Helicase SKI2W (SKIV2L)

The protein contains 1246 amino acids for an estimated molecular weight of 137755 Da.

 

Helicase; has ATPase activity. Component of the SKI complex which is thought to be involved in exosome-mediated RNA decay and associates with transcriptionally active genes in a manner dependent on PAF1 complex (PAF1C). (updated: March 4, 2015)

Protein identification was indicated in the following studies:

  1. Goodman and co-workers. (2013) The proteomics and interactomics of human erythrocytes. Exp Biol Med (Maywood) 238(5), 509-518.
  2. Hegedűs and co-workers. (2015) Inconsistencies in the red blood cell membrane proteome analysis: generation of a database for research and diagnostic applications. Database (Oxford) 1-8.
  3. Bryk and co-workers. (2017) Quantitative Analysis of Human Red Blood Cell Proteome. J Proteome Res. 16(8), 2752-2761.
  4. D'Alessandro and co-workers. (2017) Red blood cell proteomics update: is there more to discover? Blood Transfus. 15(2), 182-187.
  5. Chu and co-workers. (2018) Quantitative mass spectrometry of human reticulocytes reveal proteome-wide modifications during maturation. Br J Haematol. 180(1), 118-133.

Methods

The following articles were analysed to gather the proteome content of erythrocytes.

The gene or protein list provided in the studies were processed using the ID mapping API of Uniprot in September 2018. The number of proteins identified and mapped without ambiguity in these studies is indicated below.
Only Swiss-Prot entries (reviewed) were considered for protein evidence assignation.

PublicationIdentification 1Uniprot mapping 2Not mapped /
Obsolete
TrEMBLSwiss-Prot
Goodman (2013)2289 (gene list)227853205992269
Lange (2014)123412347281224
Hegedus (2015)2638262202352387
Wilson (2016)165815281702911068
d'Alessandro (2017)18261817201815
Bryk (2017)20902060101081942
Chu (2018)18531804553621387

1 as available in the article and/or in supplementary material
2 uniprot mapping returns all protein isoforms as one entry

The compilation of older studies can be retrieved from the Red Blood Cell Collection database.

The data and differentiation stages presented below come from the proteomic study and analysis performed by our partners of the GReX consortium, more details are available in their published work.

No sequence conservation computed yet.

Interpro domains
Total structural coverage: 92%
Model score: 45

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VariantDescription
dbSNP:rs438999
a breast cancer sample; somatic mutation
dbSNP:rs437179
dbSNP:rs36038685
THES2
a colorectal cancer sample
dbSNP:rs3911893
dbSNP:rs106287
dbSNP:rs449643
dbSNP:rs2734329
dbSNP:rs2746400

The reference OMIM entry for this protein is 600478

Superkiller viralicidic activity 2, s. cerevisiae, homolog-like; skiv2l
Ski2, s. cerevisiae, homolog of; ski2
Ski2w

CLONING

Lee et al. (1995) identified a human cDNA with sequence homology to the yeast nucleolar protein gene SKI2. SKI2 belongs to a group of 6 yeast genes that repress the copy number of single- and double-stranded RNA viruses. Lee et al. (1995) identified the cDNA by immunoscreening an expression library with a monoclonal antibody raised against bovine pigmented retinal cells. The antibody recognizes a 90-kD nuclear antigen in a number of species. Helicases are involved in DNA replication, DNA repair, recombination, transcription, RNA splicing, and translation. Dangel et al. (1995) cloned a putative human helicase, which they designated SKI2W, that is located between the RD gene (154040) and a gene they called RP1 (D6S60E; see Shen et al., 1994) in the class III region of the major histocompatibility complex on chromosome 6. The gene occurs within an approximately 11-kb span between RD and RP1. The cDNA was isolated from a set of lymphocyte libraries and the predicted 1,246-amino acid protein (137 kD) contains motifs associated with RNA helicases and has a leucine zipper domain. The protein shares extensive similarity (39% identity) to the yeast Ski2p gene which is involved in the inhibition of translation of non-polyadenylated RNA and has an important role in defense against infection by single- and double-stranded RNA viruses. The authors showed that the recombinant SKI2W protein exhibits ATPase activity. Northern blots indicated a 3.9-kb transcript in a variety of human transformed lines. Dangel et al. (1995) stated that this gene was very similar in sequence to that reported by Lee et al. (1995) and that discrepancies between the 2 sequences were probably the result of cloning artifacts. Inherently unstable mammalian mRNAs contain AU-rich elements (AREs) within their 3-prime untranslated regions. In yeast, 3-prime-to-5-prime mRNA degradation is mediated by the exosome, a multisubunit particle. Chen et al. (2001) purified and characterized the human exosome by mass spectrometry and found its composition to be similar to its yeast counterpart. They identified the following protein subunits within the human exosome: p7, which is homologous to the yeast Rrp4 protein (602238); p8, which is homologous to the yeast Rrp42 protein (606488); p9, which is homologous to the yeast Rrp43 protein (OIP2; 606019); p10, which is homologous to the yeast Rrp40 protein (606489); p11, which is homologous to the yeast Mtr3 protein (606490); p12A, which is homologous to the yeast Rrp41 protein (606491); p12B, which is homologous to the yeast Rrp46 protein (606492); and p13, which is homologous to the yeast Csl4 protein (606493). They also identified 2 exosome-associated factors, p1 (SKIV2L) and p14 (MPP6; 605500), that were not homologous to any yeast exosome components.

GENE STRUCTURE

By genomic sequence analysis, Yang et al. (1998) determined that SKIV2L is a polymorphic gene that spans 11 kb and contains 28 exons.

MAPPING

Lee et al. (1995) isolated genomic clones and mapped the human homolog of SKI2 gene to 6p21 by fluorescence in situ hybridization. By genomic sequence analysis, Yang et al. (1998) determined that the SKIV2L gene is located 171 bp downstream from the RD gene.

GENE FUNCTION

Using a cell-free RNA decay system, Chen et al. (2001) demonstrated that the mammalian exosome is required for rapid degradation of ARE-containing RNAs but not for poly(A) shortening. They found that the mammalian exosome ... More on the omim web site

Subscribe to this protein entry history

Feb. 2, 2018: Protein entry updated
Automatic update: Uniprot description updated

Dec. 19, 2017: Protein entry updated
Automatic update: Uniprot description updated

Nov. 23, 2017: Protein entry updated
Automatic update: Uniprot description updated

June 20, 2017: Protein entry updated
Automatic update: comparative model was added.

March 16, 2016: Protein entry updated
Automatic update: OMIM entry 600478 was added.