Biology:TMEM106A

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

TMEM106A is a gene that encodes the transmembrane protein 106A (TMEM106A) in Homo sapiens.[1] It is located at 17q21.31 on the plus strand next to cancer-related genes NBR1 and BRCA1.[1][2] The TMEM106A gene contains a domain of unknown function, DUF1356.[1]

Protein structure

The TMEM106A protein has a molecular weight of 28.9 kdal. It has 262 amino acids, 240 of which are in the domain of function.[1] The protein has a transmembrane region.[3] There is evidence for a secondary transmembrane region in humans but this region is not conserved in related orthologs.[4] The protein does not contain a peptide signal protein.[5] The protein structure contains a similar proportion of alpha-helix and beta-strand secondary structures (this does not include transmembrane structures).[6][7]

TMEM106A protein with beta-sheets (red), alpha-helices (blue), and transmembrane region (grey)

There are several areas for post-translational modification for TMEM106A including:

Homology

Paralogs

The TMEM106A gene has two paralogs: TMEM106B and TMEM106C. These paralogs belong to the gene family pfam07092, which belongs to the DUF1356 superfamily. This family consists of several mammalian proteins that are around 250 amino acids in length.[11] TMEM106B and TMEM106C are conserved in invertebrates to mammals.

Protein Accession Number Amino Acids Identity Percent Highest Expression
TMEM106A AAI46977 262 100 Kidney [12]
TMEM106B NP_001127704 274 43 Ubiquitous [13]
TMEM106C AAI07793 231 36 Ubiquitous [14]

Orthologs

Expression of TMEM106A in human tissues[15]

The TMEM106A gene has been found in only the Chordate phylum.[16] Of the three subphyla, TMEM106A is most commonly found in Vertebrata and has also been found in select members of Tunicata, which are invertebrate marine filter feeders. This phylum split occurred 722.5 million years ago.[17] TMEM106A has not been seen in bacteria, plants, or fungi.

Organism Common Name Accession Number Amino Acids Identity Percent Notes
Homo sapiens Human AAI46977.1 262 100 Mammal
Pan troglodytes Chimpanzee XP_001154896.2 262 99.2 Mammal
Pongo abelii Orangutan XP_002827523.1 262 96.2 Mammal
Callithrix jacchus Marmoset XP_002748067.1 262 90.5 Mammal
Canis lupus familiaris Dog XP_548074.2 262 84.8 Mammal
Mus musculus Mouse AAH22145.1 261 66.4 Mammal
Xenopus borealis Marsabit Clawed Frog ACC55056.1 262 59.5 Reptile
Danio rerio Zebrafish AAH50177.1 282 34.5 Fish
Oikopleura dioica Sea-squirt CBY08060.1 249 27.8 Invertebrate

Expression

TMEM106A is expressed in several human tissues. The tissues with highest expression are uterus, kidneys, small intestine, and stomach.[12][18] EST profiles for orthologs show expression is conserved with greatest expression in kidneys and lesser expression in several other areas.[19] Some tissues never show expression including: muscle, adipose tissue, and bone.

Gene neighborhood

In Homo sapiens, TMEM106A is located next to NBR1, a gene identified as an ovarian tumor antigen monitored in ovarian cancer.[20] It is also located near BRCA1, a breast cancer tumor suppressor gene.[21] The first 140 amino acids of the TMEM106A protein, including portions of DUF1356 and a transmembrane region, are deleted along with BRCA1 during early-onset breast cancer.[22]

Gene neighborhood of TMEM106A

References

  1. ↑ 1.0 1.1 1.2 1.3 "Entrez Gene: TMEM106A transmembrane protein 106A". https://www.ncbi.nlm.nih.gov/gene/113277. 
  2. ↑ "Genecards: TMEM106A transmembrane protein 106A". https://www.genecards.org/cgi-bin/carddisp.pl?gene=TMEM106A&search=tmem106a. 
  3. ↑ "PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization". Trends Biochem. Sci. 24 (1): 34–6. January 1999. doi:10.1016/S0968-0004(98)01336-X. PMID 10087920. http://psort.hgc.jp. 
  4. ↑ "Prediction of transmembrane segments in proteins utilising multiple sequence alignments". J. Mol. Biol. 237 (2): 182–92. March 1994. doi:10.1006/jmbi.1994.1220. PMID 8126732. 
  5. ↑ "Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites". Protein Eng. 10 (1): 1–6. January 1997. doi:10.1093/protein/10.1.1. PMID 9051728. 
  6. ↑ "Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins". J. Mol. Biol. 120 (1): 97–120. March 1978. doi:10.1016/0022-2836(78)90297-8. PMID 642007. 
  7. ↑ "Prediction of the secondary structure of proteins from their amino acid sequence". Advances in Enzymology and Related Areas of Molecular Biology. Advances in Enzymology - and Related Areas of Molecular Biology. 47. 1978. 45–148. doi:10.1002/9780470122921.ch2. ISBN 9780470122921. https://archive.org/details/advancesinenzymo0047unse/page/45. 
  8. ↑ "Sequence and structure-based prediction of eukaryotic protein phosphorylation sites". J. Mol. Biol. 294 (5): 1351–62. December 1999. doi:10.1006/jmbi.1999.3310. PMID 10600390. 
  9. ↑ Prediction of N-glycosylation sites in human proteins. 2004. http://www.cbs.dtu.dk/services/NetNGlyc/abstract.php. 
  10. ↑ "Analysis and prediction of mammalian protein glycation". Glycobiology 16 (9): 844–53. September 2006. doi:10.1093/glycob/cwl009. PMID 16762979. 
  11. ↑ "NCBI Conserved Domains: DUF1356". https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam07092. 
  12. ↑ 12.0 12.1 "EST profile: TMEM106A transmembrane protein 106A". https://www.ncbi.nlm.nih.gov/UniGene/ESTProfileViewer.cgi?uglist=Hs.536474. .
  13. ↑ "EST profile: TMEM106B transmembrane protein 106B". https://www.ncbi.nlm.nih.gov/UniGene/ESTProfileViewer.cgi?uglist=Hs.396358. .
  14. ↑ "EST profile: TMEM106C transmembrane protein 106C". https://www.ncbi.nlm.nih.gov/UniGene/ESTProfileViewer.cgi?uglist=Hs.396358. .
  15. ↑ "BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources". Genome Biol. 10 (11): R130. 2009. doi:10.1186/gb-2009-10-11-r130. PMID 19919682. 
  16. ↑ "NCBI Homologene: TMEM106A". https://www.ncbi.nlm.nih.gov/sites/homologene/1699. 
  17. ↑ "TimeTree: a public knowledge-base of divergence times among organisms". Bioinformatics 22 (23): 2971–2. December 2006. doi:10.1093/bioinformatics/btl505. PMID 17021158. http://biogps.org/#goto=genereport&id=113277. 
  18. ↑ "GEO Profiles: TMEM106A transmembrane protein 106A". http://biogps.org/#goto=genereport&id=113277. 
  19. ↑ "EST profiles". https://www.ncbi.nlm.nih.gov/est/. .
  20. ↑ "NBR1 interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB) and shows developmentally restricted expression in the neural tube". Eur. J. Biochem. 269 (2): 538–45. January 2002. doi:10.1046/j.0014-2956.2001.02681.x. PMID 11856312. 
  21. ↑ "A de novo complete BRCA1 gene deletion identified in a Spanish woman with early bilateral breast cancer". BMC Med. Genet. 12: 134. 2011. doi:10.1186/1471-2350-12-134. PMID 21989022. 
  22. ↑ "Identification and comprehensive characterization of large genomic rearrangements in the BRCA1 and BRCA2 genes". Breast Cancer Res. Treat. 122 (3): 733–43. August 2010. doi:10.1007/s10549-009-0613-9. PMID 19894111. https://hal.archives-ouvertes.fr/hal-00535410/file/PEER_stage2_10.1007%252Fs10549-009-0613-9.pdf. 

External links




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