CAP-Gly Domain Containing Linker Protein Family Member 4 is a protein that in humans is encoded by the CLIP4 gene. In terms of conserved domains, the CLIP4 gene contains primarily ankyrin repeats and the eponymous CAP-Gly domains. The structure of the CLIP4 protein is largely made up of coil, with alpha helices dominating the rest of the protein. CLIP4 mRNA expression occurs largely in the adrenal cortex and atrioventricular node. The literature encompassing CLIP4's conserved domains and paralogs points toward microtubule regulation as a possible function of CLIP4.
Gene The human CLIP4 gene, also known as Restin-Like Protein 2 (RSNL2), is located on the plus strand of the short (p) arm of chromosome 2 at region 2, band 3 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.
Transcript
Transcript variants TranscriptmRNA size (nucleotides)CLIP4 transcript variant 14299CLIP4 transcript variant 24295CLIP4 transcript variant 32353
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. 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.
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. The molecular weight is about 65 kD. The most abundant amino acid in CLIP4 is Serine, which makes up 10.7% of the protein. 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. 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. 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. 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.
Protein isoforms IsoformProtein size (amino acids)CLIP4 isoform 1705CLIP4 isoform 2599
Expression CLIP4 RNA expression is consistently measured to a high degree in the thyroid. Additionally, high degrees of transcription occur in the adrenal cortex and atrioventricular node. 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. 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.
CLIP4 protein expression seems to be highly expressed during Ada3 deficiency. There also exists a higher trend towards higher CLIP4 expression in the absence of U28.
Regulation
Gene
Common transcription factor binding sites These transcription factors were chosen and organized based on proximity to the promoter and matrix similarity. Transcription factor Detailed Matrix Info Anchor base Matrix similarity SequenceNOLFEarly B-cell factor 1170.98taagagTCCCcagggcagaaacaPAX2Zebrafish PAX2 paired domain protein180.8aagagtccccagggcagAAACaaAP2FTranscription factor AP-2, alpha160.98ctgcCCTGgggactcAP2FTranscription factor AP-2, beta160.899gagTCCCcagggcagSORYSRY (sex-determining region Y) box 9, dimeric binding sites350.768aAACAaaatccagtgagggagagHNF6CUT-homeodomain transcription factor Onecut-2320.827aaacaaAATCcagtgagPAX5B-cell-specific activator protein400.815acaaaaTCCAgtgagggagagatgcagggZF16PR/SET domain 15360.852aaatccagtgaGGGASORYHMGI(Y) high-mobility-group protein I (Y), architectural transcription factor organizing the framework of a nuclear protein-DNA transcriptional complex780.945tggaAATTttctaccttaggagcNFATNuclear factor of activated T-cells 5830.955ttttGGAAattttctacctNFATNuclear factor of activated T-cells 5830.871aggtAGAAaatttccaaaaCEBPCCAAT/enhancer binding protein (C/EBP), epsilon890.975agccttttGGAAattCAATCellular and viral CCAAT box1100.91gcagCCATttaatctCAATAvian C-type LTR CCAAT box 1650.875cccaCCAAgcagtggCEBPCCAAT/enhancer binding protein (C/EBP), gamma6500.866ctaaTTGCtcaacgtCEBPCCAAT/enhancer binding protein alpha6510.971cacgttgaGCAAttaVTBPMammalian C-type LTR TATA box6800.903tgctgTAAAaggcctaaTF2BTranscription factor II B (TFIIB) recognition element9831ccgCGCCTF2BTranscription factor II B (TFIIB) recognition element11571ccgCGCCTF2BTranscription factor II B (TFIIB) recognition element12281ccgCGCC
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.
Protein The human CLIP4 protein is localized within the cellular nuclear membrane. CLIP4 does not have a signal peptide due to its intracellular localization. It also does not have N-linked glycosylation sites for that same reason. CLIP4 is not cleaved. However, numerous O-linked glycosylation sites are present. 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.
Function CAP-Gly domains are often associated with microtubule regulation. In addition, ankyrin repeats are known to mediate protein-protein interactions. Furthermore, CLIP1, a paralog of CLIP4 in humans, is known to bind to microtubules and regulate the microtubule cytoskeleton. The CLIP4 protein is also predicted to interact with various microtubule-associated proteins. 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.
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. 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. This indicates that CLIP4 could be used for early detection of gastric cancer. A similar finding was also documented for prostate cancer, in which CLIP4 was found to be hypermethylated in patients with prostate cancer.
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). 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.
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. 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)HumanPrimate0AAP97312601100100Aotus nancymaae (Ana)Ma's night monkeyPrimate43.2XP_01233089570483.583.7Sorex araneus (Sar)Common shrewEulipotyphla96XP_0046200567077478.5Antrostomus carolinensis (Aca)Chuck-will's-widowAves312XP_02894299770266.575.4Gekko japonicus (Gja)Schlegel's Japanese geckoReptilia312XP_01527036670263.873.1Rhinatrema bivittatum (Rbi)Two-lined caecilianAmphibians351.8XP_02944886270759.570.5Callorhinchus milii (Cmi)Elephant sharkChondrichthyes473XP_00789501671552.565.6Branchiostoma floridae (Bfl)Florida lanceletLeptocardii684XP_00260682448140.452.8Saccoglossus kowalevskii (Sko)Acorn wormEnteropneusta684XP_00682268664835.747.5Ixodes scapularis (Isc)Black-legged tickArachnid797XP_02983109052738.953Limulus polyphemus (Lpo)Atlantic horseshoe crabArachnid797XP_0137863764623851.6Lottia gigantea (Lgi)Owl limpet Gastropods797XP_00904684366936.349.3Mizuhopecten yessoensis (Mye)Yesso scallopBivalvia797XP_02135974763335.447.2Parasteatoda tepidariorum (Pte)Common house spiderArachnid797XP_01591496661634.747.6Aplysia californica (Aca)California sea hareGastropods797XP_01294534665333.745.7Crassostrea virginica (Cvi)Eastern oysterBivalvia797XP_02231587964632.745.1Tetranychus urticae (Tur)Two-spotted spider miteArachnid797XP_01579053665231.943.5Centruroides sculpturatus (Csc)Bark scorpionArachnid797XP_02322948460530.643.4Penaeus vannamei (Pva)Pacific white shrimpMalacostracans797XP_02720674668122.934Monosiga brevicollis (Mbr)ChoanoflagellateChoanoflagellatea1023XP_00174858057625.340.8
References