Biology:TMTC4

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A representation of the 3D structure of the protein myoglobin showing turquoise α-helices.
Generic protein structure example

Transmembrane and Tetratricopeptide repeat containing 4 is a protein that in humans is encoded by the TMTC4 gene.[1] This protein crosses the plasma membrane 10 times, and resides in the ER lumen and cytosol. The predicted structure of the TMTC4 protein is a series of alpha-helices.

Gene

TMTC4 is located on chromosome 13 at 13q32.3. The gene is flanked by ADP ribosylation factor 4 pseudogene 3 (ARF4P3) on the left, and ribosomal protein S26 pseudogene 47 (RPS26P47) on the right. TMTC4 spans 4043 bp and has a total of 23 exons.[1]

mRNA

TMTC4 has seven isoform variants, the most common being isoform 1 at 4043 bp.[1]

Isoform Length (bp)
1 4043
2 3833
3 3500
4 4217
5 4120
6 4037
7 3827

The 5’ UTR for TMTC4 is short and in many of the shorter isoforms, portions of this untranslated region are cut. In comparison, the 3’ UTR is long and is often complete across the seven isoforms.

Protein

Physical properties

The molecular weight for TMTC4 is 85.0 kdal, and there are no positive, negative, or neutral clusters of amino acids or charge runs exceeding the normal lengths. When looking at a distant ortholog (purple sea urchin) the molecular weight of TMTC4 is 85.5 kdal and there, again, are no charge runs, positive, negative or neutral clusters, or unusual spacings. There are strong similarities in protein composition across species. The isoelectric point for the domain of unknown function (DUF 1736) is lower than that of the protein overall.

Schematic illustration of known and predicted domains and motifs for TMTC4
Domain Amino Acids Molecular Weight (kdal) Isoelectric Point
Human TMTC4 760 85.0 9.135
DUF 1736 75 8.6 4.123
TPR repeats 234 26.7 9.509

Domains

Predicted secondary structure of TMTC4. Starting at blue and going to red, the diagram illustrates the n-terminus through the c-terminus.

TMTC4 has ten transmembrane regions, all of them spaced within the first half of the protein.[2]

TMTC4 is layered with tetratricopeptide (TPR) repeat sequences that are a part of the TPR superfamily of proteins. DUF1736 is present upstream of the TPR region. A seven residue repeat (SRR) is located toward the end of the protein, and it is thought to encode a coiled-coil structure.[3] Another member of the TPR family, PFTA (protein prenyltransferases alpha subunit repeat), is located within the protein’s TPR region and is believed to be involved in signal transduction and vesicular traffic regulation.[4] LSPR coagulation factor V, also a repeat motif, is located within the TPR region, and is thought to be a central regulator of hemostasis.[5]

Secondary structure

TMTC4 takes on a series of alpha-helix structures, especially within the TPR region, though there are a minimal amount of beta-strand structures spaced throughout the beginning half of the protein.[6]

Post-translational modifications

Predicted post-translational modifications of TMTC4 protein

There are four predicted nuclear localization signals, each tagging the protein for nuclear import.[2] At the very end of the protein, however, there is a predicted ER retention signal which would prevent the protein from leaving the ER. The protein has three predicted N-glycosylation sites, potentially altering its structure and function and there are ten predicted phosphorylation sites, each a possible activation site for a regulatory mechanism.[2]

Expression

TMTC4 is expressed in all human tissues. The gene, however, is most highly expressed in the brain and in the spinal cord.[7]

Protein abundance seems to be lower than normal for TMTC4.

Regulation

There is one possible promoter for the TMTC4 gene, located in the 5’ UTR but before the start of the coding sequence.

Function

Currently the function of TMTC4 has not been characterized.

Interacting proteins

Possible interacting proteins are NRG1, PEX19, HERC3, TXNDC15, and COL1A1 . All of these were detected through affinity chromatography.[8]

Protein Name Known function Location
Neuregulin 1 [NRG1] mediates cell to cell signaling[9] membrane glycoprotein[9]
Peroxisomal Biogenesis Factor 19 [PEX19] cytosolic chaperone[10] membrane receptor protein[10]
ECT And RLD Domain Containing E3 Ubiquitin Protein Ligase 3 [HERC3] member of the ubiquitin ligase family[11] cytosol[11]
Thioredoxin Domain Containing 15 [TXNDC15] Not known Not known
Collagen Type I Alpha 1 Chain [COL1A1] triple helix collagen protein[12] extracellular[12]

Homology

Orthologs

Ortholog space for TMTC4 spans a large portion of evolutionary time. TMTC4 is present in mammals, reptiles, amphibians, birds, fish, and invertebrates. It is not present in plants, bacteria, archaea, or fungi.[13]

Sequence Number Genus and Species Common Name Accession # (protein) Identity Date of Divergence (MYA)
1 Heterocephalus glaber Naked mole rat EHB03258.1 88% 94
2 Rattus norvegicus Brown rat NP_001127886.1 90% 94
3 Myotis brandtii Brandt's bat EPQ01527.1 90% 94
4 Pteropus alecto Black flying fox XP_006909447.1 93% 88
5 Erinaceus europaeus European hedgehog XP_016040457.1 85% 94
6 Sorex araneus Common shrew XP_004614101.1 86% 94
7 Sus scrofa Wild boar NP_001239134.1 91% 94
8 Lipotes vexillifer Baiji XP_007461591.1 90% 88
9 Ailuropoda melanoleuca Giant panda XP_019650336.1 90% 94
10 Acinonyx jubatus Cheetah XP_014931490.1 93% 94
11 Tyto alba Barn owl KFV56414.1 85% 320
12 Charadrius vociferus Killdeer KGL87053.1 84% 320
13 Python bivittatus Burmese python XP_007425712.1 81% 320
14 Anolis carolinensis Carolina anole XP_008105174.1 82% 320
15 Xenopus tropicalis Western clawed frog NP_001121486.1 38% 353
16 Nanorana parkeri Nanorana parkeri XP_018432106.1 73% 353
17 Callorhinchus milii Australian ghostshark XP_007885231.1 68% 465
18 Crassostrea gigas Pacific oyster XP_011422949.1 50% 758
19 Strongylocentrotus purpuratus Purple sea urchin XP_011670776.1 49% 627

Paralogs

Paralog space for TMTC4 spans the gene family TMTC. There are four genes in this gene family: TMTC1, TMTC2, TMTC3, and TMTC4. TMTC1 and TMTC3 split from TMTC4 about 1200 million years ago, while TMTC2 split from TMTC4 1400 million years ago. Both of these events happened somewhere between invertebrates and plants.

References

  1. ↑ 1.0 1.1 1.2 "TMTC4 transmembrane and tetratricopeptide repeat containing 4". Entrez Gene. https://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=84899. 
  2. ↑ 2.0 2.1 2.2 "Motif Scan". Swiss Institute of Bioinformatics. http://myhits.isb-sib.ch/cgi-bin/motif_scan. 
  3. ↑ "Structural specificity in coiled-coil interactions". Current Opinion in Structural Biology 18 (4): 477–83. 2008. doi:10.1016/j.sbi.2008.04.008. PMID 18555680. 
  4. ↑ "The alpha-subunit of protein prenyltransferases is a member of the tetratricopeptide repeat family". Protein Science 8 (8): 1658–67. August 1999. doi:10.1110/ps.8.8.1658. PMID 10452610. 
  5. ↑ "Coagulation factor V, LSPD (IPR009271)". InterPro. EMBL-EBI. http://www.ebi.ac.uk/interpro/entry/IPR009271. 
  6. ↑ "I-TASSER results". I-TASSER. University of Michigan. http://zhanglab.ccmb.med.umich.edu/I-TASSER/output/S325695/j2663g/. 
  7. ↑ "2906582". GEO Profiles. NCBI. https://www.ncbi.nlm.nih.gov/geoprofiles/2906582. 
  8. ↑ "The BioPlex Network: A Systematic Exploration of the Human Interactome". Cell 162 (2): 425–40. July 2015. doi:10.1016/j.cell.2015.06.043. PMID 26186194. 
  9. ↑ 9.0 9.1 "NRG1 Gene". GeneCards. https://www.genecards.org/cgi-bin/carddisp.pl?gene=nrg1. 
  10. ↑ 10.0 10.1 "PEX19 Gene". GeneCards. https://www.genecards.org/cgi-bin/carddisp.pl?gene=pex19. 
  11. ↑ 11.0 11.1 "HERC3 Gene". GeneCards. https://www.genecards.org/cgi-bin/carddisp.pl?gene=herc3. 
  12. ↑ 12.0 12.1 "COL1A1 Gene". GeneCards. https://www.genecards.org/cgi-bin/carddisp.pl?gene=col1a1. 
  13. ↑ "BLAST: Basic Local Alignment Search Tool". NCBI. https://blast.ncbi.nlm.nih.gov/Blast.cgi. 

Further reading




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