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Q96DZ5

- CLIP3_HUMAN

UniProt

Q96DZ5 - CLIP3_HUMAN

Protein

CAP-Gly domain-containing linker protein 3

Gene

CLIP3

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 115 (01 Oct 2014)
      Sequence version 3 (17 Oct 2006)
      Previous versions | rss
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    Functioni

    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.1 Publication

    GO - Molecular functioni

    1. ganglioside binding Source: UniProtKB
    2. microtubule binding Source: UniProtKB

    GO - Biological processi

    1. chaperone-mediated protein transport Source: UniProtKB
    2. fat cell differentiation Source: UniProtKB
    3. membrane biogenesis Source: UniProtKB
    4. negative regulation of microtubule polymerization Source: UniProtKB
    5. peptidyl-L-cysteine S-palmitoylation Source: UniProtKB
    6. positive regulation of apoptotic process Source: UniProtKB
    7. positive regulation of endocytosis Source: UniProtKB
    8. positive regulation of establishment of protein localization to plasma membrane Source: UniProtKB
    9. positive regulation of glucose transport Source: UniProtKB
    10. positive regulation of protein phosphorylation Source: UniProtKB

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    CAP-Gly domain-containing linker protein 3
    Alternative name(s):
    Cytoplasmic linker protein 170-related 59 kDa protein
    Short name:
    CLIP-170-related 59 kDa protein
    Short name:
    CLIPR-59
    Gene namesi
    Name:CLIP3
    Synonyms:CLIPR59
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 19

    Organism-specific databases

    HGNCiHGNC:24314. CLIP3.

    Subcellular locationi

    Cell membrane 1 Publication; Lipid-anchor 1 Publication. Cytoplasm 1 Publication. Golgi apparatusGolgi stack 1 Publication
    Note: Localized to Golgi stacks as well as on tubulovesicular elements juxtaposed to Golgi cisternae.

    GO - Cellular componenti

    1. early endosome membrane Source: UniProtKB
    2. Golgi stack Source: UniProtKB-SubCell
    3. membrane raft Source: UniProtKB
    4. plasma membrane Source: UniProtKB
    5. recycling endosome membrane Source: UniProtKB
    6. trans-Golgi network Source: UniProtKB
    7. trans-Golgi network membrane Source: UniProtKB

    Keywords - Cellular componenti

    Cell membrane, Cytoplasm, Golgi apparatus, Membrane

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi534 – 5352CC → AA: Strongly reduced plasma membrane association and decrease in the levels of Akt at the plasma membrane. 1 Publication

    Organism-specific databases

    PharmGKBiPA162382439.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 547547CAP-Gly domain-containing linker protein 3PRO_0000076212Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Lipidationi534 – 5341S-palmitoyl cysteine1 Publication
    Lipidationi535 – 5351S-palmitoyl cysteine1 Publication

    Post-translational modificationi

    Palmitoylation by ZDHHC17 regulates association with the plasma membrane.1 Publication

    Keywords - PTMi

    Lipoprotein, Palmitate

    Proteomic databases

    PaxDbiQ96DZ5.
    PRIDEiQ96DZ5.

    PTM databases

    PhosphoSiteiQ96DZ5.

    Expressioni

    Gene expression databases

    ArrayExpressiQ96DZ5.
    BgeeiQ96DZ5.
    CleanExiHS_CLIP3.
    GenevestigatoriQ96DZ5.

    Organism-specific databases

    HPAiHPA041429.

    Interactioni

    Subunit structurei

    Homodimer. Interacts with AKT1 and AKT2; when AKT1 and AKT2 are phosphorylated and activated, affinity is higher for AKT2.1 Publication

    Protein-protein interaction databases

    BioGridi117475. 9 interactions.
    STRINGi9606.ENSP00000353732.

    Structurei

    Secondary structure

    1
    547
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi288 – 2925
    Beta strandi299 – 3024
    Turni303 – 3053
    Beta strandi306 – 3149
    Beta strandi317 – 3193
    Beta strandi323 – 3319
    Beta strandi337 – 3393
    Beta strandi348 – 3503
    Beta strandi352 – 3554
    Helixi357 – 3593
    Beta strandi360 – 3623

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2CP0NMR-A285-366[»]
    ProteinModelPortaliQ96DZ5.
    SMRiQ96DZ5. Positions 99-238, 286-370, 409-491.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ96DZ5.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Repeati117 – 15842ANK 1Add
    BLAST
    Repeati160 – 19132ANK 2Add
    BLAST
    Repeati197 – 22933ANK 3Add
    BLAST
    Domaini314 – 35643CAP-Gly 1PROSITE-ProRule annotationAdd
    BLAST
    Domaini436 – 47843CAP-Gly 2PROSITE-ProRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni488 – 54760GoLDAdd
    BLAST

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi16 – 2510Poly-Glu

    Domaini

    Microtubule association is inhibited by the ANK repeats and the Golgi localization region (GoLD).

    Sequence similaritiesi

    Contains 3 ANK repeats.PROSITE-ProRule annotation
    Contains 2 CAP-Gly domains.PROSITE-ProRule annotation

    Keywords - Domaini

    ANK repeat, Repeat

    Phylogenomic databases

    eggNOGiCOG5244.
    HOGENOMiHOG000007206.
    HOVERGENiHBG057079.
    InParanoidiQ96DZ5.
    KOiK10423.
    OMAiDNVGAKK.
    OrthoDBiEOG75QR3B.
    PhylomeDBiQ96DZ5.
    TreeFamiTF326096.

    Family and domain databases

    Gene3Di1.25.40.20. 1 hit.
    2.30.30.190. 2 hits.
    InterProiIPR002110. Ankyrin_rpt.
    IPR020683. Ankyrin_rpt-contain_dom.
    IPR000938. CAP-Gly_domain.
    [Graphical view]
    PfamiPF12796. Ank_2. 1 hit.
    PF01302. CAP_GLY. 2 hits.
    [Graphical view]
    SMARTiSM00248. ANK. 3 hits.
    SM01052. CAP_GLY. 2 hits.
    [Graphical view]
    SUPFAMiSSF48403. SSF48403. 1 hit.
    SSF74924. SSF74924. 2 hits.
    PROSITEiPS50297. ANK_REP_REGION. 1 hit.
    PS50088. ANK_REPEAT. 1 hit.
    PS00845. CAP_GLY_1. 2 hits.
    PS50245. CAP_GLY_2. 2 hits.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q96DZ5-1 [UniParc]FASTAAdd to Basket

    « Hide

    MTKTDPAPMA PPPRGEEEEE EEEDEPVPEA PSPTQERRQK PVVHPSAPAP    50
    LPKDYAFTFF DPNDPACQEI LFDPQTTIPE LFAIVRQWVP QVQHKIDVIG 100
    NEILRRGCHV NDRDGLTDMT LLHYACKAGA HGVGDPAAAV RLSQQLLALG 150
    ADVTLRSRWT NMNALHYAAY FDVPDLVRVL LKGARPRVVN STCSDFNHGS 200
    ALHIAASSLC LGAAKCLLEH GANPALRNRK GQVPAEVVPD PMDMSLDKAE 250
    AALVAKELRT LLEEAVPLSC ALPKVTLPNY DNVPGNLMLS ALGLRLGDRV 300
    LLDGQKTGTL RFCGTTEFAS GQWVGVELDE PEGKNDGSVG GVRYFICPPK 350
    QGLFASVSKI SKAVDAPPSS VTSTPRTPRM DFSRVTGKGR REHKGKKKTP 400
    SSPSLGSLQQ RDGAKAEVGD QVLVAGQKQG IVRFYGKTDF APGYWYGIEL 450
    DQPTGKHDGS VFGVRYFTCP PRHGVFAPAS RIQRIGGSTD SPGDSVGAKK 500
    VHQVTMTQPK RTFTTVRTPK DIASENSISR LLFCCWFPWM LRAEMQS 547
    Length:547
    Mass (Da):59,560
    Last modified:October 17, 2006 - v3
    Checksum:iA718D9673EC1CF4B
    GO

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti175 – 1751D → V.1 Publication
    Corresponds to variant rs17851002 [ dbSNP | Ensembl ].
    VAR_027962

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AJ427922 mRNA. Translation: CAD20873.1.
    AK094738 mRNA. Translation: BAG52921.1.
    AK289509 mRNA. Translation: BAF82198.1.
    BC013116 mRNA. Translation: AAH13116.2.
    BC014486 mRNA. Translation: AAH14486.2.
    AL117468 mRNA. Translation: CAB55943.1.
    CCDSiCCDS12486.1.
    PIRiT17253.
    RefSeqiNP_001186499.1. NM_001199570.1.
    NP_056341.1. NM_015526.2.
    UniGeneiHs.466539.

    Genome annotation databases

    EnsembliENST00000360535; ENSP00000353732; ENSG00000105270.
    ENST00000593074; ENSP00000466832; ENSG00000105270.
    GeneIDi25999.
    KEGGihsa:25999.
    UCSCiuc002ocz.2. human.

    Polymorphism databases

    DMDMi116241302.

    Keywords - Coding sequence diversityi

    Polymorphism

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AJ427922 mRNA. Translation: CAD20873.1 .
    AK094738 mRNA. Translation: BAG52921.1 .
    AK289509 mRNA. Translation: BAF82198.1 .
    BC013116 mRNA. Translation: AAH13116.2 .
    BC014486 mRNA. Translation: AAH14486.2 .
    AL117468 mRNA. Translation: CAB55943.1 .
    CCDSi CCDS12486.1.
    PIRi T17253.
    RefSeqi NP_001186499.1. NM_001199570.1.
    NP_056341.1. NM_015526.2.
    UniGenei Hs.466539.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2CP0 NMR - A 285-366 [» ]
    ProteinModelPortali Q96DZ5.
    SMRi Q96DZ5. Positions 99-238, 286-370, 409-491.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 117475. 9 interactions.
    STRINGi 9606.ENSP00000353732.

    PTM databases

    PhosphoSitei Q96DZ5.

    Polymorphism databases

    DMDMi 116241302.

    Proteomic databases

    PaxDbi Q96DZ5.
    PRIDEi Q96DZ5.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000360535 ; ENSP00000353732 ; ENSG00000105270 .
    ENST00000593074 ; ENSP00000466832 ; ENSG00000105270 .
    GeneIDi 25999.
    KEGGi hsa:25999.
    UCSCi uc002ocz.2. human.

    Organism-specific databases

    CTDi 25999.
    GeneCardsi GC19M036505.
    H-InvDB HIX0040341.
    HGNCi HGNC:24314. CLIP3.
    HPAi HPA041429.
    MIMi 607382. gene.
    neXtProti NX_Q96DZ5.
    PharmGKBi PA162382439.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi COG5244.
    HOGENOMi HOG000007206.
    HOVERGENi HBG057079.
    InParanoidi Q96DZ5.
    KOi K10423.
    OMAi DNVGAKK.
    OrthoDBi EOG75QR3B.
    PhylomeDBi Q96DZ5.
    TreeFami TF326096.

    Miscellaneous databases

    EvolutionaryTracei Q96DZ5.
    GenomeRNAii 25999.
    NextBioi 47718.
    PROi Q96DZ5.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi Q96DZ5.
    Bgeei Q96DZ5.
    CleanExi HS_CLIP3.
    Genevestigatori Q96DZ5.

    Family and domain databases

    Gene3Di 1.25.40.20. 1 hit.
    2.30.30.190. 2 hits.
    InterProi IPR002110. Ankyrin_rpt.
    IPR020683. Ankyrin_rpt-contain_dom.
    IPR000938. CAP-Gly_domain.
    [Graphical view ]
    Pfami PF12796. Ank_2. 1 hit.
    PF01302. CAP_GLY. 2 hits.
    [Graphical view ]
    SMARTi SM00248. ANK. 3 hits.
    SM01052. CAP_GLY. 2 hits.
    [Graphical view ]
    SUPFAMi SSF48403. SSF48403. 1 hit.
    SSF74924. SSF74924. 2 hits.
    PROSITEi PS50297. ANK_REP_REGION. 1 hit.
    PS50088. ANK_REPEAT. 1 hit.
    PS00845. CAP_GLY_1. 2 hits.
    PS50245. CAP_GLY_2. 2 hits.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "CLIPR-59, a new trans-Golgi/TGN cytoplasmic linker protein belonging to the CLIP-170 family."
      Perez F., Pernet-Gallay K., Nizak C., Goodson H.V., Kreis T.E., Goud B.
      J. Cell Biol. 156:631-642(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    2. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
      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.
      Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Tissue: Brain and Cerebellum.
    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], VARIANT VAL-175.
      Tissue: Brain and Skin.
    4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 387-547.
      Tissue: Uterus.
    5. "ClipR-59 interacts with Akt and regulates Akt cellular compartmentalization."
      Ding J., Du K.
      Mol. Cell. Biol. 29:1459-1471(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, INTERACTION WITH AKT1 AND AKT2.
    6. "DHHC17 palmitoylates ClipR-59 and modulates ClipR-59 association with the plasma membrane."
      Ren W., Sun Y., Du K.
      Mol. Cell. Biol. 33:4255-4265(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: PALMITOYLATION AT CYS-534 AND CYS-535, SUBCELLULAR LOCATION, MUTAGENESIS OF 534-CYS--CYS-535.
    7. "Solution structure of the 1st CAP-GLY domain in human clip-170-related protein CLIPR59."
      RIKEN structural genomics initiative (RSGI)
      Submitted (NOV-2005) to the PDB data bank
      Cited for: STRUCTURE BY NMR OF 285-366.

    Entry informationi

    Entry nameiCLIP3_HUMAN
    AccessioniPrimary (citable) accession number: Q96DZ5
    Secondary accession number(s): A8K0E4
    , Q8WWL1, Q96C99, Q9UFT7
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 10, 2006
    Last sequence update: October 17, 2006
    Last modified: October 1, 2014
    This is version 115 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program
    DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

    Miscellaneousi

    Miscellaneous

    The N-terminal half is dispensable for proper Golgi targeting, whereas the GoLD region is required.

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Human chromosome 19
      Human chromosome 19: entries, gene names and cross-references to MIM
    2. Human entries with polymorphisms or disease mutations
      List of human entries with polymorphisms or disease mutations
    3. Human polymorphisms and disease mutations
      Index of human polymorphisms and disease mutations
    4. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    5. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    6. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3