SubmitCancel

Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.

P46467

- VPS4B_MOUSE

UniProt

P46467 - VPS4B_MOUSE

(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

Protein
Vacuolar protein sorting-associated protein 4B
Gene
Vps4b, Skd1
Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

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.2 Publications

Catalytic activityi

ATP + H2O = ADP + phosphate.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi174 – 1818ATP Reviewed prediction

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. ATPase activity Source: MGI
  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
Complete GO annotation...

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; Peripheral membrane protein By similarity
Note: Membrane-associated in the prevacuolar endosomal compartment.2 Publications

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
Complete GO annotation...

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 4B
PRO_0000084768Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei102 – 1021Phosphoserine1 Publication
Modified residuei108 – 1081Phosphoserine By 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.3 Publications

Protein-protein interaction databases

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

Structurei

Secondary structure

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.

Miscellaneous databases

EvolutionaryTraceiP46467.

Family & Domainsi

Domains and Repeats

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

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili19 – 8264 Reviewed prediction
Add
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.
Contains 1 MIT domain.

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

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti90 – 901E → A in AAA50497. 1 Publication
Sequence conflicti339 – 3391A → V in AAA50497. 1 Publication

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

« Hide 'large scale' publications
  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: September 3, 2014
This is version 130 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

Similar proteinsi