P52917
PR
Gene name |
VPS4 (CSC1, DID6, END13, GRD13, VPL4, VPT10) |
Protein name |
Vacuolar protein sorting-associated protein 4 |
Names |
DOA4-independent degradation protein 6, Protein END13, Vacuolar protein-targeting protein 10 |
Species |
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) |
KEGG Pathway |
sce:YPR173C |
EC number |
|
Protein Class |
|
Descriptions
(Annotation based on sequence homology with Q9UN37)
VPS4 proteins are AAA+ ATPases required to form multivesicular bodies, release viral particles, and complete cytokinesis. VPS4 proteins act by disassembling ESCRT-III heteropolymers during or after their proposed function in membrane scission. Deleting the N-terminal MIT domain and adjacent linker from VPS4A increases both basal and liposome-enhanced ATPase activity, indicating that these elements play a role in autoinhibiting VPS4A until it encounters ESCRT-III polymers. The interactions between acidic ESCRT-III residues and sequences in VPS4A, in particular in the linker connecting the MIT and AAA+ domains, are involved in regulating the intrinsic autoinhibition of the enzyme.
Autoinhibitory domains (AIDs)
Target domain |
|
Relief mechanism |
|
Assay |
cis-regPred |
Accessory elements
No accessory elements
Autoinhibited structure
Activated structure
18 structures for P52917
| Entry ID | Method | Resolution | Chain | Position | Source |
|---|---|---|---|---|---|
| 2QP9 | X-ray | 290 A | X | 83-437 | PDB |
| 2QPA | X-ray | 320 A | A/B/C | 83-437 | PDB |
| 2RKO | X-ray | 335 A | A | 124-437 | PDB |
| 2V6X | X-ray | 198 A | A | 1-82 | PDB |
| 3EIE | X-ray | 270 A | A | 122-437 | PDB |
| 3EIH | X-ray | 325 A | A/B/C | 104-437 | PDB |
| 3MHV | X-ray | 310 A | C | 299-413 | PDB |
| 4NIQ | X-ray | 230 A | A/B | 1-82 | PDB |
| 5FVK | X-ray | 166 A | A/B | 1-82 | PDB |
| 5FVL | X-ray | 197 A | A/B | 1-82 | PDB |
| 5UIE | EM | 570 A | A/B/C/D/E/F | 1-437 | PDB |
| 5XMI | EM | 390 A | A/B/C/D/E/F | 1-437 | PDB |
| 5XMK | EM | 418 A | A/B/C/D/E/F | 1-437 | PDB |
| 6AP1 | EM | 320 A | A/B/C/D/E/F | 101-437 | PDB |
| 6BMF | EM | 320 A | A/B/C/D/E | 101-437 | PDB |
| 6NDY | EM | 360 A | A/B/C/D/E | 101-437 | PDB |
| 6OO2 | EM | 440 A | A/B/C/D/E/F | 101-437 | PDB |
| AF-P52917-F1 | Predicted | AlphaFoldDB |
4 variants for P52917
| Variant ID(s) | Position | Change | Description | Diseaes Association | Provenance |
|---|---|---|---|---|---|
| s16-887548 | 96 | N>Y | No | SGRP | |
| s16-887498 | 112 | N>K | No | SGRP | |
| s16-886857 | 326 | T>N | No | SGRP | |
| s16-886732 | 368 | D>N | No | SGRP |
No associated diseases with P52917
9 GO annotations of cellular component
| Name | Definition |
|---|---|
| ATPase complex | A protein complex which is capable of ATPase activity. |
| cytoplasm | The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. |
| endoplasmic reticulum | The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached). |
| endosome | A vacuole to which materials ingested by endocytosis are delivered. |
| ESCRT IV complex | An ESCRT complex that has AAA-ATPase activity and is involved in ESCRT-mediated intralumenal vesicle formation and the final stages of cytokinesis. The complex catalyzes disassembly of the ESCRT III filament around the neck of the budding vesicle in an ATP-driven reaction, resulting in membrane scission and recycling of the ESCRT III components back to the cytosol. In yeast, it is formed by the AAA ATPase Vps4 and its cofactor Vta1. |
| membrane | A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. |
| midbody | A thin cytoplasmic bridge formed between daughter cells at the end of cytokinesis. The midbody forms where the contractile ring constricts, and may persist for some time before finally breaking to complete cytokinesis. |
| nuclear pore | A protein complex providing a discrete opening in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined. |
| plasma membrane | The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. |
4 GO annotations of molecular function
| Name | Definition |
|---|---|
| ATP binding | Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. |
| ATP hydrolysis activity | Catalysis of the reaction: ATP + H2O = ADP + H+ phosphate. ATP hydrolysis is used in some reactions as an energy source, for example to catalyze a reaction or drive transport against a concentration gradient. |
| identical protein binding | Binding to an identical protein or proteins. |
| protein homodimerization activity | Binding to an identical protein to form a homodimer. |
21 GO annotations of biological process
| Name | Definition |
|---|---|
| autophagosome maturation | Removal of PI3P and Atg8/LC3 after the closure of the phagophore and before the fusion with the endosome/lysosome (e.g. mammals and insects) or vacuole (yeast), and that very likely destabilizes other Atg proteins and thus enables their efficient dissociation and recycling. |
| autophagy | The cellular catabolic process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation. |
| endosomal transport | The directed movement of substances mediated by an endosome, a membrane-bounded organelle that carries materials enclosed in the lumen or located in the endosomal membrane. |
| intralumenal vesicle formation | The invagination of the endosome membrane and resulting formation of a vesicle within the lumen of the endosome. |
| late endosome to lysosome transport via multivesicular body sorting pathway | The directed movement of substances from late endosomes to lysosomes by a pathway in which molecules are sorted into multivesicular bodies, which then fuse with the lysosome. |
| late endosome to vacuole transport | The directed movement of substances from late endosomes to the vacuole. In yeast, after transport to the prevacuolar compartment, endocytic content is delivered to the late endosome and on to the vacuole. This pathway is analogous to endosome to lysosome transport. |
| late endosome to vacuole transport via multivesicular body sorting pathway | The directed movement of substances from endosomes to vacuoles by a pathway in which molecules are sorted into multivesicular bodies, which then fuse with the vacuole. |
| macroautophagy | The major inducible pathway for the general turnover of cytoplasmic constituents in eukaryotic cells, it is also responsible for the degradation of active cytoplasmic enzymes and organelles during nutrient starvation. Macroautophagy involves the formation of double-membrane-bounded autophagosomes which enclose the cytoplasmic constituent targeted for degradation in a membrane-bounded structure. Autophagosomes then fuse with a lysosome (or vacuole) releasing single-membrane-bounded autophagic bodies that are then degraded within the lysosome (or vacuole). Some types of macroautophagy, e.g. pexophagy, mitophagy, involve selective targeting of the targets to be degraded. |
| membrane fission | A process that is carried out at the cellular level which results in the separation of a single continuous membrane into two membranes. |
| midbody abscission | The process by which the midbody, the cytoplasmic bridge that connects the two prospective daughter cells, is severed at the end of mitotic cytokinesis, resulting in two separate daughter cells. |
| multivesicular body assembly | The aggregation, arrangement and bonding together of a set of components to form a multivesicular body, a type of late endosome in which regions of the limiting endosomal membrane invaginate to form internal vesicles; membrane proteins that enter the internal vesicles are sequestered from the cytoplasm. |
| multivesicular body sorting pathway | A vesicle-mediated transport process in which transmembrane proteins are ubiquitylated to facilitate their entry into luminal vesicles of multivesicular bodies (MVBs); upon subsequent fusion of MVBs with lysosomes or vacuoles, the cargo proteins are degraded. |
| negative regulation of cell death | Any process that decreases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death. |
| nuclear membrane reassembly | The reformation of the nuclear membranes following their breakdown in the context of a normal process. |
| nucleus organization | A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus. |
| plasma membrane repair | The resealing of a cell plasma membrane after cellular wounding due to, for instance, mechanical stress. |
| protein retention in Golgi apparatus | The retention of proteins within the Golgi apparatus. Golgi-localized carbohydrate-modifying enzymes have a short N-terminal domain that faces the cytosol, a single transmembrane alpha helix, and a large C-terminal domain that faces the Golgi lumen and that contains the catalytic site. How the membrane-spanning alpha helix in a Golgi enzyme causes its localization and prevents its movement to the plasma membrane is not known. |
| protein transport | The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. |
| reticulophagy | The selective autohagy process in which parts of the endoplasmic reticulum are loaded into autophagosomes, delivered to the vacuole, and degraded in response to changing cellular conditions. |
| sterol metabolic process | The chemical reactions and pathways involving sterols, steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule. |
| vacuole organization | A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vacuole. |
7 homologous proteins in AiPD
| UniProt AC | Gene Name | Protein Name | Species | Evidence Code |
|---|---|---|---|---|
| Q0VD48 | VPS4B | Vacuolar protein sorting-associated protein 4B | Bos taurus (Bovine) | SS |
| O75351 | VPS4B | Vacuolar protein sorting-associated protein 4B | Homo sapiens (Human) | PR |
| Q9UN37 | VPS4A | Vacuolar protein sorting-associated protein 4A | Homo sapiens (Human) | EV |
| P46467 | Vps4b | Vacuolar protein sorting-associated protein 4B | Mus musculus (Mouse) | PR |
| Q8VEJ9 | Vps4a | Vacuolar protein sorting-associated protein 4A | Mus musculus (Mouse) | PR |
| Q793F9 | Vps4a | Vacuolar protein sorting-associated protein 4A | Rattus norvegicus (Rat) | PR |
| Q9ZNT0 | SKD1 | Protein SUPPRESSOR OF K(+) TRANSPORT GROWTH DEFECT 1 | Arabidopsis thaliana (Mouse-ear cress) | PR |
| 10 | 20 | 30 | 40 | 50 | 60 |
| MSTGDFLTKG | IELVQKAIDL | DTATQYEEAY | TAYYNGLDYL | MLALKYEKNP | KSKDLIRAKF |
| 70 | 80 | 90 | 100 | 110 | 120 |
| TEYLNRAEQL | KKHLESEEAN | AAKKSPSAGS | GSNGGNKKIS | QEEGEDNGGE | DNKKLRGALS |
| 130 | 140 | 150 | 160 | 170 | 180 |
| SAILSEKPNV | KWEDVAGLEG | AKEALKEAVI | LPVKFPHLFK | GNRKPTSGIL | LYGPPGTGKS |
| 190 | 200 | 210 | 220 | 230 | 240 |
| YLAKAVATEA | NSTFFSVSSS | DLVSKWMGES | EKLVKQLFAM | ARENKPSIIF | IDEVDALTGT |
| 250 | 260 | 270 | 280 | 290 | 300 |
| RGEGESEASR | RIKTELLVQM | NGVGNDSQGV | LVLGATNIPW | QLDSAIRRRF | ERRIYIPLPD |
| 310 | 320 | 330 | 340 | 350 | 360 |
| LAARTTMFEI | NVGDTPCVLT | KEDYRTLGAM | TEGYSGSDIA | VVVKDALMQP | IRKIQSATHF |
| 370 | 380 | 390 | 400 | 410 | 420 |
| KDVSTEDDET | RKLTPCSPGD | DGAIEMSWTD | IEADELKEPD | LTIKDFLKAI | KSTRPTVNED |
| 430 | |||||
| DLLKQEQFTR | DFGQEGN |