EMC1

23065

EMC1
EMC1
Identifiers
AliasesEMC1, KIAA0090, CAVIPMR, ER membrane protein complex subunit 1
External IDsOMIM: 616846; MGI: 2443696; GeneCards: EMC1
Orthologs
DatabasesNCBI: entry; OMA: entry
SpeciesHumanMouse
Entrez

23065

230866

Ensembl

ENSG00000127463

ENSMUSG00000078517

UniProt

Q8N766

Q8C7X2

RefSeq (mRNA)

NM_001039200
NM_146157

RefSeq (protein)

NP_001034289
NP_666269

Location (UCSC)Chr 1: 19.22 – 19.25 MbChr 4: 139.08 – 139.11 Mb
PubMed search[3][4]
Wikidata
View/Edit HumanView/Edit Mouse

ER membrane protein complex subunit 1 is a protein which in humans is encoded by the gene EMC1 (previously KIAA0090).[5] The EMC1 protein is a type I single-pass membrane protein and part of the endoplasmic reticulum membrane protein complex.[5]

Characterization of the KIAA0090 gene and its transcript products

Figure 1: A graphical summary of the KIAA0090 gene neighborhood, regions of promotion, exons/introns, and variant transcript products

KIAA0090 is located on chromosome one in the p arm at location 1p36.132.[6] It covers 36.74 kb, from base pairs 19451486 to 19414744. The gene is composed of 37 gt-at introns/alternative introns with 57 exons expressed in 1 unspliced form of 4253 bp and 20 alternatively spliced forms of varying lengths.[7] The gene has 8 probable promoters.[8] The gene is flanked by UBR4 on its right and MRTO4 on its left.[5] This Information is graphically displayed in Figure 1.

Expressed Sequence Tags and isolated cDNA clones indicate KIAA0090 is expressed ubiquitously in low to moderate levels throughout the body.[9] This includes but is not limited to testis, tongue, lung, cerebellum, brain, mammary gland, trachea, placenta, esophageal, salivary gland, brain, hippocampus, amygdale, bone marrow, thalamus, spleen, uterus, thymus, kidney, eye, heart, gall bladder, prostate, liver, parathyroid gland, ovary, stomach, skeletal muscle, colon, pancreas, and skin. Expression of KIAA0090 changes throughout development (embryogenesis, fetal, adult, etc.)and during carcinogenesis. Evidence indicates a correlation between conditions and expression level but no data exists to suggest KIAA0090 is responsible for any disease or stage of development.

The mRNA for this gene codes for 18 protein isoforms6. The remaining 3 splice variants have no evidence supporting their ability to be translated.

Characterization of the KIAA0090 protein product

Analysis indicates the KIAA0090 unspliced protein product to be 993 amino acids long with an isoelectric point of 7.418 and a molecular weight of 111765.73 daltons.[10][11] The primary structure of this protein contains 4 conserved domains.[12] This includes a signal peptide from position 1 to 22, a COG1520 WD40 like domain, a leucine zipper domain, a DUF1620 domain (domain of unknown function), and a transmembrane domain. These can be viewed in Figure 2. Several conserved cysteine residues are present at positions 226,235, 335, 364,449, 581, 675, 925, and 985.[13] Several internal localization signals are also present.[14][15][16][17][18] Dependent on splice outcome and posttranslational modification, these additional signals indicate the protein could localize to the peroxisome, the plasma membrane, outside the cell, the cytosol, the nucleus, or mitochondria.

Figure 2: An annotated protein map of KIAA0090 with domain residence and function

Post translational modification of KIAA0090 can occur. 54 possible sites of phosphorylation exist; 33 serines, 10 threonines, and 11 tyrosines.[19] 3 sites of N-linked glycosylation are present at residues 370, 818, and 913[20] The signal peptide can be cleaved between residues 21 and 22.[17]

Figure 3: A conceptual translation of KIAA0090 with domains, sites of phosphorylation, sites of N-linked glycosylation, and signal peptide.

This information is graphically displayed in Figure 3. Structure beyond the primary remains predicative. Bioinformatic analysis yields consensus data that is also displayed in Figure 3.[21][22] The protein is highly conserved throughout Eukaryotes both in multi and single cellular organisms. This includes but is not limited to animals, plants, fungi, and protists.

Figure 4: KIAA0090/Protein Interactions

The WD40 like domain COG1520 is KIAA0090s only identified functional effector domain. WD40 containing proteins are signal transducers involved in transduction of signals to binding factors, the centromeres, and other effectors.[23] Coimmunoprecipitation experiments have proven KIAA0090 interaction with these types of proteins; specifically the centromeric protein CENPH, the BAX Inhibitor TMBI4, the ADP ribosylation factor ARF6, the kinase TNIK, and the transcriptional repressor T22D1.[24] The number of splice variants indicates this list is probably not definitive. As further characterization is completed additional interactions would be expected.

References

  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000127463 – Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000078517 – Ensembl, May 2017
  3. ^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  4. ^ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  5. ^ a b c "Enterez Gene, KIAA0090". NCBI. March 2010. Retrieved 2010-03-21.
  6. ^ "Enterez Nucleotide, KIAA0090". NCBI. April 2010. Retrieved 2010-04-23.
  7. ^ "Aceview". NCBI. April 2010. Retrieved 2010-04-23.
  8. ^ Genomatix. "El Dorado, KIAA0090". Genomatix. Archived from the original on 2021-12-02. Retrieved 2010-05-10.
  9. ^ "Unigene, KIAA0090". NCBI. March 2010. Retrieved 2010-04-05.{{cite web}}: CS1 maint: deprecated archival service (link)
  10. ^ AASTATS; Jack Kramer, 1990. http://seqtool.sdsc.edu Archived 2003-08-11 at the Wayback Machine Accessed April 21, 2010
  11. ^ PI; Program by Dr. Luca Toldo, developed at http://www.embl-heidelberg.de. Changed by Bjoern Kindler to print also the lowest found net charge. http://seqtool.sdsc.edu Archived 2003-08-11 at the Wayback Machine Accessed April 22, 2010
  12. ^ "Gene cards". Retrieved 2010-02-14.
  13. ^ Brendel V, Bucher P, Nourbakhsh IR, Blaisdell BE, Karlin S (March 1992). "Methods and algorithms for statistical analysis of protein sequences". Proc. Natl. Acad. Sci. U.S.A. 89 (6): 2002–6. Bibcode:1992PNAS...89.2002B. doi:10.1073/pnas.89.6.2002. PMC 48584. PMID 1549558.
  14. ^ Horton P, Park KJ, Obayashi T, Fujita N, Harada H, Adams-Collier CJ, Nakai K (July 2007). "WoLF PSORT: protein localization predictor". Nucleic Acids Res. 35 (Web Server issue): W585–7. doi:10.1093/nar/gkm259. PMC 1933216. PMID 17517783.
  15. ^ la Cour T, Kiemer L, Mølgaard A, Gupta R, Skriver K, Brunak S (June 2004). "Analysis and prediction of leucine-rich nuclear export signals". Protein Eng. Des. Sel. 17 (6): 527–36. doi:10.1093/protein/gzh062. PMID 15314210.
  16. ^ Bendtsen JD, Jensen LJ, Blom N, Von Heijne G, Brunak S (April 2004). "Feature-based prediction of non-classical and leaderless protein secretion". Protein Eng. Des. Sel. 17 (4): 349–56. doi:10.1093/protein/gzh037. PMID 15115854.
  17. ^ a b Bendtsen JD, Nielsen H, von Heijne G, Brunak S (July 2004). "Improved prediction of signal peptides: SignalP 3.0". J. Mol. Biol. 340 (4): 783–95. CiteSeerX 10.1.1.165.2784. doi:10.1016/j.jmb.2004.05.028. PMID 15223320. {{cite journal}}: Cite uses deprecated parameter |citeseerx= (help)
  18. ^ Gupta R, Brunak S (2002). "Prediction of glycosylation across the human proteome and the correlation to protein function". Pac Symp Biocomput: 310–22. doi:10.1142/9789812799623_0029. ISBN 978-981-02-4777-5. PMID 11928486.{{cite journal}}: CS1 maint: periodical has ISBN (link)
  19. ^ Blom N, Gammeltoft S, Brunak S (December 1999). "Sequence and structure-based prediction of eukaryotic protein phosphorylation sites". J. Mol. Biol. 294 (5): 1351–62. doi:10.1006/jmbi.1999.3310. PMID 10600390.
  20. ^ NetNGlyc; Prediction of N-glycosylation sites in human proteins.R. Gupta, E. Jung and S. Brunak. In preparation, 2004. http://www.cbs.dtu.dk/services/NetNGlyc/ Accessed April 20, 2010.
  21. ^ McGuffin LJ, Bryson K, Jones DT (April 2000). "The PSIPRED protein structure prediction server". Bioinformatics. 16 (4): 404–5. doi:10.1093/bioinformatics/16.4.404. PMID 10869041.
  22. ^ PROF; Aberystwyth University Computational Biology Group. Department of Computer Science, Aberystwyth SY23 3DB, Wales, UK. http://www.aber.ac.uk/~phiwww/prof/ Accessed: April 23, 2010
  23. ^ Neer EJ, Schmidt CJ, Nambudripad R, Smith TF (September 1994). "The ancient regulatory-protein family of WD-repeat proteins". Nature. 371 (6495): 297–300. Bibcode:1994Natur.371..297N. doi:10.1038/371297a0. PMID 8090199. S2CID 600856.
  24. ^ Prieto C, De Las Rivas J (July 2006). "APID: Agile Protein Interaction DataAnalyzer". Nucleic Acids Res. 34 (Web Server issue): W298–302. doi:10.1093/nar/gkl128. PMC 1538863. PMID 16845013.

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