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P46467

- VPS4B_MOUSE

UniProt

P46467 - VPS4B_MOUSE

Protein

Vacuolar protein sorting-associated protein 4B

Gene

Vps4b

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 131 (01 Oct 2014)
      Sequence version 2 (16 Jan 2004)
      Previous versions | rss
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    Functioni

    Involved in late steps of the endosomal multivesicular bodies (MVB) pathway. Recognizes membrane-associated ESCRT-III assemblies and catalyzes their disassembly, possibly in combination with membrane fission. Redistributes the ESCRT-III components to the cytoplasm for further rounds of MVB sorting. MVBs contain intraluminal vesicles (ILVs) that are generated by invagination and scission from the limiting membrane of the endosome and mostly are delivered to lysosomes enabling degradation of membrane proteins, such as stimulated growth factor receptors, lysosomal enzymes and lipids. In conjunction with the ESCRT machinery also appears to function in topologically equivalent membrane fission events, such as the terminal stages of cytokinesis By similarity.By similarity

    Catalytic activityi

    ATP + H2O = ADP + phosphate.

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi174 – 1818ATPSequence Analysis

    GO - Molecular functioni

    1. ATPase activity Source: MGI
    2. ATP binding Source: UniProtKB-KW
    3. protein binding Source: UniProtKB

    GO - Biological processi

    1. cell cycle Source: UniProtKB-KW
    2. cell division Source: UniProtKB-KW
    3. cholesterol transport Source: MGI
    4. endosomal transport Source: MGI
    5. endosome organization Source: MGI
    6. endosome to lysosome transport via multivesicular body sorting pathway Source: Ensembl
    7. intracellular cholesterol transport Source: Ensembl
    8. potassium ion transport Source: MGI
    9. protein transport Source: UniProtKB-KW
    10. response to lipid Source: Ensembl

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Cell cycle, Cell division, Protein transport, Transport

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding

    Enzyme and pathway databases

    ReactomeiREACT_198518. Endosomal Sorting Complex Required For Transport (ESCRT).

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Vacuolar protein sorting-associated protein 4B (EC:3.6.4.6)
    Alternative name(s):
    Suppressor of K(+) transport growth defect 1
    Short name:
    Protein SKD1
    Gene namesi
    Name:Vps4b
    Synonyms:Skd1
    OrganismiMus musculus (Mouse)
    Taxonomic identifieri10090 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
    ProteomesiUP000000589: Chromosome 1

    Organism-specific databases

    MGIiMGI:1100499. Vps4b.

    Subcellular locationi

    Prevacuolar compartment membrane; Peripheral membrane protein. Late endosome membrane By similarity; Peripheral membrane protein By similarity
    Note: Membrane-associated in the prevacuolar endosomal compartment.

    GO - Cellular componenti

    1. cytosol Source: MGI
    2. early endosome Source: Ensembl
    3. endosome Source: MGI
    4. late endosome membrane Source: UniProtKB-SubCell
    5. lysosome Source: Ensembl
    6. nucleus Source: Ensembl
    7. vacuolar membrane Source: Ensembl

    Keywords - Cellular componenti

    Endosome, Membrane

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi180 – 1801K → Q: Defective in ATP-binding. Causes membrane association. Induces vacuolation of endosomal compartments and impairs cholesterol sorting. 1 Publication
    Mutagenesisi235 – 2351E → Q: Defective in ATP-hydrolysis. Causes membrane-association. Induces vacuolation of endosomal compartments and impairs cholesterol and protein sorting. Increased perinuclear localization. 4 Publications
    Mutagenesisi290 – 2912RR → AA: Abolishes ATP-dependent oligomerization.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 444444Vacuolar protein sorting-associated protein 4BPRO_0000084768Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei102 – 1021Phosphoserine1 Publication
    Modified residuei108 – 1081PhosphoserineBy similarity

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiP46467.
    PaxDbiP46467.
    PRIDEiP46467.

    PTM databases

    PhosphoSiteiP46467.

    Expressioni

    Tissue specificityi

    High level expression seen in the kidney. It is also expressed in the heart, brain, spleen, lung, liver, skeletal muscle, and testis.2 Publications

    Gene expression databases

    ArrayExpressiP46467.
    BgeeiP46467.
    CleanExiMM_VPS4B.
    GenevestigatoriP46467.

    Interactioni

    Subunit structurei

    Proposed to be monomeric or homodimeric in nucleotide-free form and to oligomerize upon binding to ATP to form two stacked hexameric or heptameric rings with a central pore through which ESCRT-III substrates are translocated in an ATP-dependent manner. In vitro, associates on the inside of a helical tubular structure formed by a CHMP2A-CHMP3 polymer. Interacts with CHMP1A, CHMP1B, CHMP2A, CHMP4B and CHMP6. Interacts with VPS4A; the interaction suggests a heteromeric assembly with VPS4A. Interacts with VTA1 By similarity.By similarity

    Protein-protein interaction databases

    BioGridi203266. 2 interactions.
    IntActiP46467. 2 interactions.
    MINTiMINT-4134751.

    Structurei

    Secondary structure

    1
    444
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi133 – 1353
    Helixi140 – 15011
    Helixi152 – 1554
    Turni157 – 1604
    Helixi162 – 1643
    Beta strandi168 – 1736
    Helixi180 – 19011
    Beta strandi193 – 1997
    Turni203 – 2053
    Helixi216 – 22510
    Beta strandi228 – 2347
    Turni236 – 2394
    Helixi249 – 2513
    Helixi252 – 2598
    Turni260 – 2634
    Beta strandi265 – 2673
    Beta strandi273 – 2797
    Helixi281 – 2833
    Helixi286 – 2894
    Beta strandi294 – 2974
    Helixi303 – 31412
    Beta strandi317 – 3193
    Helixi323 – 33210
    Turni333 – 3353
    Helixi338 – 34912
    Helixi351 – 3588
    Beta strandi360 – 3656
    Beta strandi373 – 3764
    Beta strandi380 – 3845
    Beta strandi386 – 3883
    Beta strandi391 – 3933
    Turni396 – 3983
    Helixi401 – 4033
    Helixi411 – 4199
    Helixi427 – 43610
    Turni441 – 4433

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2ZAMX-ray3.50A1-444[»]
    2ZANX-ray3.00A1-444[»]
    2ZAOX-ray3.20A1-444[»]
    ProteinModelPortaliP46467.
    SMRiP46467. Positions 7-108, 123-444.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP46467.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini4 – 8279MITAdd
    BLAST

    Coiled coil

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Coiled coili19 – 8264Sequence AnalysisAdd
    BLAST

    Domaini

    The MIT domain serves as an adapter for ESCRT-III proteins. It forms an asymmetric three-helix bundle that binds amphipathic MIM (MIT interacting motif) helices along the groove between MIT helices 2 and 3 present in a subset of ESCRT-III proteins thus establishing the canonical MIM-MIT interaction. In an extended conformation along the groove between helices 1 and 3, also binds to a type-2 MIT interacting motif (MIM2).

    Sequence similaritiesi

    Belongs to the AAA ATPase family.Curated
    Contains 1 MIT domain.Curated

    Keywords - Domaini

    Coiled coil

    Phylogenomic databases

    eggNOGiCOG0464.
    HOGENOMiHOG000225146.
    HOVERGENiHBG057074.
    InParanoidiP46467.
    KOiK12196.
    OMAiRRTEMYS.
    OrthoDBiEOG74BJS2.
    PhylomeDBiP46467.
    TreeFamiTF105012.

    Family and domain databases

    Gene3Di1.20.58.280. 1 hit.
    3.40.50.300. 1 hit.
    InterProiIPR003593. AAA+_ATPase.
    IPR003959. ATPase_AAA_core.
    IPR003960. ATPase_AAA_CS.
    IPR007330. MIT.
    IPR027417. P-loop_NTPase.
    IPR015415. Vps4_C.
    [Graphical view]
    PfamiPF00004. AAA. 1 hit.
    PF04212. MIT. 1 hit.
    PF09336. Vps4_C. 1 hit.
    [Graphical view]
    SMARTiSM00382. AAA. 1 hit.
    SM00745. MIT. 1 hit.
    [Graphical view]
    SUPFAMiSSF116846. SSF116846. 1 hit.
    SSF52540. SSF52540. 1 hit.
    PROSITEiPS00674. AAA. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P46467-1 [UniParc]FASTAAdd to Basket

    « Hide

    MASTNTNLQK AIDLASKAAQ EDKAGNYEEA LQLYQHAVQY FLHVVKYEAQ    50
    GDKAKQSIRA KCTEYLDRAE KLKEYLKKKE KKPQKPVKEE QSGPVDEKGN 100
    DSDGEAESDD PEKKKLQNQL QGAIVIERPN VKWSDVAGLE GAKEALKEAV 150
    ILPIKFPHLF TGKRTPWRGI LLFGPPGTGK SYLAKAVATE ANNSTFFSIS 200
    SSDLVSKWLG ESEKLVKNLF QLARENKPSI IFIDEIDSLC GSRSENESEA 250
    ARRIKTEFLV QMQGVGVDND GILVLGATNI PWVLDSAIRR RFEKRIYIPL 300
    PEAHARAAMF RLHLGSTQNS LTEADFQELG RKTDGYSGAD ISIIVRDALM 350
    QPVRKVQSAT HFKKVRGPSR ADPNCIVNDL LTPCSPGDPG AIEMTWMDVP 400
    GDKLLEPVVS MWDMLRSLSS TKPTVNEQDL LKLKKFTEDF GQEG 444
    Length:444
    Mass (Da):49,419
    Last modified:January 16, 2004 - v2
    Checksum:iAA95B607DF8706A1
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti90 – 901E → A in AAA50497. (PubMed:8082782)Curated
    Sequence conflicti339 – 3391A → V in AAA50497. (PubMed:8082782)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U10119 mRNA. Translation: AAA50497.1.
    AF134119 Genomic DNA. Translation: AAD47570.1.
    BC003799 mRNA. Translation: AAH03799.1.
    CCDSiCCDS15211.1.
    PIRiS48696.
    RefSeqiNP_033216.2. NM_009190.2.
    UniGeneiMm.18705.
    Mm.483448.

    Genome annotation databases

    EnsembliENSMUST00000094646; ENSMUSP00000092230; ENSMUSG00000009907.
    ENSMUST00000112736; ENSMUSP00000108356; ENSMUSG00000009907.
    GeneIDi20479.
    KEGGimmu:20479.
    UCSCiuc007cgz.2. mouse.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U10119 mRNA. Translation: AAA50497.1 .
    AF134119 Genomic DNA. Translation: AAD47570.1 .
    BC003799 mRNA. Translation: AAH03799.1 .
    CCDSi CCDS15211.1.
    PIRi S48696.
    RefSeqi NP_033216.2. NM_009190.2.
    UniGenei Mm.18705.
    Mm.483448.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2ZAM X-ray 3.50 A 1-444 [» ]
    2ZAN X-ray 3.00 A 1-444 [» ]
    2ZAO X-ray 3.20 A 1-444 [» ]
    ProteinModelPortali P46467.
    SMRi P46467. Positions 7-108, 123-444.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 203266. 2 interactions.
    IntActi P46467. 2 interactions.
    MINTi MINT-4134751.

    PTM databases

    PhosphoSitei P46467.

    Proteomic databases

    MaxQBi P46467.
    PaxDbi P46467.
    PRIDEi P46467.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSMUST00000094646 ; ENSMUSP00000092230 ; ENSMUSG00000009907 .
    ENSMUST00000112736 ; ENSMUSP00000108356 ; ENSMUSG00000009907 .
    GeneIDi 20479.
    KEGGi mmu:20479.
    UCSCi uc007cgz.2. mouse.

    Organism-specific databases

    CTDi 9525.
    MGIi MGI:1100499. Vps4b.

    Phylogenomic databases

    eggNOGi COG0464.
    HOGENOMi HOG000225146.
    HOVERGENi HBG057074.
    InParanoidi P46467.
    KOi K12196.
    OMAi RRTEMYS.
    OrthoDBi EOG74BJS2.
    PhylomeDBi P46467.
    TreeFami TF105012.

    Enzyme and pathway databases

    Reactomei REACT_198518. Endosomal Sorting Complex Required For Transport (ESCRT).

    Miscellaneous databases

    EvolutionaryTracei P46467.
    NextBioi 298605.
    PROi P46467.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi P46467.
    Bgeei P46467.
    CleanExi MM_VPS4B.
    Genevestigatori P46467.

    Family and domain databases

    Gene3Di 1.20.58.280. 1 hit.
    3.40.50.300. 1 hit.
    InterProi IPR003593. AAA+_ATPase.
    IPR003959. ATPase_AAA_core.
    IPR003960. ATPase_AAA_CS.
    IPR007330. MIT.
    IPR027417. P-loop_NTPase.
    IPR015415. Vps4_C.
    [Graphical view ]
    Pfami PF00004. AAA. 1 hit.
    PF04212. MIT. 1 hit.
    PF09336. Vps4_C. 1 hit.
    [Graphical view ]
    SMARTi SM00382. AAA. 1 hit.
    SM00745. MIT. 1 hit.
    [Graphical view ]
    SUPFAMi SSF116846. SSF116846. 1 hit.
    SSF52540. SSF52540. 1 hit.
    PROSITEi PS00674. AAA. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Identification of a novel mammalian member of the NSF/CDC48p/Pas1p/TBP-1 family through heterologous expression in yeast."
      Perier F., Coulter K.L., Liang H., Radeke C.M., Gaber R.F., Vandenberg C.A.
      FEBS Lett. 351:286-290(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY.
      Strain: BALB/c.
    2. "Cloning, characterisation, and functional expression of the Mus musculus SKD1 gene in yeast demonstrates that the mouse SKD1 and the yeast VPS4 genes are orthologues and involved in intracellular protein trafficking."
      Scheuring S., Bodor O., Rohricht R.A., Muller S., Beyer A., Kohrer K.
      Gene 234:149-159(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION.
    3. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
      The MGC Project Team
      Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Tissue: Mammary tumor.
    4. "Comparative sequence and expression analyses of four mammalian VPS4 genes."
      Beyer A., Scheuring S., Mueller S., Mincheva A., Lichter P., Koehrer K.
      Gene 305:47-59(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: PARTIAL NUCLEOTIDE SEQUENCE [GENOMIC DNA], SUBCELLULAR LOCATION, TISSUE SPECIFICITY, INTERACTION WITH VPS4A, MUTAGENESIS OF GLU-235.
    5. "ATPase-defective mammalian VPS4 localizes to aberrant endosomes and impairs cholesterol trafficking."
      Bishop N., Woodman P.
      Mol. Biol. Cell 11:227-239(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBCELLULAR LOCATION, MUTAGENESIS OF LYS-180 AND GLU-235.
    6. "The mouse SKD1, a homologue of yeast Vps4p, is required for normal endosomal trafficking and morphology in mammalian cells."
      Yoshimori T., Yamagata F., Yamamoto A., Mizushima N., Kabeya Y., Nara A., Miwako I., Ohashi M., Ohsumi M., Ohsumi Y.
      Mol. Biol. Cell 11:747-763(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, MUTAGENESIS OF GLU-235.
    7. "Mammalian class E Vps proteins, SBP1 and mVps2/CHMP2A, interact with and regulate the function of an AAA-ATPase SKD1/Vps4B."
      Fujita H., Umezuki Y., Imamura K., Ishikawa D., Uchimura S., Nara A., Yoshimori T., Hayashizaki Y., Kawai J., Ishidoh K., Tanaka Y., Himeno M.
      J. Cell Sci. 117:2997-3009(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH CHMP2A.
    8. "The phagosomal proteome in interferon-gamma-activated macrophages."
      Trost M., English L., Lemieux S., Courcelles M., Desjardins M., Thibault P.
      Immunity 30:143-154(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-102, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    9. "Nucleotide-dependent conformational changes and assembly of the AAA ATPase SKD1/VPS4B."
      Inoue M., Kamikubo H., Kataoka M., Kato R., Yoshimori T., Wakatsuki S., Kawasaki M.
      Traffic 9:2180-2189(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 123-444, SUBUNIT, MUTAGENESIS OF GLU-235 AND 290-ARG-ARG-291.

    Entry informationi

    Entry nameiVPS4B_MOUSE
    AccessioniPrimary (citable) accession number: P46467
    Secondary accession number(s): Q91W22, Q9R1C9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1995
    Last sequence update: January 16, 2004
    Last modified: October 1, 2014
    This is version 131 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. MGD cross-references
      Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3