Tetratricopeptide repeat 39A
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Tetratricopeptide repeat 39A is a human protein encoded by the TTC39A gene.[1] TTC39A is also known as DEME-6 (differentially expressed in MCF7 with estradiol protein 6), KIAA0452, and c1orf34.[1] The function of TTC39A is currently not well understood. The main feature within tetratricopeptide repeat 39A is the domain of unknown function 3808 (DUF3808), spanning almost the entire protein.[2] KIAA0452 can also be seen as an isoform of TTC39A because of differences in genome sequence, but overlap in DUF domain.[3]
Gene
The gene for TTC39A is located on the first chromosome at 1p32.3.[1] The genomic DNA is 57,859 bases long, consists of 19 exons and is located on the minus strand.[4] The mRNA has a length of 2759 bases.[4] TTC39A is surrounded by genes for RNF11 and EPS15.[2] Neither of these genes have a known interaction or similar function as TTC39A.[2] There are not any known medical disorders resulting from the deletion of TTC39A.[2]
The gene for KIAA0452 is also located on the first chromosome at 1p32.3. The genomic DNA is 34,096 bases long, consists of 11 exons and is located on the minus strand.[5] The mRNA has a length of 6256 bases.[6]
Homology
TTC39A has several orthologs that have been found in eukaryotes, archea, and bacteria.[4] Two paralogs, TTC39B and TTC39C, have also been identified.[4] The functions of TTC39B and TTC39C are not known.[4]
| Species | Common name | Accession number | Length | Protein identity | Protein similarity |
|---|---|---|---|---|---|
| Homo sapiens | Human | NP_001073963.1 | 613aa | 100% | 100% |
| Mus musculus | Mouse | NP_001139420.1 | 578aa | 87.9% | 91.0% |
| Macaca mulatta | Rhesus monkey | XP_002801613.1 | 550aa | 92.0% | 93.0% |
| Gallus gallus | Chicken | XP_422466.3 | 575aa | 71.3% | 81.0% |
| Taeniopygia guttata | Zebra finch | XP_002193183 | 575aa | 73.0% | 82.0% |
| Anolis carolinensis | Green anole | XP_003216860.1 | 570aa | 58.8% | 74.0% |
| Danio rerio | Zebra fish | XP_002663143.1 | 598aa | 60.8% | 76.0% |
| Branchiostoma floridae | Lancelet | XP_002591442.1 | 544aa | 41.1% | 61.0% |
| Physcomitrella patens | Moss | XP_001766901.1 | 601aa | 24.2% | 41.0% |
| Leishmania braziliensis | Euglenozoa | XP_001566995.1 | 584aa | 21.8% | 40.0% |
| Aster yellows | Phytoplasma | AAO61940.1 | 299aa | 15.1% | 42.0% |
KIAA0452 has several similar orthologs as TTC39A from eukaryotes, achea and bacteria but different protein identities and similarities.[5]
| Species | Common name | Accession number | Length | Protein identity | Protein similarity |
|---|---|---|---|---|---|
| Homo sapiens | Human | AB007921 | 453aa | 100% | 100% |
| Homo sapiens | Human | BC028374.2 | 629aa | 99% | 99% |
| Mus musculus | Mouse | AK172951.1 | 574aa | 85% | 87% |
| Macaca mulatta | Rhesus monkey | XP_002801613 | 550aa | 88% | 88% |
| Taeniopygia gutlata | Zebra finch | XP_002193183.2 | 549aa | 72% | 79% |
| Anolis carolinensis | Green anole | XP_003216860.1 | 570aa | 56% | 69% |
| Danio rerio | Zebra fish | XP_002663143 | 598aa | 60% | 71% |
| Branchiostoma floridae | Lanclet | XP_002591442.1 | 544aa | 42% | 62% |
| Physcomitrella patens | Moss | XP_001766901.1 | 601aa | 25% | 41% |
| Leishmania braziliensis | Euglenoza | XP_001566995.1 | 584aa | 28% | 48% |
| Aster yellows | Phytoplasma | AAO61940.1 | 299aa | 24% | 42% |
mRNA features
Promoter
The predicted promoter for the TTC39A gene spans 713 bp from 51,796,048 to 51,796,760.[7]
A predicted promoter for KIAA0452 gene spans 600 bp from 51,796,517 to 51,797,117.[7]
Transcription factors
Below are some of transcription factors that exist for the predicted the promoter sequence.[7]
| Detailed family information | Start | End | Strand |
|---|---|---|---|
| Myeloid zinc finger protein MZF1 | 286 | 296 | + |
| Fork head domain factors FOXK2 | 54 | 70 | - |
| X-linked zinc finger protein ZFX and ZFY | 118 | 128 | - |
| E2F transcription factor 4, p107/p130-binding protein | 475 | 491 | - |
| SPI-1 proto-oncogene; hematopoietic transcription factor PU.1 | 205 | 225 | + |
| Hematopoietically expressed homeobox, proline-rich homeodomain protein | 108 | 126 | + |
Below are some of transcription factors, with similarity of 1, that exist for the predicted promoter sequence.[7][8]
| Detailed family information | Start | End | Strand |
|---|---|---|---|
| AP1 activating protein 1 | 22 | 34 | + |
| Myeloid Zinc finger protein MZF1 | 577 | 587 | + |
| Myeloid transforming protein EVI1
(Ectotropic viral integration site 1 encoded factor, amino-terminal zinc finger domain) |
16 | 32 | + |
| C2H2 xinc finger transcription factor 2 | 539 | 561 | - |
| Fork Head domain factor alternative splice variant of FOXP1 (activated in ESCs) | 410 | 426 | - |
| Pleomorphic adenoma gene 1 | 209 | 231 | + |
Protein
The longest protein sequence consists of 613 amino acids.[9] Within TTC39A, there is a domain of unknown function, DUF 3808.[9] DUF 3808 is generally considered to be an outer mitochondrial membrane protein and has been conserved from fungi to humans.[9] DUF 3808 also contains a tetratricopeptide, TPR_16 and a predicted transmembrane domain.[9][10] The structure of TTC39A is predicted to have 12 alpha helices and a single beta sheet.[11]
KIAA0452 has a protein sequence with 453 amino acids.[12] The structure of KIAA0452 is predicted to have 11 alpha helices and 9 beta sheets.[11] KIAA0452 overlaps TTC39A via a domain of unknown function, DUF 3808.[9] KIAA0452 has a predicted molecular weight of 49.4 kdal [13] and an isoelectric point of 6.766000.[14]
Expression
There are 17 splice variants for TTC39A.[15] TTC39A is a highly expressed protein in the human body.[15] The highest levels of expression are located in mammary glands and testis.[9] The lowest levels of expression are found in the immune system.[9]
KIAA0452 expression is most prevalent in the brain, with the highest levels in the trigeminal ganglion and occipital lobe[16]
TTC39A is induced by TFAP2C in hormone responsive breast carcinoma cells[17] and TTC39A is expressed in estrogen receptor positive carcinoma cell lines.[18]
Post translational modifications
There are several predicted phosphorylation sites but none have been experimentally confirmed.[19] A single sulfination site is predicted at position 175.[20]
KIAA0452 has a single N-acetalation site at position 274.[21]
Interactions
TTC39A has been found to interact with BTNL2[22] and MAPK3.[23]
References
- ↑ 1.0 1.1 1.2 HUGO Gene Nomenclature Committee. "TTC39A". Gene Symbol Report. Human Genome Organisation.
- ↑ 2.0 2.1 2.2 2.3 "National Center of Biotechnology Information".
- ↑ "UCSC Genome Browser Aceview".
- ↑ 4.0 4.1 4.2 4.3 4.4 "TTC39A Gene". GeneCards Human Gene Database. Weizmann Institute of Science.
- ↑ 5.0 5.1 "Gene/Protein Characteristic Table for KIAA0452".
- ↑ "National Center of Biotechnology Information".
- ↑ 7.0 7.1 7.2 7.3 "Gene2Promoter". Genomatix.
- ↑ "GemsLauncher". Genomatrix.
- ↑ 9.0 9.1 9.2 9.3 9.4 9.5 9.6 "TTC39A tetratricopeptide repeat domain 39A [Homo sapiens]". NCBI Gene Report. National Center for Biotechnology Information.
- ↑ "San Diego Biology Workbench". Predicted transmembrane domains.[permanent dead link]
- ↑ 11.0 11.1 "San Diego Supercomputer Biology Workbench Pele".
- ↑ "KIAA0452 protein [Homo sapiens]".
- ↑ "San Diego Biology Workbench SAPs".[permanent dead link]
- ↑ "San Diego Biology Workbench PI".[permanent dead link]
- ↑ 15.0 15.1 "Aceview".
- ↑ "Large-scale analysis of the human transcriptome (HG-U133A".
- ↑ Woodfield GW, Chen Y, Bair TB, Domann FE, Weigel RJ (October 2010). "Identification of primary gene targets of TFAP2C in hormone responsive breast carcinoma cells". Genes Chromosomes Cancer. 49 (10): 948–62. doi:10.1002/gcc.20807. PMC 2928401. PMID 20629094.
- ↑ Kuang WW, Thompson DA, Hoch RV, Weigel RJ (February 1998). "Differential screening and suppression subtractive hybridization identified genes differentially expressed in an estrogen receptor-positive breast carcinoma cell line". Nucleic Acids Res. 26 (4): 1116–23. doi:10.1093/nar/26.4.1116. PMC 147366. PMID 9461476.
- ↑ "Netphos".
- ↑ "Expasy Sulfinator".
- ↑ "Expasy NetAcet".
- ↑ "TTC39A". STRING: functional protein association networks.
- ↑ von Kriegsheim A, Baiocchi D, Birtwistle M, Sumpton D, Bienvenut W, Morrice N, Yamada K, Lamond A, Kalna G, Orton R, Gilbert D, Kolch W (December 2009). "Cell fate decisions are specified by the dynamic ERK interactome". Nat. Cell Biol. 11 (12): 1458–64. doi:10.1038/ncb1994. PMC 3839079. PMID 19935650.