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WD repeat and FYVE domain-containing protein 3 (Autophagy-linked FYVE protein) (Alfy)

 WDFY3_HUMAN             Reviewed;        3526 AA.
Q8IZQ1; Q4W5K5; Q6P0Q5; Q8N1T2; Q8NAV6; Q96BS7; Q96D33; Q96N85;
Q9Y2J7;
27-JUN-2006, integrated into UniProtKB/Swiss-Prot.
27-JUN-2006, sequence version 2.
22-NOV-2017, entry version 144.
RecName: Full=WD repeat and FYVE domain-containing protein 3;
AltName: Full=Autophagy-linked FYVE protein;
Short=Alfy;
Name=WDFY3; Synonyms=KIAA0993;
Homo sapiens (Human).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
NCBI_TaxID=9606;
[1]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), SUBCELLULAR LOCATION, AND
BINDING TO PTDINS3P.
TISSUE=Brain;
PubMed=15292400; DOI=10.1242/jcs.01287;
Simonsen A., Birkeland H.C.G., Gillooly D.J., Mizushima N., Kuma A.,
Yoshimori T., Slagsvold T., Brech A., Stenmark H.;
"Alfy, a novel FYVE-domain-containing protein associated with protein
granules and autophagic membranes.";
J. Cell Sci. 117:4239-4251(2004).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
PubMed=15815621; DOI=10.1038/nature03466;
Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H.,
Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M.,
Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E.,
Kremitzki C., Oddy L., Du H., Sun H., Bradshaw-Cordum H., Ali J.,
Carter J., Cordes M., Harris A., Isak A., van Brunt A., Nguyen C.,
Du F., Courtney L., Kalicki J., Ozersky P., Abbott S., Armstrong J.,
Belter E.A., Caruso L., Cedroni M., Cotton M., Davidson T., Desai A.,
Elliott G., Erb T., Fronick C., Gaige T., Haakenson W., Haglund K.,
Holmes A., Harkins R., Kim K., Kruchowski S.S., Strong C.M.,
Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K.,
McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C.,
Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N.,
Swearengen-Shahid S., Snider J., Strong J.T., Thompson J., Yoakum M.,
Leonard S., Pearman C., Trani L., Radionenko M., Waligorski J.E.,
Wang C., Rock S.M., Tin-Wollam A.-M., Maupin R., Latreille P.,
Wendl M.C., Yang S.-P., Pohl C., Wallis J.W., Spieth J., Bieri T.A.,
Berkowicz N., Nelson J.O., Osborne J., Ding L., Meyer R., Sabo A.,
Shotland Y., Sinha P., Wohldmann P.E., Cook L.L., Hickenbotham M.T.,
Eldred J., Williams D., Jones T.A., She X., Ciccarelli F.D.,
Izaurralde E., Taylor J., Schmutz J., Myers R.M., Cox D.R., Huang X.,
McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C.,
Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S.,
Miller W., Eichler E.E., Bork P., Suyama M., Torrents D.,
Waterston R.H., Wilson R.K.;
"Generation and annotation of the DNA sequences of human chromosomes 2
and 4.";
Nature 434:724-731(2005).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1971-3526 (ISOFORM 1).
TISSUE=Brain;
PubMed=10231032; DOI=10.1093/dnares/6.1.63;
Nagase T., Ishikawa K., Suyama M., Kikuno R., Hirosawa M.,
Miyajima N., Tanaka A., Kotani H., Nomura N., Ohara O.;
"Prediction of the coding sequences of unidentified human genes. XIII.
The complete sequences of 100 new cDNA clones from brain which code
for large proteins in vitro.";
DNA Res. 6:63-70(1999).
[4]
SEQUENCE REVISION.
PubMed=12168954; DOI=10.1093/dnares/9.3.99;
Nakajima D., Okazaki N., Yamakawa H., Kikuno R., Ohara O., Nagase T.;
"Construction of expression-ready cDNA clones for KIAA genes: manual
curation of 330 KIAA cDNA clones.";
DNA Res. 9:99-106(2002).
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 2381-3036 (ISOFORM 2), AND
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 2650-3526 (ISOFORM 1).
TISSUE=Corpus callosum, and Kidney;
PubMed=14702039; DOI=10.1038/ng1285;
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A.,
Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M.,
Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y.,
Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M.,
Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K.,
Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S.,
Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J.,
Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y.,
Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N.,
Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S.,
Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y.,
Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T.,
Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y.,
Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S.,
Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T.,
Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M.,
Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T.,
Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K.,
Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R.,
Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.;
"Complete sequencing and characterization of 21,243 full-length human
cDNAs.";
Nat. Genet. 36:40-45(2004).
[6]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 2749-3526 (ISOFORM 1).
TISSUE=Colon, Duodenum, and Ovary;
PubMed=15489334; DOI=10.1101/gr.2596504;
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA
project: the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[7]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Cervix carcinoma;
PubMed=18669648; DOI=10.1073/pnas.0805139105;
Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E.,
Elledge S.J., Gygi S.P.;
"A quantitative atlas of mitotic phosphorylation.";
Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008).
[8]
FUNCTION, INTERACTION WITH SQSTM1, AND SUBCELLULAR LOCATION.
PubMed=20168092; DOI=10.4161/auto.6.3.11226;
Clausen T.H., Lamark T., Isakson P., Finley K., Larsen K.B., Brech A.,
Overvatn A., Stenmark H., Bjorkoy G., Simonsen A., Johansen T.;
"p62/SQSTM1 and ALFY interact to facilitate the formation of p62
bodies/ALIS and their degradation by autophagy.";
Autophagy 6:330-344(2010).
[9]
SUBCELLULAR LOCATION, INTERACTION WITH SQSTM1, AND TISSUE SPECIFICITY.
PubMed=20971078; DOI=10.1016/j.bbrc.2010.10.076;
Hocking L.J., Mellis D.J., McCabe P.S., Helfrich M.H., Rogers M.J.;
"Functional interaction between sequestosome-1/p62 and autophagy-
linked FYVE-containing protein WDFY3 in human osteoclasts.";
Biochem. Biophys. Res. Commun. 402:543-548(2010).
[10]
FUNCTION, INTERACTION WITH ATG5, ASSOCIATION WITH THE
ATG12-ATG5-ATG16L COMPLEX, AND SUBCELLULAR LOCATION.
PubMed=20417604; DOI=10.1016/j.molcel.2010.04.007;
Filimonenko M., Isakson P., Finley K.D., Anderson M., Jeong H.,
Melia T.J., Bartlett B.J., Myers K.M., Birkeland H.C., Lamark T.,
Krainc D., Brech A., Stenmark H., Simonsen A., Yamamoto A.;
"The selective macroautophagic degradation of aggregated proteins
requires the PI3P-binding protein Alfy.";
Mol. Cell 38:265-279(2010).
[11]
FUNCTION.
PubMed=24128730; DOI=10.4161/auto.26085;
Isakson P., Lystad A.H., Breen K., Koster G., Stenmark H.,
Simonsen A.;
"TRAF6 mediates ubiquitination of KIF23/MKLP1 and is required for
midbody ring degradation by selective autophagy.";
Autophagy 9:1955-1964(2013).
[12]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-2278 AND SER-3339, AND
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Cervix carcinoma, and Erythroleukemia;
PubMed=23186163; DOI=10.1021/pr300630k;
Zhou H., Di Palma S., Preisinger C., Peng M., Polat A.N., Heck A.J.,
Mohammed S.;
"Toward a comprehensive characterization of a human cancer cell
phosphoproteome.";
J. Proteome Res. 12:260-271(2013).
[13]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Liver;
PubMed=24275569; DOI=10.1016/j.jprot.2013.11.014;
Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D.,
Wang L., Ye M., Zou H.;
"An enzyme assisted RP-RPLC approach for in-depth analysis of human
liver phosphoproteome.";
J. Proteomics 96:253-262(2014).
[14]
X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) OF 3341-3354 IN COMPLEX WITH
GABARAP, INTERACTION WITH MAP1LC3C; GABARAPL1 AND GABARAPL2, LIR
MOTIF, AND MUTAGENESIS OF LYS-3343; ASP-3344; PHE-3346; ILE-3347;
PHE-3348; VAL-3349 AND TYR-3351.
PubMed=24668264; DOI=10.1002/embr.201338003;
Lystad A.H., Ichimura Y., Takagi K., Yang Y., Pankiv S., Kanegae Y.,
Kageyama S., Suzuki M., Saito I., Mizushima T., Komatsu M.,
Simonsen A.;
"Structural determinants in GABARAP required for the selective binding
and recruitment of ALFY to LC3B-positive structures.";
EMBO Rep. 15:557-565(2014).
[15]
VARIANT MCPH18 TRP-2637, CHARACTERIZATION OF VARIANT MCPH18 TRP-2637,
AND FUNCTION.
PubMed=27008544; DOI=10.1371/journal.pgen.1005919;
Kadir R., Harel T., Markus B., Perez Y., Bakhrat A., Cohen I.,
Volodarsky M., Feintsein-Linial M., Chervinski E., Zlotogora J.,
Sivan S., Birnbaum R.Y., Abdu U., Shalev S., Birk O.S.;
"ALFY-controlled DVL3 autophagy regulates Wnt signaling, determining
human brain size.";
PLoS Genet. 12:E1005919-E1005919(2016).
-!- FUNCTION: Required for selective macroautophagy (aggrephagy). Acts
as an adapter protein by linking specific proteins destined for
degradation to the core autophagic machinery members, such as the
ATG5-ATG12-ATG16L E3-like ligase, SQSTM1 and LC3
(PubMed:20417604). Along with p62/SQSTM1, involved in the
formation and autophagic degradation of cytoplasmic ubiquitin-
containing inclusions (p62 bodies, ALIS/aggresome-like induced
structures). Along with SQSTM1, required to recruit ubiquitinated
proteins to PML bodies in the nucleus (PubMed:20168092). Important
for normal brain development. Essential for the formation of
axonal tracts throughout the brain and spinal cord, including the
formation of the major forebrain commissures. Involved in the
ability of neural cells to respond to guidance cues. Required for
cortical neurons to respond to the trophic effects of netrin-
1/NTN1 (By similarity). Regulates Wnt signaling through the
removal of DVL3 aggregates, likely in an autophagy-dependent
manner. This process may be important for the determination of
brain size during embryonic development (PubMed:27008544). May
regulate osteoclastogenesis by acting on the TNFSF11/RANKL - TRAF6
pathway (By similarity). After cytokinetic abscission, involved in
midbody remnant degradation (PubMed:24128730). In vitro strongly
binds to phosphatidylinositol 3-phosphate (PtdIns3P)
(PubMed:15292400). {ECO:0000250|UniProtKB:Q6VNB8,
ECO:0000269|PubMed:15292400, ECO:0000269|PubMed:20168092,
ECO:0000269|PubMed:20417604, ECO:0000269|PubMed:24128730,
ECO:0000269|PubMed:27008544}.
-!- SUBUNIT: Directly interacts with ATG5 and associates with the
ATG12-ATG5-ATG16L complex (PubMed:20417604). Interacts with
p62/SQSTM1; this interaction is required to recruit WDFY3 to
cytoplasmic bodies and to PML bodies (PubMed:20168092,
PubMed:20971078). Directly interacts with GABARAP, GABARAPL1 and
GABARAPL2; the interaction with GABARAP is required for WDFY3
recruitment to MAP1LC3B-positive p62/SQSTM1 bodies. Weakly
interacts with MAP1LC3C; this interaction is direct. Does not
interact with MAP1LC3A, nor MAP1LC3B (PubMed:24668264). Interacts
with TRAF6 (By similarity). {ECO:0000250|UniProtKB:Q6VNB8,
ECO:0000269|PubMed:20168092, ECO:0000269|PubMed:20417604,
ECO:0000269|PubMed:20971078, ECO:0000269|PubMed:24668264}.
-!- INTERACTION:
Q9H1Y0:ATG5; NbExp=7; IntAct=EBI-1569256, EBI-1047414;
Q8TAP6:CEP76; NbExp=3; IntAct=EBI-10264625, EBI-742887;
Q6IAW1:GABARAP; NbExp=17; IntAct=EBI-1569256, EBI-10106927;
Q9H0R8:GABARAPL1; NbExp=3; IntAct=EBI-1569256, EBI-746969;
P60520:GABARAPL2; NbExp=3; IntAct=EBI-1569256, EBI-720116;
P42858:HTT; NbExp=10; IntAct=EBI-1569256, EBI-466029;
Q9GZQ8:MAP1LC3B; NbExp=6; IntAct=EBI-1569256, EBI-373144;
Q9BXW4:MAP1LC3C; NbExp=7; IntAct=EBI-1569256, EBI-2603996;
Q92569:PIK3R3; NbExp=2; IntAct=EBI-1569256, EBI-79893;
P14079:tax (xeno); NbExp=3; IntAct=EBI-1569256, EBI-9675698;
Q9HCM9:TRIM39; NbExp=3; IntAct=EBI-10264625, EBI-739510;
Q8NCP5:ZBTB44; NbExp=3; IntAct=EBI-10264625, EBI-5658292;
-!- SUBCELLULAR LOCATION: Nucleus membrane
{ECO:0000269|PubMed:15292400, ECO:0000269|PubMed:20168092,
ECO:0000269|PubMed:20417604, ECO:0000269|PubMed:20971078}.
Cytoplasm, cytosol {ECO:0000269|PubMed:15292400,
ECO:0000269|PubMed:20168092, ECO:0000269|PubMed:20417604,
ECO:0000269|PubMed:20971078}. Nucleus, PML body
{ECO:0000269|PubMed:20168092}. Membrane; Peripheral membrane
protein {ECO:0000269|PubMed:15292400}; Cytoplasmic side
{ECO:0000305}. Perikaryon {ECO:0000250|UniProtKB:Q6VNB8}. Cell
projection, axon {ECO:0000250|UniProtKB:Q6VNB8}.
Note=Relocalization from the nucleus to the cytosol is stimulated
by cellular stress, such as starvation or proteasomal inhibition.
In the cytosol of starved cells, colocalizes with autophagic
structures (PubMed:15292400, PubMed:20168092, PubMed:20971078,
PubMed:20417604). This redistribution is dependent on p62/SQSTM1
(PubMed:20168092). When nuclear export is blocked by treatment
with leptomycin B, accumulates in nuclear bodies, that completely
or partially colocalize with promyelocytic leukemia (PML) bodies
(PubMed:20168092). Localizes throughout neurons, including within
axons. In neurons, enriched in the light membrane fraction along
with the synaptosomal membrane protein synaptophysin and the
membrane-bound form of LC3/MAP1LC3A/MAP1LC3B, called LC3-II, a
classic marker for autophagic vesicles (By similarity).
{ECO:0000250|UniProtKB:Q6VNB8, ECO:0000269|PubMed:15292400,
ECO:0000269|PubMed:20168092, ECO:0000269|PubMed:20417604,
ECO:0000269|PubMed:20971078}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=2;
Name=1;
IsoId=Q8IZQ1-1; Sequence=Displayed;
Name=2;
IsoId=Q8IZQ1-2; Sequence=VSP_019475;
-!- TISSUE SPECIFICITY: Expressed in osteoclast and their mononuclear
precursors (at protein level). {ECO:0000269|PubMed:20971078}.
-!- DOMAIN: The LIR (LC3-interacting region) motif mediates the
interaction with MAP1LC3C and other ATG8 family members.
{ECO:0000269|PubMed:24668264}.
-!- DOMAIN: The FYVE domain mediates binding to phosphatidylinositol
3-phosphate (PtdIns3P). {ECO:0000269|PubMed:15292400}.
-!- DISEASE: Microcephaly 18, primary, autosomal dominant (MCPH18)
[MIM:617520]: A form of microcephaly, a disease defined as a head
circumference more than 3 standard deviations below the age, sex
and ethnically matched mean. Brain weight is markedly reduced and
the cerebral cortex is disproportionately small. MCPH18 affected
individuals manifest microcephaly with mild to moderate
intellectual disability. {ECO:0000269|PubMed:27008544}. Note=The
disease is caused by mutations affecting the gene represented in
this entry.
-!- SEQUENCE CAUTION:
Sequence=AAH13377.1; Type=Miscellaneous discrepancy; Evidence={ECO:0000305};
Sequence=BAB71020.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing.; Evidence={ECO:0000305};
Sequence=BAC04455.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};
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EMBL; AF538685; AAN15137.1; -; mRNA.
EMBL; AC095046; AAY40903.1; -; Genomic_DNA.
EMBL; AC104082; -; NOT_ANNOTATED_CDS; Genomic_DNA.
EMBL; AB023210; BAA76837.2; -; mRNA.
EMBL; AK055806; BAB71020.1; ALT_SEQ; mRNA.
EMBL; AK094910; BAC04455.1; ALT_INIT; mRNA.
EMBL; BC013377; AAH13377.1; ALT_SEQ; mRNA.
EMBL; BC015214; AAH15214.2; -; mRNA.
EMBL; BC065502; AAH65502.1; -; mRNA.
EMBL; BC119633; AAI19634.1; -; mRNA.
CCDS; CCDS3609.1; -. [Q8IZQ1-1]
RefSeq; NP_055806.2; NM_014991.4. [Q8IZQ1-1]
RefSeq; XP_011530065.1; XM_011531763.2. [Q8IZQ1-1]
RefSeq; XP_011530067.1; XM_011531765.2. [Q8IZQ1-2]
UniGene; Hs.480116; -.
UniGene; Hs.726339; -.
PDB; 3WIM; X-ray; 2.60 A; B=3341-3354.
PDBsum; 3WIM; -.
ProteinModelPortal; Q8IZQ1; -.
SMR; Q8IZQ1; -.
BioGrid; 116647; 65.
IntAct; Q8IZQ1; 43.
MINT; MINT-4829131; -.
STRING; 9606.ENSP00000295888; -.
iPTMnet; Q8IZQ1; -.
PhosphoSitePlus; Q8IZQ1; -.
BioMuta; WDFY3; -.
DMDM; 109896161; -.
EPD; Q8IZQ1; -.
MaxQB; Q8IZQ1; -.
PaxDb; Q8IZQ1; -.
PeptideAtlas; Q8IZQ1; -.
PRIDE; Q8IZQ1; -.
DNASU; 23001; -.
Ensembl; ENST00000295888; ENSP00000295888; ENSG00000163625. [Q8IZQ1-1]
GeneID; 23001; -.
KEGG; hsa:23001; -.
UCSC; uc003hpd.4; human. [Q8IZQ1-1]
CTD; 23001; -.
DisGeNET; 23001; -.
EuPathDB; HostDB:ENSG00000163625.15; -.
GeneCards; WDFY3; -.
H-InvDB; HIX0004348; -.
HGNC; HGNC:20751; WDFY3.
HPA; HPA042734; -.
HPA; HPA048572; -.
MIM; 617485; gene.
MIM; 617520; phenotype.
neXtProt; NX_Q8IZQ1; -.
OpenTargets; ENSG00000163625; -.
PharmGKB; PA134903706; -.
eggNOG; KOG1786; Eukaryota.
eggNOG; KOG1788; Eukaryota.
eggNOG; ENOG410XNQC; LUCA.
GeneTree; ENSGT00760000119083; -.
HOVERGEN; HBG094156; -.
InParanoid; Q8IZQ1; -.
OMA; TVDSGHE; -.
OrthoDB; EOG091G002Q; -.
PhylomeDB; Q8IZQ1; -.
TreeFam; TF313658; -.
SignaLink; Q8IZQ1; -.
ChiTaRS; WDFY3; human.
GeneWiki; WDFY3; -.
GenomeRNAi; 23001; -.
PRO; PR:Q8IZQ1; -.
Proteomes; UP000005640; Chromosome 4.
Bgee; ENSG00000163625; -.
CleanEx; HS_WDFY3; -.
ExpressionAtlas; Q8IZQ1; baseline and differential.
Genevisible; Q8IZQ1; HS.
GO; GO:0005776; C:autophagosome; IMP:UniProtKB.
GO; GO:0030424; C:axon; IEA:UniProtKB-SubCell.
GO; GO:0005737; C:cytoplasm; IDA:UniProtKB.
GO; GO:0005829; C:cytosol; IDA:HPA.
GO; GO:0097635; C:extrinsic component of autophagosome membrane; IEA:Ensembl.
GO; GO:0019898; C:extrinsic component of membrane; IDA:MGI.
GO; GO:0016234; C:inclusion body; IDA:UniProtKB.
GO; GO:0005635; C:nuclear envelope; IDA:UniProtKB.
GO; GO:0031965; C:nuclear membrane; IEA:UniProtKB-SubCell.
GO; GO:0005730; C:nucleolus; IDA:HPA.
GO; GO:0005634; C:nucleus; IDA:HPA.
GO; GO:0043204; C:perikaryon; IEA:UniProtKB-SubCell.
GO; GO:0005886; C:plasma membrane; IDA:HPA.
GO; GO:0016605; C:PML body; IDA:UniProtKB.
GO; GO:0005545; F:1-phosphatidylinositol binding; IDA:MGI.
GO; GO:0003831; F:beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity; IEA:Ensembl.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0035973; P:aggrephagy; IMP:UniProtKB.
GO; GO:0007275; P:multicellular organism development; IEA:UniProtKB-KW.
CDD; cd06071; Beach; 1.
CDD; cd01201; PH_BEACH; 1.
Gene3D; 1.10.1540.10; -; 1.
Gene3D; 1.25.10.10; -; 3.
Gene3D; 2.120.10.30; -; 1.
Gene3D; 3.30.40.10; -; 1.
InterPro; IPR011042; 6-blade_b-propeller_TolB-like.
InterPro; IPR011989; ARM-like.
InterPro; IPR016024; ARM-type_fold.
InterPro; IPR000409; BEACH_dom.
InterPro; IPR036372; BEACH_dom_sf.
InterPro; IPR013320; ConA-like_dom_sf.
InterPro; IPR031570; DUF4704.
InterPro; IPR023362; PH-BEACH_dom.
InterPro; IPR011993; PH-like_dom_sf.
InterPro; IPR001680; WD40_repeat.
InterPro; IPR019775; WD40_repeat_CS.
InterPro; IPR017986; WD40_repeat_dom.
InterPro; IPR036322; WD40_repeat_dom_sf.
InterPro; IPR000306; Znf_FYVE.
InterPro; IPR017455; Znf_FYVE-rel.
InterPro; IPR011011; Znf_FYVE_PHD.
InterPro; IPR013083; Znf_RING/FYVE/PHD.
Pfam; PF02138; Beach; 1.
Pfam; PF15787; DUF4704; 1.
Pfam; PF01363; FYVE; 1.
Pfam; PF14844; PH_BEACH; 1.
SMART; SM01026; Beach; 1.
SMART; SM00064; FYVE; 1.
SMART; SM00320; WD40; 5.
SUPFAM; SSF48371; SSF48371; 3.
SUPFAM; SSF49899; SSF49899; 1.
SUPFAM; SSF50729; SSF50729; 1.
SUPFAM; SSF50978; SSF50978; 2.
SUPFAM; SSF57903; SSF57903; 1.
SUPFAM; SSF81837; SSF81837; 1.
PROSITE; PS50197; BEACH; 1.
PROSITE; PS51783; PH_BEACH; 1.
PROSITE; PS00678; WD_REPEATS_1; 1.
PROSITE; PS50082; WD_REPEATS_2; 1.
PROSITE; PS50294; WD_REPEATS_REGION; 1.
PROSITE; PS50178; ZF_FYVE; 1.
1: Evidence at protein level;
3D-structure; Alternative splicing; Autophagy; Cell projection;
Complete proteome; Cytoplasm; Developmental protein; Disease mutation;
Lipid-binding; Membrane; Metal-binding; Nucleus; Phosphoprotein;
Polymorphism; Primary microcephaly; Reference proteome; Repeat;
WD repeat; Zinc; Zinc-finger.
CHAIN 1 3526 WD repeat and FYVE domain-containing
protein 3.
/FTId=PRO_0000242693.
DOMAIN 2531 2656 BEACH-type PH. {ECO:0000255|PROSITE-
ProRule:PRU01119}.
DOMAIN 2683 2976 BEACH. {ECO:0000255|PROSITE-
ProRule:PRU00026}.
REPEAT 3077 3115 WD 1.
REPEAT 3125 3164 WD 2.
REPEAT 3167 3206 WD 3.
REPEAT 3210 3254 WD 4.
REPEAT 3408 3447 WD 5.
ZN_FING 3454 3514 FYVE-type. {ECO:0000255|PROSITE-
ProRule:PRU00091}.
REGION 2285 2981 Sufficient for localization to p62
bodies/ALIS.
{ECO:0000269|PubMed:20168092}.
REGION 2586 3526 Interaction with SQSTM1.
{ECO:0000269|PubMed:20168092}.
REGION 2981 3526 Interaction with ATG5.
{ECO:0000269|PubMed:20417604}.
REGION 3313 3363 Interaction with GABARAP.
{ECO:0000269|PubMed:24668264}.
MOTIF 3346 3349 LC3-interacting region (LIR).
{ECO:0000303|PubMed:24668264}.
COMPBIAS 472 475 Poly-Ser.
COMPBIAS 2516 2519 Poly-Glu.
MOD_RES 1942 1942 Phosphoserine.
{ECO:0000250|UniProtKB:Q6VNB8}.
MOD_RES 2278 2278 Phosphoserine.
{ECO:0000244|PubMed:23186163}.
MOD_RES 2492 2492 Phosphoserine.
{ECO:0000250|UniProtKB:Q6VNB8}.
MOD_RES 3335 3335 Phosphoserine.
{ECO:0000250|UniProtKB:Q6VNB8}.
MOD_RES 3339 3339 Phosphoserine.
{ECO:0000244|PubMed:23186163}.
VAR_SEQ 2408 2424 Missing (in isoform 2).
{ECO:0000303|PubMed:14702039}.
/FTId=VSP_019475.
VARIANT 2637 2637 R -> W (in MCPH18; increased cellular
DVL3 protein levels as compared to the
wild-type protein and loss of attenuation
of Wnt signaling; when expressed in
Drosophila, causes brain anomalies).
{ECO:0000269|PubMed:27008544}.
/FTId=VAR_079130.
VARIANT 3032 3032 I -> V (in dbSNP:rs17368018).
/FTId=VAR_026864.
MUTAGEN 3343 3343 K->A: Decreased interaction with GABARAP,
no effect on interaction with MAP1LC3B;
when associated with A-3344 and A-3351.
{ECO:0000269|PubMed:24668264}.
MUTAGEN 3344 3344 D->A: Decreased interaction with GABARAP,
no effect on interaction with MAP1LC3B;
when associated with A-3343 and A-3351.
{ECO:0000269|PubMed:24668264}.
MUTAGEN 3346 3346 F->A: Abolishes interaction with GABARAP
and MAP1LC3C.
{ECO:0000269|PubMed:24668264}.
MUTAGEN 3347 3347 I->A: Decreases interaction with GABARAP
and MAP1LC3C.
{ECO:0000269|PubMed:24668264}.
MUTAGEN 3348 3348 F->A: Decreases interaction with GABARAP
and MAP1LC3C.
{ECO:0000269|PubMed:24668264}.
MUTAGEN 3349 3349 V->A: Decreases interaction with GABARAP
and MAP1LC3C.
{ECO:0000269|PubMed:24668264}.
MUTAGEN 3351 3351 Y->A: Decreased interaction with GABARAP,
no effect on interaction with MAP1LC3B;
when associated with A-3343 and A-3344.
{ECO:0000269|PubMed:24668264}.
CONFLICT 2944 2944 N -> T (in Ref. 1; AAN15137).
{ECO:0000305}.
CONFLICT 3396 3396 L -> P (in Ref. 5; BAB71020).
{ECO:0000305}.
STRAND 3346 3348 {ECO:0000244|PDB:3WIM}.
SEQUENCE 3526 AA; 395258 MW; F4D518E8C9C12E23 CRC64;
MNMVKRIMGR PRQEECSPQD NALGLMHLRR LFTELCHPPR HMTQKEQEEK LYMMLPVFNR
VFGNAPPNTM TEKFSDLLQF TTQVSRLMVT EIRRRASNKS TEAASRAIVQ FLEINQSEEA
SRGWMLLTTI NLLASSGQKT VDCMTTMSVP STLVKCLYLF FDLPHVPEAV GGAQNELPLA
ERRGLLQKVF VQILVKLCSF VSPAEELAQK DDLQLLFSAI TSWCPPYNLP WRKSAGEVLM
TISRHGLSVN VVKYIHEKEC LSTCVQNMQQ SDDLSPLEIV EMFAGLSCFL KDSSDVSQTL
LDDFRIWQGY NFLCDLLLRL EQAKEAESKD ALKDLVNLIT SLTTYGVSEL KPAGITTGAP
FLLPGFAVPQ PAGKGHSVRN VQAFAVLQNA FLKAKTSFLA QIILDAITNI YMADNANYFI
LESQHTLSQF AEKISKLPEV QNKYFEMLEF VVFSLNYIPC KELISVSILL KSSSSYHCSI
IAMKTLLKFT RHDYIFKDVF REVGLLEVMV NLLHKYAALL KDPTQALNEQ GDSRNNSSVE
DQKHLALLVM ETLTVLLQGS NTNAGIFREF GGARCAHNIV KYPQCRQHAL MTIQQLVLSP
NGDDDMGTLL GLMHSAPPTE LQLKTDILRA LLSVLRESHR SRTVFRKVGG FVYITSLLVA
MERSLSCPPK NGWEKVNQNQ VFELLHTVFC TLTAAMRYEP ANSHFFKTEI QYEKLADAVR
FLGCFSDLRK ISAMNVFPSN TQPFQRLLEE DVISIESVSP TLRHCSKLFI YLYKVATDSF
DSRAEQIPPC LTSESSLPSP WGTPALSRKR HAYHSVSTPP VYPPKNVADL KLHVTTSSLQ
SSDAVIIHPG AMLAMLDLLA SVGSVTQPEH ALDLQLAVAN ILQSLVHTER NQQVMCEAGL
HARLLQRCSA ALADEDHSLH PPLQRMFERL ASQALEPMVL REFLRLASPL NCGAWDKKLL
KQYRVHKPSS LSYEPEMRSS MITSLEGLGT DNVFSLHEDN HYRISKSLVK SAEGSTVPLT
RVKCLVSMTT PHDIRLHGSS VTPAFVEFDT SLEGFGCLFL PSLAPHNAPT NNTVTTGLID
GAVVSGIGSG ERFFPPPSGL SYSSWFCIEH FSSPPNNHPV RLLTVVRRAN SSEQHYVCLA
IVLSAKDRSL IVSTKEELLQ NYVDDFSEES SFYEILPCCA RFRCGELIIE GQWHHLVLVM
SKGMLKNSTA ALYIDGQLVN TVKLHYVHST PGGSGSANPP VVSTVYAYIG TPPAQRQIAS
LVWRLGPTHF LEEVLPSSNV TTIYELGPNY VGSFQAVCMP CKDAKSEGVV PSPVSLVPEE
KVSFGLYALS VSSLTVARIR KVYNKLDSKA IAKQLGISSH ENATPVKLIH NSAGHLNGSA
RTIGAALIGY LGVRTFVPKP VATTLQYVGG AAAILGLVAM ASDVEGLYAA VKALVCVVKS
NPLASKEMER IKGYQLLAML LKKKRSLLNS HILHLTFSLV GTVDSGHETS IIPNSTAFQD
LLCDFEVWLH APYELHLSLF EHFIELLTES SEASKNAKLM REFQLIPKLL LTLRDMSLSQ
PTIAAISNVL SFLLQGFPSS NDLLRFGQFI SSTLPTFAVC EKFVVMEINN EEKLDTGTEE
EFGGLVSANL ILLRNRLLDI LLKLIYTSKE KTSINLQACE ELVKTLGFDW IMMFMEEHLH
STTVTAAMRI LVVLLSNQSI LIKFKEGLSG GGWLEQTDSV LTNKIGTVLG FNVGRSAGGR
STVREINRDA CHFPGFPVLQ SFLPKHTNVP ALYFLLMALF LQQPVSELPE NLQVSVPVIS
CRSKQGCQFD LDSIWTFIFG VPASSGTVVS SIHNVCTEAV FLLLGMLRSM LTSPWQSEEE
GSWLREYPVT LMQFFRYLYH NVPDLASMWM SPDFLCALAA TVFPFNIRPY SEMVTDLDDE
VGSPAEEFKA FAADTGMNRS QSEYCNVGTK TYLTNHPAKK FVFDFMRVLI IDNLCLTPAS
KQTPLIDLLL EASPERSTRT QQKEFQTYIL DSVMDHLLAA DVLLGEDASL PITSGGSYQV
LVNNVFYFTQ RVVDKLWQGM FNKESKLLID FIIQLIAQSK RRSQGLSLDA VYHCLNRTIL
YQFSRAHKTV PQQVALLDSL RVLTVNRNLI LGPGNHDQEF ISCLAHCLIN LHVGSNVDGF
GLEAEARMTT WHIMIPSDIE PDGSYSQDIS EGRQLLIKAV NRVWTELIHS KKQVLEELFK
VTLPVNERGH VDIATARPLI EEAALKCWQN HLAHEKKCIS RGEALAPTTQ SKLSRVSSGF
GLSKLTGSRR NRKESGLNKH SLSTQEISQW MFTHIAVVRD LVDTQYKEYQ ERQQNALKYV
TEEWCQIECE LLRERGLWGP PIGSHLDKWM LEMTEGPCRM RKKMVRNDMF YNHYPYVPET
EQETNVASEI PSKQPETPDD IPQKKPARYR RAVSYDSKEY YMRLASGNPA IVQDAIVESS
EGEAAQQEPE HGEDTIAKVK GLVKPPLKRS RSAPDGGDEE NQEQLQDQIA EGSSIEEEEK
TDNATLLRLL EEGEKIQHMY RCARVQGLDT SEGLLLFGKE HFYVIDGFTM TATREIRDIE
TLPPNMHEPI IPRGARQGPS QLKRTCSIFA YEDIKEVHKR RYLLQPIAVE VFSGDGRNYL
LAFQKGIRNK VYQRFLAVVP SLTDSSESVS GQRPNTSVEQ GSGLLSTLVG EKSVTQRWER
GEISNFQYLM HLNTLAGRSY NDLMQYPVFP WILADYDSEE VDLTNPKTFR NLAKPMGAQT
DERLAQYKKR YKDWEDPNGE TPAYHYGTHY SSAMIVASYL VRMEPFTQIF LRLQGGHFDL
ADRMFHSVRE AWYSASKHNM ADVKELIPEF FYLPEFLFNS NNFDLGCKQN GTKLGDVILP
PWAKGDPREF IRVHREALEC DYVSAHLHEW IDLIFGYKQQ GPAAVEAVNV FHHLFYEGQV
DIYNINDPLK ETATIGFINN FGQIPKQLFK KPHPPKRVRS RLNGDNAGIS VLPGSTSDKI
FFHHLDNLRP SLTPVKELKE PVGQIVCTDK GILAVEQNKV LIPPTWNKTF AWGYADLSCR
LGTYESDKAM TVYECLSEWG QILCAICPNP KLVITGGTST VVCVWEMGTS KEKAKTVTLK
QALLGHTDTV TCATASLAYH IIVSGSRDRT CIIWDLNKLS FLTQLRGHRA PVSALCINEL
TGDIVSCAGT YIHVWSINGN PIVSVNTFTG RSQQIICCCM SEMNEWDTQN VIVTGHSDGV
VRFWRMEFLQ VPETPAPEPA EVLEMQEDCP EAQIGQEAQD EDSSDSEADE QSISQDPKDT
PSQPSSTSHR PRAASCRATA AWCTDSGSDD SRRWSDQLSL DEKDGFIFVN YSEGQTRAHL
QGPLSHPHPN PIEVRNYSRL KPGYRWERQL VFRSKLTMHT AFDRKDNAHP AEVTALGISK
DHSRILVGDS RGRVFSWSVS DQPGRSAADH WVKDEGGDSC SGCSVRFSLT ERRHHCRNCG
QLFCQKCSRF QSEIKRLKIS SPVRVCQNCY YNLQHERGSE DGPRNC


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