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CAP-Gly domain-containing linker protein 3 (Cytoplasmic linker protein 170-related 59 kDa protein) (CLIP-170-related 59 kDa protein) (CLIPR-59)

 CLIP3_HUMAN             Reviewed;         547 AA.
Q96DZ5; A8K0E4; Q8WWL1; Q96C99; Q9UFT7;
10-JAN-2006, integrated into UniProtKB/Swiss-Prot.
17-OCT-2006, sequence version 3.
18-JUL-2018, entry version 150.
RecName: Full=CAP-Gly domain-containing linker protein 3;
AltName: Full=Cytoplasmic linker protein 170-related 59 kDa protein;
Short=CLIP-170-related 59 kDa protein;
Short=CLIPR-59;
Name=CLIP3; Synonyms=CLIPR59;
Homo sapiens (Human).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
NCBI_TaxID=9606;
[1]
NUCLEOTIDE SEQUENCE [MRNA].
PubMed=11854307; DOI=10.1083/jcb.200111003;
Perez F., Pernet-Gallay K., Nizak C., Goodson H.V., Kreis T.E.,
Goud B.;
"CLIPR-59, a new trans-Golgi/TGN cytoplasmic linker protein belonging
to the CLIP-170 family.";
J. Cell Biol. 156:631-642(2002).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
TISSUE=Brain, and Cerebellum;
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).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], AND VARIANT VAL-175.
TISSUE=Brain, and Skin;
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).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 387-547.
TISSUE=Uterus;
PubMed=17974005; DOI=10.1186/1471-2164-8-399;
Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U.,
Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H.,
Heubner D., Hoerlein A., Michel G., Wedler H., Koehrer K.,
Ottenwaelder B., Poustka A., Wiemann S., Schupp I.;
"The full-ORF clone resource of the German cDNA consortium.";
BMC Genomics 8:399-399(2007).
[5]
FUNCTION, AND INTERACTION WITH AKT1 AND AKT2.
PubMed=19139280; DOI=10.1128/MCB.00754-08;
Ding J., Du K.;
"ClipR-59 interacts with Akt and regulates Akt cellular
compartmentalization.";
Mol. Cell. Biol. 29:1459-1471(2009).
[6]
PALMITOYLATION AT CYS-534 AND CYS-535, SUBCELLULAR LOCATION, AND
MUTAGENESIS OF 534-CYS--CYS-535.
PubMed=24001771; DOI=10.1128/MCB.00527-13;
Ren W., Sun Y., Du K.;
"DHHC17 palmitoylates ClipR-59 and modulates ClipR-59 association with
the plasma membrane.";
Mol. Cell. Biol. 33:4255-4265(2013).
[7]
INTERACTION WITH ZDHHC17 AND ZDHHC13, AND MUTAGENESIS OF PRO-509.
PubMed=26198635; DOI=10.1074/jbc.M115.657668;
Lemonidis K., Sanchez-Perez M.C., Chamberlain L.H.;
"Identification of a novel sequence motif recognized by the ankyrin
repeat domain of zDHHC17/13 S-acyltransferases.";
J. Biol. Chem. 290:21939-21950(2015).
[8]
INTERACTION WITH ZDHHC17.
PubMed=28882895; DOI=10.1074/jbc.M117.799650;
Lemonidis K., MacLeod R., Baillie G.S., Chamberlain L.H.;
"Peptide array based screening reveals a large number of proteins
interacting with the ankyrin repeat domain of the zDHHC17 S-
acyltransferase.";
J. Biol. Chem. 292:17190-17202(2017).
[9]
STRUCTURE BY NMR OF 285-366.
RIKEN structural genomics initiative (RSGI);
"Solution structure of the 1st CAP-GLY domain in human clip-170-
related protein CLIPR59.";
Submitted (NOV-2005) to the PDB data bank.
-!- FUNCTION: Functions as a cytoplasmic linker protein. Involved in
TGN-endosome dynamics. May modulate the cellular
compartmentalization of AKT kinase family and promote its cell
membrane localization, thereby playing a role in glucose transport
in adipocytes. {ECO:0000269|PubMed:19139280}.
-!- SUBUNIT: Homodimer. Interacts with AKT1 and AKT2; when AKT1 and
AKT2 are phosphorylated and activated, affinity is higher for AKT2
(PubMed:19139280). Interacts with ZDHHC13 (via ANK repeats)
(PubMed:26198635). Interacts with ZDHHC17 (via ANK repeats)
(PubMed:26198635, PubMed:28882895). {ECO:0000269|PubMed:19139280,
ECO:0000269|PubMed:26198635, ECO:0000269|PubMed:28882895}.
-!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000269|PubMed:24001771};
Lipid-anchor {ECO:0000269|PubMed:24001771}. Cytoplasm
{ECO:0000269|PubMed:24001771}. Golgi apparatus, Golgi stack
{ECO:0000269|PubMed:24001771}. Note=Localized to Golgi stacks as
well as on tubulovesicular elements juxtaposed to Golgi cisternae.
-!- DOMAIN: Microtubule association is inhibited by the ANK repeats
and the Golgi localization region (GoLD).
-!- PTM: Palmitoylation by ZDHHC17 regulates association with the
plasma membrane. {ECO:0000269|PubMed:24001771}.
-!- MISCELLANEOUS: The N-terminal half is dispensable for proper Golgi
targeting, whereas the GoLD region is required.
-----------------------------------------------------------------------
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EMBL; AJ427922; CAD20873.1; -; mRNA.
EMBL; AK094738; BAG52921.1; -; mRNA.
EMBL; AK289509; BAF82198.1; -; mRNA.
EMBL; BC013116; AAH13116.2; -; mRNA.
EMBL; BC014486; AAH14486.2; -; mRNA.
EMBL; AL117468; CAB55943.1; -; mRNA.
CCDS; CCDS12486.1; -.
PIR; T17253; T17253.
RefSeq; NP_001186499.1; NM_001199570.1.
RefSeq; NP_056341.1; NM_015526.2.
UniGene; Hs.466539; -.
PDB; 2CP0; NMR; -; A=285-366.
PDBsum; 2CP0; -.
ProteinModelPortal; Q96DZ5; -.
SMR; Q96DZ5; -.
BioGrid; 117475; 9.
IntAct; Q96DZ5; 4.
STRING; 9606.ENSP00000353732; -.
iPTMnet; Q96DZ5; -.
PhosphoSitePlus; Q96DZ5; -.
SwissPalm; Q96DZ5; -.
BioMuta; CLIP3; -.
DMDM; 116241302; -.
EPD; Q96DZ5; -.
PaxDb; Q96DZ5; -.
PeptideAtlas; Q96DZ5; -.
PRIDE; Q96DZ5; -.
ProteomicsDB; 76346; -.
Ensembl; ENST00000360535; ENSP00000353732; ENSG00000105270.
Ensembl; ENST00000593074; ENSP00000466832; ENSG00000105270.
GeneID; 25999; -.
KEGG; hsa:25999; -.
UCSC; uc002ocz.3; human.
CTD; 25999; -.
EuPathDB; HostDB:ENSG00000105270.14; -.
GeneCards; CLIP3; -.
H-InvDB; HIX0040341; -.
HGNC; HGNC:24314; CLIP3.
MIM; 607382; gene.
neXtProt; NX_Q96DZ5; -.
OpenTargets; ENSG00000105270; -.
PharmGKB; PA162382439; -.
eggNOG; KOG4568; Eukaryota.
eggNOG; COG5244; LUCA.
GeneTree; ENSGT00760000119173; -.
HOGENOM; HOG000007206; -.
HOVERGEN; HBG057079; -.
InParanoid; Q96DZ5; -.
KO; K10423; -.
OMA; ICPPKLG; -.
OrthoDB; EOG091G04NK; -.
PhylomeDB; Q96DZ5; -.
TreeFam; TF326096; -.
Reactome; R-HSA-5357905; Regulation of TNFR1 signaling.
EvolutionaryTrace; Q96DZ5; -.
GenomeRNAi; 25999; -.
PRO; PR:Q96DZ5; -.
Proteomes; UP000005640; Chromosome 19.
Bgee; ENSG00000105270; -.
CleanEx; HS_CLIP3; -.
ExpressionAtlas; Q96DZ5; baseline and differential.
Genevisible; Q96DZ5; HS.
GO; GO:0005829; C:cytosol; TAS:Reactome.
GO; GO:0031901; C:early endosome membrane; IDA:UniProtKB.
GO; GO:0005795; C:Golgi stack; IEA:UniProtKB-SubCell.
GO; GO:0045121; C:membrane raft; IDA:UniProtKB.
GO; GO:0005886; C:plasma membrane; IDA:UniProtKB.
GO; GO:0055038; C:recycling endosome membrane; IDA:UniProtKB.
GO; GO:0005802; C:trans-Golgi network; ISS:UniProtKB.
GO; GO:0032588; C:trans-Golgi network membrane; IDA:UniProtKB.
GO; GO:0035594; F:ganglioside binding; IDA:UniProtKB.
GO; GO:0008017; F:microtubule binding; IDA:UniProtKB.
GO; GO:0072321; P:chaperone-mediated protein transport; IMP:UniProtKB.
GO; GO:0045444; P:fat cell differentiation; ISS:UniProtKB.
GO; GO:0044091; P:membrane biogenesis; IMP:UniProtKB.
GO; GO:0031115; P:negative regulation of microtubule polymerization; IMP:UniProtKB.
GO; GO:0018230; P:peptidyl-L-cysteine S-palmitoylation; IMP:UniProtKB.
GO; GO:0043065; P:positive regulation of apoptotic process; IMP:UniProtKB.
GO; GO:0045807; P:positive regulation of endocytosis; IMP:UniProtKB.
GO; GO:0010828; P:positive regulation of glucose transmembrane transport; ISS:UniProtKB.
GO; GO:1903078; P:positive regulation of protein localization to plasma membrane; ISS:UniProtKB.
GO; GO:0001934; P:positive regulation of protein phosphorylation; ISS:UniProtKB.
GO; GO:0010803; P:regulation of tumor necrosis factor-mediated signaling pathway; TAS:Reactome.
CDD; cd00204; ANK; 1.
Gene3D; 1.25.40.20; -; 1.
Gene3D; 2.30.30.190; -; 2.
InterPro; IPR002110; Ankyrin_rpt.
InterPro; IPR020683; Ankyrin_rpt-contain_dom.
InterPro; IPR036770; Ankyrin_rpt-contain_sf.
InterPro; IPR036859; CAP-Gly_dom_sf.
InterPro; IPR000938; CAP-Gly_domain.
Pfam; PF12796; Ank_2; 1.
Pfam; PF01302; CAP_GLY; 2.
SMART; SM00248; ANK; 3.
SMART; SM01052; CAP_GLY; 2.
SUPFAM; SSF48403; SSF48403; 1.
SUPFAM; SSF74924; SSF74924; 2.
PROSITE; PS50297; ANK_REP_REGION; 1.
PROSITE; PS50088; ANK_REPEAT; 1.
PROSITE; PS00845; CAP_GLY_1; 2.
PROSITE; PS50245; CAP_GLY_2; 2.
1: Evidence at protein level;
3D-structure; ANK repeat; Cell membrane; Complete proteome; Cytoplasm;
Golgi apparatus; Lipoprotein; Membrane; Palmitate; Phosphoprotein;
Polymorphism; Reference proteome; Repeat.
CHAIN 1 547 CAP-Gly domain-containing linker protein
3.
/FTId=PRO_0000076212.
REPEAT 117 158 ANK 1.
REPEAT 160 191 ANK 2.
REPEAT 197 229 ANK 3.
DOMAIN 314 356 CAP-Gly 1. {ECO:0000255|PROSITE-
ProRule:PRU00045}.
DOMAIN 436 478 CAP-Gly 2. {ECO:0000255|PROSITE-
ProRule:PRU00045}.
REGION 488 547 GoLD.
COMPBIAS 16 25 Poly-Glu.
MOD_RES 374 374 Phosphothreonine.
{ECO:0000250|UniProtKB:B9EHT4}.
MOD_RES 401 401 Phosphoserine.
{ECO:0000250|UniProtKB:B9EHT4}.
LIPID 534 534 S-palmitoyl cysteine.
{ECO:0000269|PubMed:24001771}.
LIPID 535 535 S-palmitoyl cysteine.
{ECO:0000269|PubMed:24001771}.
VARIANT 175 175 D -> V (in dbSNP:rs17851002).
{ECO:0000269|PubMed:15489334}.
/FTId=VAR_027962.
MUTAGEN 509 509 P->A: Inhibits interaction with ZDHHC13
and ZDHHC17.
{ECO:0000269|PubMed:26198635}.
MUTAGEN 534 535 CC->AA: Strongly reduced plasma membrane
association and decrease in the levels of
Akt at the plasma membrane.
{ECO:0000269|PubMed:24001771}.
HELIX 288 292 {ECO:0000244|PDB:2CP0}.
STRAND 299 302 {ECO:0000244|PDB:2CP0}.
TURN 303 305 {ECO:0000244|PDB:2CP0}.
STRAND 306 314 {ECO:0000244|PDB:2CP0}.
STRAND 317 319 {ECO:0000244|PDB:2CP0}.
STRAND 323 331 {ECO:0000244|PDB:2CP0}.
STRAND 337 339 {ECO:0000244|PDB:2CP0}.
STRAND 348 350 {ECO:0000244|PDB:2CP0}.
STRAND 352 355 {ECO:0000244|PDB:2CP0}.
HELIX 357 359 {ECO:0000244|PDB:2CP0}.
STRAND 360 362 {ECO:0000244|PDB:2CP0}.
SEQUENCE 547 AA; 59560 MW; A718D9673EC1CF4B CRC64;
MTKTDPAPMA PPPRGEEEEE EEEDEPVPEA PSPTQERRQK PVVHPSAPAP LPKDYAFTFF
DPNDPACQEI LFDPQTTIPE LFAIVRQWVP QVQHKIDVIG NEILRRGCHV NDRDGLTDMT
LLHYACKAGA HGVGDPAAAV RLSQQLLALG ADVTLRSRWT NMNALHYAAY FDVPDLVRVL
LKGARPRVVN STCSDFNHGS ALHIAASSLC LGAAKCLLEH GANPALRNRK GQVPAEVVPD
PMDMSLDKAE AALVAKELRT LLEEAVPLSC ALPKVTLPNY DNVPGNLMLS ALGLRLGDRV
LLDGQKTGTL RFCGTTEFAS GQWVGVELDE PEGKNDGSVG GVRYFICPPK QGLFASVSKI
SKAVDAPPSS VTSTPRTPRM DFSRVTGKGR REHKGKKKTP SSPSLGSLQQ RDGAKAEVGD
QVLVAGQKQG IVRFYGKTDF APGYWYGIEL DQPTGKHDGS VFGVRYFTCP PRHGVFAPAS
RIQRIGGSTD SPGDSVGAKK VHQVTMTQPK RTFTTVRTPK DIASENSISR LLFCCWFPWM
LRAEMQS


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