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Protein

CAP-Gly domain-containing linker protein 3

Gene

CLIP3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

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

Miscellaneous

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

GO - Molecular functioni

  • ganglioside binding Source: UniProtKB
  • microtubule binding Source: UniProtKB

GO - Biological processi

  • chaperone-mediated protein transport Source: UniProtKB
  • fat cell differentiation Source: UniProtKB
  • membrane biogenesis Source: UniProtKB
  • negative regulation of microtubule polymerization Source: UniProtKB
  • peptidyl-L-cysteine S-palmitoylation Source: UniProtKB
  • positive regulation of apoptotic process Source: UniProtKB
  • positive regulation of endocytosis Source: UniProtKB
  • positive regulation of glucose transmembrane transport Source: UniProtKB
  • positive regulation of protein localization to plasma membrane Source: UniProtKB
  • positive regulation of protein phosphorylation Source: UniProtKB
  • regulation of tumor necrosis factor-mediated signaling pathway Source: Reactome

Enzyme and pathway databases

ReactomeiR-HSA-5357905 Regulation of TNFR1 signaling

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
Proteomesi
  • UP000005640 Componenti: Chromosome 19

Organism-specific databases

EuPathDBiHostDB:ENSG00000105270.14
HGNCiHGNC:24314 CLIP3
MIMi607382 gene
neXtProtiNX_Q96DZ5

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cell membrane, Cytoplasm, Golgi apparatus, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi509P → A: Inhibits interaction with ZDHHC13 and ZDHHC17. 1 Publication1
Mutagenesisi534 – 535CC → AA: Strongly reduced plasma membrane association and decrease in the levels of Akt at the plasma membrane. 1 Publication2

Organism-specific databases

OpenTargetsiENSG00000105270
PharmGKBiPA162382439

Polymorphism and mutation databases

BioMutaiCLIP3
DMDMi116241302

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000762121 – 547CAP-Gly domain-containing linker protein 3Add BLAST547

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei374PhosphothreonineBy similarity1
Modified residuei401PhosphoserineBy similarity1
Lipidationi534S-palmitoyl cysteine1 Publication1
Lipidationi535S-palmitoyl cysteine1 Publication1

Post-translational modificationi

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

Keywords - PTMi

Lipoprotein, Palmitate, Phosphoprotein

Proteomic databases

EPDiQ96DZ5
PaxDbiQ96DZ5
PeptideAtlasiQ96DZ5
PRIDEiQ96DZ5
ProteomicsDBi76346

PTM databases

iPTMnetiQ96DZ5
PhosphoSitePlusiQ96DZ5
SwissPalmiQ96DZ5

Expressioni

Gene expression databases

BgeeiENSG00000105270
CleanExiHS_CLIP3
ExpressionAtlasiQ96DZ5 baseline and differential
GenevisibleiQ96DZ5 HS

Interactioni

Subunit structurei

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).3 Publications

GO - Molecular functioni

  • microtubule binding Source: UniProtKB

Protein-protein interaction databases

BioGridi117475, 9 interactors
IntActiQ96DZ5, 3 interactors
STRINGi9606.ENSP00000353732

Structurei

Secondary structure

1547
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi288 – 292Combined sources5
Beta strandi299 – 302Combined sources4
Turni303 – 305Combined sources3
Beta strandi306 – 314Combined sources9
Beta strandi317 – 319Combined sources3
Beta strandi323 – 331Combined sources9
Beta strandi337 – 339Combined sources3
Beta strandi348 – 350Combined sources3
Beta strandi352 – 355Combined sources4
Helixi357 – 359Combined sources3
Beta strandi360 – 362Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2CP0NMR-A285-366[»]
ProteinModelPortaliQ96DZ5
SMRiQ96DZ5
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ96DZ5

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati117 – 158ANK 1Add BLAST42
Repeati160 – 191ANK 2Add BLAST32
Repeati197 – 229ANK 3Add BLAST33
Domaini314 – 356CAP-Gly 1PROSITE-ProRule annotationAdd BLAST43
Domaini436 – 478CAP-Gly 2PROSITE-ProRule annotationAdd BLAST43

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni488 – 547GoLDAdd BLAST60

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi16 – 25Poly-Glu10

Domaini

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

Keywords - Domaini

ANK repeat, Repeat

Phylogenomic databases

eggNOGiKOG4568 Eukaryota
COG5244 LUCA
GeneTreeiENSGT00760000119173
HOGENOMiHOG000007206
HOVERGENiHBG057079
InParanoidiQ96DZ5
KOiK10423
OMAiICPPKLG
OrthoDBiEOG091G04NK
PhylomeDBiQ96DZ5
TreeFamiTF326096

Family and domain databases

CDDicd00204 ANK, 1 hit
Gene3Di1.25.40.20, 1 hit
2.30.30.190, 2 hits
InterProiView protein in InterPro
IPR002110 Ankyrin_rpt
IPR020683 Ankyrin_rpt-contain_dom
IPR036770 Ankyrin_rpt-contain_sf
IPR036859 CAP-Gly_dom_sf
IPR000938 CAP-Gly_domain
PfamiView protein in Pfam
PF12796 Ank_2, 1 hit
PF01302 CAP_GLY, 2 hits
SMARTiView protein in SMART
SM00248 ANK, 3 hits
SM01052 CAP_GLY, 2 hits
SUPFAMiSSF48403 SSF48403, 1 hit
SSF74924 SSF74924, 2 hits
PROSITEiView protein in PROSITE
PS50297 ANK_REP_REGION, 1 hit
PS50088 ANK_REPEAT, 1 hit
PS00845 CAP_GLY_1, 2 hits
PS50245 CAP_GLY_2, 2 hits

Sequencei

Sequence statusi: Complete.

Q96DZ5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTKTDPAPMA PPPRGEEEEE EEEDEPVPEA PSPTQERRQK PVVHPSAPAP
60 70 80 90 100
LPKDYAFTFF DPNDPACQEI LFDPQTTIPE LFAIVRQWVP QVQHKIDVIG
110 120 130 140 150
NEILRRGCHV NDRDGLTDMT LLHYACKAGA HGVGDPAAAV RLSQQLLALG
160 170 180 190 200
ADVTLRSRWT NMNALHYAAY FDVPDLVRVL LKGARPRVVN STCSDFNHGS
210 220 230 240 250
ALHIAASSLC LGAAKCLLEH GANPALRNRK GQVPAEVVPD PMDMSLDKAE
260 270 280 290 300
AALVAKELRT LLEEAVPLSC ALPKVTLPNY DNVPGNLMLS ALGLRLGDRV
310 320 330 340 350
LLDGQKTGTL RFCGTTEFAS GQWVGVELDE PEGKNDGSVG GVRYFICPPK
360 370 380 390 400
QGLFASVSKI SKAVDAPPSS VTSTPRTPRM DFSRVTGKGR REHKGKKKTP
410 420 430 440 450
SSPSLGSLQQ RDGAKAEVGD QVLVAGQKQG IVRFYGKTDF APGYWYGIEL
460 470 480 490 500
DQPTGKHDGS VFGVRYFTCP PRHGVFAPAS RIQRIGGSTD SPGDSVGAKK
510 520 530 540
VHQVTMTQPK RTFTTVRTPK DIASENSISR LLFCCWFPWM LRAEMQS
Length:547
Mass (Da):59,560
Last modified:October 17, 2006 - v3
Checksum:iA718D9673EC1CF4B
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_027962175D → V1 PublicationCorresponds to variant dbSNP:rs17851002Ensembl.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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.3 human

Keywords - Coding sequence diversityi

Polymorphism

Similar proteinsi

Entry informationi

Entry nameiCLIP3_HUMAN
AccessioniPrimary (citable) accession number: Q96DZ5
Secondary accession number(s): A8K0E4
, Q8WWL1, Q96C99, Q9UFT7
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 10, 2006
Last sequence update: October 17, 2006
Last modified: June 20, 2018
This is version 149 of the entry and version 3 of the sequence. See 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

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

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