEFKNLISSGVEKVTRSQKDLFTLKYKRVQRIVPHNDTLIELFDQDIVMHMSELQLVLTPRSVLTLMNYAMLTFTDP NAPEMPADVLRHNKEDRDDAPQKINMKIKMEAVNVIFNDDSIKLATLVLSAGEFTMVLLPERYNINLKLGGLELTDETNESFSRDSVFRKIIQMKGQELVELSYESFDPATNTKDYDSFLKYSTGSMHVN FIESAVNRMVNFFAKFQKSKVSFDRARLAAYNQAPSIDAVNNMKMDIVIKAPIIQFPKLVGTQENNYDTMRFYLGEFFIENKFSVIDESHKINHIKLGVREGQLSSNLNFDGSSQQLYLVENIGLLFNID RDPLPQDDTPELKVTSNFESFALDLTENQLTYLLEISNKVSSAFNITDENSGESGGKGEIKSPSPDPASLSSESERTATPQSLQGSNKSNIKNPEQKYLDFSFKAPKIALTLYNKTKGVTSLNDCGLTRI MFQDIGCSLGLKNDGTVDGQAHVAAFRIEDVRNIKDNKHTELIPKSKNKEYQFVANISRKNLEVGRLLNISMTMDSPKMILAMDYLVSLKEFFDAIMSKSHENNLYYPENTNQKPENKAIVESVQEGGDV TKIQYSVNIIETALILLADPCDMNSEAISFKIGQFLVTDQNIMTVAANNVGIFLFKMNSSEEKLRLLDDFSSSLTIDKRNSTPQTLMTNIQLSVQPLLMRISLRDIRLAMLIFKRVTTLLNKMTEKEDNG EEEESTDKIQFSHEFERKLAVLDPSILGERSRASQSSDSESIEVPTAILKNETFNADLGGLRFILIGDVHEMPILDMNVNEITASAKDWSTDFEALASLETYVNIFNYSRSSWEPLLEMIPITFHLSKGH SEMDPAFSFDILTQRIAEITLSARSIAMLSHIPASLTEELPLASRVSQKPYQLVNDTELDFDVWIQDKTTEDNKNEVVLLKANTSLPWEFEDWRSIREKLDIDKSKNILGVCVSGQNYKTIMNIDATTEG ENLHVLSPPRNNVHNRIVCEARCDENNVKIITFRSTLVIENTTSTEIELLVDSKDPNKPSLKYAIKPHQSKSVPVEYAYDSDIRIRPASEDIYDWSQQTLSWKSLLSNQMSIFCSSKEDSNQRFHFEIGA KYDEREPLAKIFPHMKIVVSASMTIENLLPADINFSIFDKREEKRTDFLKTGESMEVHHISLDSFLLMSVQPLQDEASASKPSIVNTPHKSPLNPEDSLSLTLSGGQNLLLKLDYKNIDGTRSKVIRIYS PYIIMNSTDRELYIQSSLLNIAQSKILLENEKRYTIPKMFSFDKEDDKSNRARIRFKESEWSSKLSFDAIGQSFDASVRIKNKEQESNLGINISEGKGKYLLSKVIEIAPRYIISNTLDIPIEVCETGSM DVQQIESNITKPLYRMRNIVDKQLVLKFLGGDSNWSQPFFIKNVGVTYLKVLKNSRHKLLKIEILLDKATIFIRIKDGGDRWPFSIRNFSDHDFIFYQRDPRKVSDPYKDDQSNESSSRSFKPIFYRIPS KSIMPYAWDFPTAKEKYLVLESGTRTREVRLAEIGELPPLRLDKRSKDKPAPIVGLHVVADDDMQALVIVNYKANVGLYKLKTASATTTSSVSVNSSVTDGFVQKDEDEKVNTQIVVSFKGVGISLINGR LQELLYINMRGIELRYNESKAYQTFSWKMKWMQIDNQLFSGNYSNILYPTEIPYTEKEIENHPVISGSISKVNDSLQAVPYFKHVTLLIQEFSIQLDEDMLYAMMDFIKFPGSPWIMDSRDYKYDEEIQL PDVSELKTAGDIYFEIFHIQPTVLHLSFIRSDEISPGLAEETEESFSSSLYYVHMFAMTLGNINEAPVKVNSLFMDNVRVPLPILMDHIERHYTTQFVYQIHKILGSADCFGNPVGLFNTISSGVWDLFY EPYQGYMMNDRPQEIGIHLAKGGLSFAKKTVFGLSDSMSKFTGSMAKGLSVTQDLEFQRVRRLQQRINKNNRNALANSAQSFASTLGSGLSGIALDPYKAMQKEGAAGFLKGLGKGIVGLPTKTAIGFLD LTSNLSQGVKSTTTVLDMQKGCRVRLPRYVDHDQIIKPYDLREAQGQYWLKTVNGGVFMNDEYLSHVILPGKELAVIVSMQHIAEVQMATQELMWSTGYPSIQGITLERSGLQIKLKSQSEYFIPISDPE ERRSLYRNIAIAVREYNKYCEAIL

Subcellular Location

Description
Endosome membrane {Experimental EvidencePubMed:27280386, Experimental EvidencePubMed:28334785, Experimental EvidencePubMed:28864540, Experimental EvidencePubMed:30018089, Experimental EvidencePubMed:32690699, Curator InferencePubMed:22442115, Curator InferencePubMed:24036347}; Peripheral membrane protein {Experimental EvidencePubMed:28122955}. Mitochondrion outer membrane {Experimental EvidencePubMed:26370498, Experimental EvidencePubMed:27280386, Experimental EvidencePubMed:30018089, Experimental EvidencePubMed:34830155}; Peripheral membrane protein {Experimental EvidencePubMed:28122955}. Prospore membrane {ECO:0000269\|PubMed:22442115, ECO:0000269\|PubMed:24036347, Experimental EvidencePubMed:27280386}; Peripheral membrane protein {Experimental EvidencePubMed:28122955}. Vacuole membrane {Experimental EvidencePubMed:26370498, Experimental EvidencePubMed:27280386, Experimental EvidencePubMed:30018089, Experimental EvidencePubMed:32690699}; Peripheral membrane protein {Experimental EvidencePubMed:28122955}. Nucleus outer membrane {Experimental EvidencePubMed:26370498, Experimental EvidencePubMed:27280386, Experimental EvidencePubMed:30018089}; Peripheral membrane protein {Experimental EvidencePubMed:28122955}. Peroxisome {Experimental EvidencePubMed:28864540}. Golgi apparatus, trans-Golgi network membrane {Experimental EvidencePubMed:34830155}; Peripheral membrane protein {Experimental EvidencePubMed:28122955}. Note=Found at different interorganellar contact sites depending on the growth state of the cell (PubMed:26370498, PubMed:27280386, PubMed:30018089, PubMed:32690699). Localizes from endosomes to the vacuolar membrane during starvation (PubMed:32690699). Localizes to mitochondrial-endosome contacts (PubMed:27280386). Localizes to nuclear envelope-vacuole contact sites (nuclear-vacuole junction; NVJ) during respiration (PubMed:26370498, PubMed:27280386, PubMed:30018089). {Experimental EvidencePubMed:26370498, Experimental EvidencePubMed:27280386, Experimental EvidencePubMed:30018089, Experimental EvidencePubMed:32690699}.
Position in the Nuclear Envelope
Location	Location ID	Description
Nuclear Envelope	SL-0178	The nuclear envelope is a membrane system which surrounds the nucleoplasm of eukaryotic cells. It is composed of the nuclear lamina, nuclear pore complexes and two nuclear membranes. The space between the two membranes is called the nuclear intermembrane space.
Nuclear Membrane	SL-0182	The membrane surrounding the nucleus. This term is used when it is not known if the protein is found in or associated with the inner or outer nuclear membrane.
Nuclear Outer Membrane	SL-0183	The outer membrane of the nucleus is the membrane facing the cytoplasm. In mammals, the outer nuclear membrane is continuous in many places with the rough endoplasmic reticulum and is dotted with ribosomes.
Membrane Topology
Topology	Source	Annotation Type
Peripheral	UniProt	Experimental Evidence {ECO:0000269\|PubMed:28122955}
Assigned Ontology terms

Cellular Component	Endosome (GO:0005768) Endosome Membrane (GO:0010008) Extrinsic Component Of Membrane (GO:0019898) Golgi Apparatus (GO:0005794) Golgi-Associated Vesicle (GO:0005798) Mitochondrial Membrane (GO:0031966) Mitochondrial Outer Membrane (GO:0005741) Mitochondrion (GO:0005739) Nuclear Outer Membrane (GO:0005640) Nucleus-Vacuole Junction (GO:0071561) Peroxisome (GO:0005777) Prospore Membrane (GO:0005628) Vacuolar Membrane (GO:0005774) Vacuole (GO:0005773) Vacuole-Mitochondrion Membrane Contact Site (GO:1990816)

Biology & Function

Description
Mediates the transfer of lipids between membranes at organelle contact sites (PubMed:30093493, PubMed:24036347, PubMed:22442115). Binds phospholipids, including phosphatidic acid (PA), phosphorylated phosphatidylinositol (PI), phosphatidylcholine (PC), phosphatidylethanolamine (PE), ceramide, and phosphatidylserine (PS) (PubMed:30093493, PubMed:34830155, PubMed:28122955, PubMed:28334785). Involved in mitochondrial lipid homeostasis, in a MCP1-dependent manner (PubMed:27280386, PubMed:34830155, PubMed:32690699). Involved in cortical reticulophagy (also known as cortical endoplasmic reticulum (ER) macroautophagy), acting at the late endosome to package ER into autophagosomes (PubMed:32690699). Involved in the formation of the prospore membrane during sporulation, in a SPO71-dependent manner (PubMed:24036347, PubMed:22442115). Involved in Golgi vesicle transport, in a CDC31-dependent and ARF1-dependent manner (PubMed:28122955, PubMed:9314526, PubMed:34830155). Plays a role in actin cytoskeleton organization (PubMed:28334785). {Experimental EvidencePubMed:22442115, Experimental EvidencePubMed:24036347, Experimental EvidencePubMed:27280386, Experimental EvidencePubMed:28122955, Experimental EvidencePubMed:28334785, Experimental EvidencePubMed:30093493, Experimental EvidencePubMed:32690699, Experimental EvidencePubMed:34830155, Experimental EvidencePubMed:9314526}.
Assigned Ontology terms

Biological Process	Ascospore-Type Prospore Membrane Formation (GO:0032120) Golgi Vesicle Transport (GO:0048193) Intermembrane Lipid Transfer (GO:0120009) Late Endosome To Vacuole Transport (GO:0045324) Mitochondrion Organization (GO:0007005) Protein Retention In Golgi Apparatus (GO:0045053) Protein Targeting To Vacuole (GO:0006623) Regulation Of Inclusion Body Assembly (GO:0090083) Reticulophagy (GO:0061709)
Molecular Function	Lipid Binding (GO:0008289) Phospholipid Binding (GO:0005543) Phospholipid Transfer Activity (GO:0120014)

Protein-Protein Interactions

Interactions with other proteins (30 interactors)

Partner (UniProt)		IntAct	Confidence score
P30656	Proteasome subunit beta type-5 (EC 3.4.25.1) (Macropain subunit PRE2) (Multicatalytic endopeptidase complex subunit PRE2) (Proteasome component PRE2) (Proteinase YSCE subunit PRE2)	EBI-7116059	0.40
P23639	Proteasome subunit alpha type-2 (Macropain subunit Y7) (Multicatalytic endopeptidase complex subunit Y7) (Proteasome component Y7) (Proteinase YSCE subunit 7)	EBI-7116127	0.40
P49956	Chromosome transmission fidelity protein 18	EBI-785954	0.44
P16140	V-type proton ATPase subunit B (V-ATPase subunit B) (V-ATPase 57 kDa subunit) (Vacuolar proton pump subunit B)	EBI-797353	0.35
P09733	Tubulin alpha-1 chain (EC 3.6.5.-)	EBI-797353	0.35
P02994	Elongation factor 1-alpha (EF-1-alpha) (Eukaryotic elongation factor 1A) (eEF1A) (Translation elongation factor 1A)	EBI-797353	0.35
P11484	Ribosome-associated molecular chaperone SSB1 (EC 3.6.4.10) (Cold-inducible protein YG101) (Heat shock protein SSB1) (Hsp70 chaperone Ssb)	EBI-797353	0.35
P10592	Heat shock protein SSA2	EBI-797353	0.35
P10659	S-adenosylmethionine synthase 1 (AdoMet synthase 1) (EC 2.5.1.6) (Methionine adenosyltransferase 1) (MAT 1)	EBI-797353	0.35
P40495	Homoisocitrate dehydrogenase, mitochondrial (HIcDH) (EC 1.1.1.87)	EBI-797353	0.35
P06787	Calmodulin (CaM)	EBI-797353	0.53
P16550	Protein APA1 [Includes: Diadenosine 5',5'''-P1,P4-tetraphosphate phosphorylase 1 (Ap4A phosphorylase 1) (EC 2.7.7.53) (ADP-sulfurylase) (EC 2.7.7.5) (ATP adenylyltransferase) (Diadenosine tetraphosphate alpha,beta-phosphorylase (ADP-forming))]	EBI-799867	0.35
P07259	Protein URA2 [Includes: Glutamine-dependent carbamoyl-phosphate synthase (EC 6.3.5.5); Aspartate carbamoyltransferase (EC 2.1.3.2)]	EBI-800803	0.35
P17255	V-type proton ATPase catalytic subunit A (V-ATPase subunit A) (EC 7.1.2.2) (Vacuolar proton pump subunit A) [Cleaved into: Endonuclease PI-SceI (EC 3.1.-.-) (Sce VMA intein) (VMA1-derived endonuclease) (VDE)]	EBI-800803	0.35
P38764	26S proteasome regulatory subunit RPN1 (HMG-CoA reductase degradation protein 2) (Proteasome non-ATPase subunit 1)	EBI-800803	0.35
P41940	Mannose-1-phosphate guanyltransferase (EC 2.7.7.13) (ATP-mannose-1-phosphate guanylyltransferase) (GDP-mannose pyrophosphorylase) (NDP-hexose pyrophosphorylase)	EBI-800803	0.35
P16474	Endoplasmic reticulum chaperone BiP (EC 3.6.4.10) (78 kDa glucose-regulated protein homolog) (GRP-78) (Immunoglobulin heavy chain-binding protein homolog) (BiP)	EBI-800803	0.35
P14742	Glutamine--fructose-6-phosphate aminotransferase [isomerizing] (GFAT) (EC 2.6.1.16) (D-fructose-6-phosphate amidotransferase) (Hexosephosphate aminotransferase)	EBI-800803	0.35
P43535	Protein GCN20 (General control non-derepressible protein 20)	EBI-800803	0.35
P32324	Elongation factor 2 (EF-2) (Eukaryotic elongation factor 2) (eEF2) (Ribosomal translocase) (Translation elongation factor 2)	EBI-800803	0.35
Q00955	Acetyl-CoA carboxylase (ACC) (EC 6.4.1.2) (Fatty acid synthetase 3) (mRNA transport-defective protein 7) [Includes: Biotin carboxylase (EC 6.3.4.14)]	EBI-812797	0.27
P18239	ADP,ATP carrier protein 2 (ADP/ATP translocase 2) (Adenine nucleotide translocator 2) (ANT 2) (Petite colonies protein 9)	EBI-813508	0.27
P37898	Alanine/arginine aminopeptidase (EC 3.4.11.-)	EBI-813689	0.27
P60010	Actin (EC 3.6.4.-)	EBI-820657	0.27
Q12250	26S proteasome regulatory subunit RPN5 (Proteasome non-ATPase subunit 5)	EBI-7638438	0.40
P38236	Protein MUM2 (Muddled meiosis protein 2)	EBI-8445626	0.44
P38041	Protein BOB1 (BEM1-binding protein) (Growth inhibitory protein 7)	EBI-7370461	0.37
Q08273	RING-box protein HRT1 (RING-box protein 1) (E3 ubiquitin-protein ligase complex SCF subunit HRT1) (High level expression reduces Ty3 transposition protein 1) (Regulator of cullins protein 1)	EBI-16271112	0.35
P06244	cAMP-dependent protein kinase type 1 (PKA 1) (EC 2.7.11.11) (CDC25-suppressing protein kinase) (PK-25)	EBI-16285450	0.35
P38815	Endosomal/vacuolar adapter protein YPT35 (PX domain-containing protein YPT35)	EBI-16289368	0.40

Cross-References

Database	Links
UNIPROT	Q07878 D6VXW6 O00040
Pfam	PF12624 PF06650 PF16908 PF16909 PF16910

NucEnvDB

NucEnvDB

A database of Nuclear Envelope Proteins and their Interactions

Intermembrane lipid transfer protein VPS13 (Saccharomyces cerevisiae S288C)

General Information

Protein Information

Subcellular Location

Description

Position in the Nuclear Envelope

Membrane Topology

Assigned Ontology terms

Biology & Function

Description

Assigned Ontology terms

Protein-Protein Interactions

Interactions with other proteins (30 interactors)

Cross-References

Database

Links

Intermembrane lipid transfer protein VPS13 (Saccharomyces cerevisiae S288C)

General Information

Protein Information

Subcellular Location

Description Show

Position in the Nuclear Envelope

Membrane Topology

Assigned Ontology terms

Biology & Function

Description Hide

Assigned Ontology terms

Protein-Protein Interactions

Interactions with other proteins (30 interactors)

Cross-References

Database

Links

Description

Description