CLIP4

Last updated
CLIP4 protein predicted tertiary structure. Taken from PhyreRisk. CLIP4 tertiary structure.png
CLIP4 protein predicted tertiary structure. Taken from PhyreRisk.
CLIP4
Available structures
PDB Ortholog search: PDBe RCSB
Identifiers
Aliases CLIP4 , RSNL2, CAP-Gly domain containing linker protein family member 4
External IDs MGI: 1919100; HomoloGene: 11662; GeneCards: CLIP4; OMA:CLIP4 - orthologs
Orthologs
SpeciesHumanMouse
Entrez

79745

78785

Ensembl

ENSG00000115295

ENSMUSG00000024059

UniProt

Q8N3C7

Q8CI96

RefSeq (mRNA)

NM_001287527
NM_001287528
NM_024692

NM_001271483
NM_001271484
NM_030179
NM_175378

RefSeq (protein)

NP_001274456
NP_001274457
NP_078968

NP_001258412
NP_001258413
NP_084455
NP_780587

Location (UCSC) Chr 2: 29.1 – 29.2 Mb Chr 17: 72.08 – 72.17 Mb
PubMed search [4] [5]
Wikidata
View/Edit Human View/Edit Mouse

CAP-Gly Domain Containing Linker Protein Family Member 4 is a protein that in humans is encoded by the CLIP4 gene. [6] In terms of conserved domains, the CLIP4 gene contains primarily ankyrin repeats and the eponymous CAP-Gly domains. [6] The structure of the CLIP4 protein is largely made up of coil, with alpha helices dominating the rest of the protein. [7] CLIP4 mRNA expression occurs largely in the adrenal cortex and atrioventricular node. [8] The literature encompassing CLIP4's conserved domains and paralogs points toward microtubule regulation as a possible function of CLIP4.

Contents

Gene

The human CLIP4 gene, also known as Restin-Like Protein 2 (RSNL2), [9] is located on the plus strand of the short (p) arm of chromosome 2 at region 2, band 3 [9] from base pair 29,096,676 to base pair 29,189,643. CLIP4 is 92,968 base pairs in length and consists of 23 exons. [9]

Transcript

Transcript variants

TranscriptmRNA size (nucleotides)
CLIP4 transcript variant 1 [10] 4299
CLIP4 transcript variant 2 [11] 4295
CLIP4 transcript variant 3 [12] 2353

Protein

The human CLIP4 protein is 705 amino acids in length and is composed of two main types of conserved domains: Two CAP-Gly domains and numerous ankyrin repeats. [9] The secondary structure of CLIP4 consists largely of random coil, with alpha helices as the second-most abundant structure and beta sheets as the third-most abundant structure. [7]

The isoelectronic point of the unprocessed CLIP4 protein is slightly basic (8.62 pI), meaning there is a slight excess of basic amino acids compared to acidic amino acids. [13] The molecular weight is about 65 kD. [13] The most abundant amino acid in CLIP4 is Serine, which makes up 10.7% of the protein. [14] Aligned matching blocks of separated, tandem, and periodic repeats are found between positions 340-345 and 542-547, as well as 447-547 and 564-568. [14] The unusual 9-figure periodic element of a singular Lysine followed by eight other amino acids occurs five times within the protein when compared to the swp23s.q dataset. [14] Another unusual phenomenon is a 7-figure periodic element of a negatively charged amino acid followed by six other hydrophobic amino acids, which occurs six times within the protein when compared to the swp23s.q dataset. [14] There are two instances of Serine spacing and two instances of Phenylalanine spacing that comprise unusually large distances when compared to the swp23s.q dataset. [14]

Protein isoforms

IsoformProtein size (amino acids)
CLIP4 isoform 1 [15] 705
CLIP4 isoform 2 [16] 599

Expression

CLIP4 RNA expression is consistently measured to a high degree in the thyroid. [6] Additionally, high degrees of transcription occur in the adrenal cortex and atrioventricular node. [8] The Human Protein Atlas points toward high RNA expression values in the muscle tissues, as well as some in the skin, endocrine tissues, and proximal digestive tract. [17] Greatest protein expression values appeared in the muscle tissues as well, in addition to some in the lung, gastrointestinal tract, liver & gallbladder, and bone marrow & lymphoid tissues. [17]

CLIP4 protein expression seems to be highly expressed during Ada3 deficiency. [18] There also exists a higher trend towards higher CLIP4 expression in the absence of U28. [18]

Regulation

Gene

Common transcription factor binding sites

These transcription factors were chosen and organized based on proximity to the promoter and matrix similarity. [19]

Transcription FactorDetailed Matrix InfoAnchor BaseMatrix SimilaritySequence
NOLFEarly B-cell factor 1


17
0.98taagagTCCCcagggcagaaaca


PAX2Zebrafish PAX2 paired domain protein


180.8aagagtccccagggcagAAACaa


AP2FTranscription factor AP-2, alpha


160.98ctgcCCTGgggactc


AP2FTranscription factor AP-2, beta


160.899gagTCCCcagggcag


SORYSRY (sex-determining region Y) box 9, dimeric binding sites


350.768aAACAaaatccagtgagggagag


HNF6CUT-homeodomain transcription factor Onecut-2


320.827aaacaaAATCcagtgag


PAX5B-cell-specific activator protein


400.815acaaaaTCCAgtgagggagagatgcaggg


ZF16PR/SET domain 15


360.852aaatccagtgaGGGA


SORYHMGI(Y) high-mobility-group protein I (Y), architectural transcription factor organizing the framework of a nuclear protein-DNA transcriptional complex


780.945tggaAATTttctaccttaggagc


NFATNuclear factor of activated T-cells 5


830.955ttttGGAAattttctacct


NFATNuclear factor of activated T-cells 5


830.871aggtAGAAaatttccaaaa


CEBPCCAAT/enhancer binding protein (C/EBP), epsilon


890.975agccttttGGAAatt


CAATCellular and viral CCAAT box


1100.91gcagCCATttaatct


CAATAvian C-type LTR CCAAT box            


1650.875cccaCCAAgcagtgg


CEBPCCAAT/enhancer binding protein (C/EBP), gamma


6500.866ctaaTTGCtcaacgt


CEBPCCAAT/enhancer binding protein alpha


6510.971cacgttgaGCAAtta


VTBPMammalian C-type LTR TATA box


6800.903tgctgTAAAaggcctaa


TF2BTranscription factor II B (TFIIB) recognition element


9831ccgCGCC


TF2BTranscription factor II B (TFIIB) recognition element


11571ccgCGCC


TF2BTranscription factor II B (TFIIB) recognition element


12281ccgCGCC


Transcriptional

The human CLIP4 mRNA sequence has 12 stem-loop structures in its 5' UTR and 13 stem-loop structures in its 3' UTR. Of those secondary structures, there are 12 conserved stem-loop secondary structures in the 5'UTR as well as 1 conserved stem-loop secondary structure in the 3' UTR. [20]

Protein

The human CLIP4 protein is localized within the cellular nuclear membrane. [21] CLIP4 does not have a signal peptide due to its intracellular localization. [22] It also does not have N-linked glycosylation sites for that same reason. [23] CLIP4 is not cleaved. [24] However, numerous O-linked glycosylation sites are present. [25] A high density of phosphorylation sites are present in the 400-599 amino acid positions on the CLIP4 protein, although many are also present throughout the rest of the protein. [26]

Function

CAP-Gly domains are often associated with microtubule regulation. [27] In addition, ankyrin repeats are known to mediate protein-protein interactions. [28] Furthermore, CLIP1, a paralog of CLIP4 in humans, is known to bind to microtubules and regulate the microtubule cytoskeleton. [29] The CLIP4 protein is also predicted to interact with various microtubule-associated proteins. [30] As a result, it is likely that the CLIP4 protein, although uncharacterized, is associated with microtubule regulation.

Interacting Proteins

The CLIP4 protein is predicted to interact with many proteins associated with microtubules; namely, MAPRE1, MAPRE2, and MAPRE3. It is also predicted to interact with CKAP5 and DCTN1, a cytoskeleton-associated protein and dynactin-associated protein respectively. [30]

Clinical significance

Importance in various cancers

CLIP4 activity is correlated with the spread of renal cell carcinomas (RCCs) within the host and could therefore be a potential biomarker for RCC metastasis in cancer patients. [31] Additionally, measurement of promotor methylation levels of CLIP4 using a Global Methylation DNA Index reveals that higher methylation of CLIP4 is associated with an increase in severity of gastritis to possibly gastric cancer. [32] This indicates that CLIP4 could be used for early detection of gastric cancer. [33] A similar finding was also documented for prostate cancer, in which CLIP4 was found to be hypermethylated in patients with prostate cancer. [34]

Importance in other diseases

The presence of CLIP4 was found to be highly increased in samples with predicted severe fibrosis as a result of Chronic Hepatitis C virus (HCV). [35] Additionally, the presence of CLIP4 as a novel self-antigen in Systemic Lupus Arythematosus points to it having a potential role in the disease mechanism. [36]

Homology

CLIP4 orthologs

These orthologs were chosen and organized based on estimated date of divergence from the human protein as well as the global sequence identity. [37]

Binomial NomenclatureCommon NameTaxonomic GroupEstimated DoD from Human (MYA)Accession NumberSequence Length (AA)Global Sequence Identity to Human Protein (%)Global Sequence Similarity to Human Protein (%)
Homo sapiens (Hsa)HumanPrimate0AAP97312601100100
Aotus nancymaae (Ana)Ma's night monkeyPrimate43.2XP_01233089570483.583.7
Sorex araneus (Sar)Common shrewEulipotyphla96XP_0046200567077478.5
Antrostomus carolinensis (Aca)Chuck-will's-widowAves312XP_02894299770266.575.4
Gekko japonicus (Gja)Schlegel's Japanese geckoReptilia312XP_01527036670263.873.1
Rhinatrema bivittatum (Rbi)Two-lined caecilianAmphibians351.8XP_02944886270759.570.5
Callorhinchus milii (Cmi)Elephant sharkChondrichthyes473XP_00789501671552.565.6
Branchiostoma floridae (Bfl)Florida lanceletLeptocardii684XP_00260682448140.452.8
Saccoglossus kowalevskii (Sko)Acorn wormEnteropneusta684XP_00682268664835.747.5
Ixodes scapularis (Isc)Black-legged tickArachnid797XP_02983109052738.953
Limulus polyphemus (Lpo)Atlantic horseshoe crabArachnid797XP_0137863764623851.6
Lottia gigantea (Lgi)Owl limpet  Gastropods797XP_00904684366936.349.3
Mizuhopecten yessoensis (Mye)Yesso scallopBivalvia797XP_02135974763335.447.2
Parasteatoda tepidariorum (Pte)Common house spiderArachnid797XP_01591496661634.747.6
Aplysia californica (Aca)California sea hareGastropods797XP_01294534665333.745.7
Crassostrea virginica (Cvi)Eastern oysterBivalvia797XP_02231587964632.745.1
Tetranychus urticae (Tur)Two-spotted spider miteArachnid797XP_01579053665231.943.5
Centruroides sculpturatus (Csc)Bark scorpionArachnid797XP_02322948460530.643.4
Penaeus vannamei (Pva)Pacific white shrimpMalacostracans797XP_02720674668122.934
Monosiga brevicollis (Mbr)ChoanoflagellateChoanoflagellatea1023XP_00174858057625.340.8

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References

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  2. 1 2 3 GRCh38: Ensembl release 89: ENSG00000115295 – Ensembl, May 2017
  3. 1 2 3 GRCm38: Ensembl release 89: ENSMUSG00000024059 – Ensembl, May 2017
  4. ↑ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  5. ↑ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  6. 1 2 3 "CLIP4 CAP-Gly domain containing linker protein family member 4 [Homo sapiens (human)] - Gene - NCBI". ncbi.nlm.nih.gov. Retrieved 2020-05-01.
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  8. 1 2 "BioGPS - your Gene Portal System". biogps.org. Retrieved 2020-05-01.
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  10. ↑ "Homo sapiens CAP-Gly domain containing linker protein family member 4 (CLIP4), transcript variant 1, mRNA". 2020-04-25.{{cite journal}}: Cite journal requires |journal= (help)
  11. ↑ "Homo sapiens CAP-Gly domain containing linker protein family member 4 (CLIP4), transcript variant 2, mRNA". 2020-04-25.{{cite journal}}: Cite journal requires |journal= (help)
  12. ↑ "Homo sapiens CAP-Gly domain containing linker protein family member 4 (CLIP4), transcript variant 3, mRNA". 2020-04-25.{{cite journal}}: Cite journal requires |journal= (help)
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  14. 1 2 3 4 5 "SAPS < Sequence Statistics < EMBL-EBI". ebi.ac.uk. Retrieved 2020-05-03.
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  16. ↑ "CAP-Gly domain-containing linker protein 4 isoform 2 [Homo sapiens] - Protein - NCBI". ncbi.nlm.nih.gov. Retrieved 2020-05-03.
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  27. ↑ Weisbrich A, Honnappa S, Jaussi R, Okhrimenko O, Frey D, Jelesarov I, et al. (October 2007). "Structure-function relationship of CAP-Gly domains". Nature Structural & Molecular Biology. 14 (10): 959–67. doi:10.1038/nsmb1291. PMID   17828277. S2CID   37088265.
  28. ↑ Li J, Mahajan A, Tsai MD (December 2006). "Ankyrin repeat: a unique motif mediating protein-protein interactions". Biochemistry. 45 (51): 15168–78. doi:10.1021/bi062188q. PMID   17176038.
  29. ↑ "UniProtKB - P30622 (CLIP1_HUMAN)". UniProt. Archived from the original on 2010-12-16. Retrieved 3 May 2020.
  30. 1 2 "CLIP4 protein (human) - STRING interaction network". string-db.org. Retrieved 2020-05-03.
  31. ↑ "CLIP4 - CAP-Gly domain-containing linker protein 4 - Homo sapiens (Human) - CLIP4 gene & protein". uniprot.org. Retrieved 2020-05-01.
  32. ↑ Pirini F, Noazin S, Jahuira-Arias MH, Rodriguez-Torres S, Friess L, Michailidi C, et al. (June 2017). "Early detection of gastric cancer using global, genome-wide and IRF4, ELMO1, CLIP4 and MSC DNA methylation in endoscopic biopsies". Oncotarget. 8 (24): 38501–38516. doi:10.18632/oncotarget.16258. PMC   5503549 . PMID   28418867.
  33. ↑ Pirini F, Noazin S, Jahuira-Arias MH, Rodriguez-Torres S, Friess L, Michailidi C, et al. (June 2017). "Early detection of gastric cancer using global, genome-wide and IRF4, ELMO1, CLIP4 and MSC DNA methylation in endoscopic biopsies". Oncotarget. 8 (24): 38501–38516. doi:10.18632/oncotarget.16258. PMC   5503549 . PMID   28418867.
  34. ↑ Kron K, Pethe V, Briollais L, Sadikovic B, Ozcelik H, Sunderji A, et al. (2009-03-13). "Discovery of novel hypermethylated genes in prostate cancer using genomic CpG island microarrays". PLOS ONE. 4 (3): e4830. Bibcode:2009PLoSO...4.4830K. doi: 10.1371/journal.pone.0004830 . PMC   2653233 . PMID   19283074.
  35. ↑ Gehrau R, Mas V, Archer K, Maluf D (2012-06-06). "Biomarkers of disease differentiation: HCV recurrence versus acute cellular rejection". Fibrogenesis & Tissue Repair. 5 (Suppl 1): S11. doi: 10.1186/1755-1536-5-S1-S11 . PMC   3368799 . PMID   23259646.
  36. ↑ "Barbara Dema". Discovery Medicine.
  37. ↑ "Nucleotide BLAST: Search nucleotide databases using a nucleotide query". blast.ncbi.nlm.nih.gov. Retrieved 2020-05-03.
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