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Transmembrane protein 53

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Identifiers
Aliases
External IDsGeneCards: [1]
Orthologs
SpeciesHumanMouse
Entrez

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Ensembl

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UniProt

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RefSeq (mRNA)

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RefSeq (protein)

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Location (UCSC)n/an/a
PubMed searchn/an/a
Wikidata
View/Edit Human
transmembrane protein 53
Identifiers
SymbolTMEM53
Alt. symbolsFLJ22353, RP4-678E16.2
Entrez79639
HUGO26186
RefSeqNP_078863
UniProtQ6P2H8
Other data
LocusChr. 1 p34.1

Transmembrane protein 53, or TMEM53, is a protein that is encoded on chromosome 1 in humans.[1] It has no paralogs but is predicted to have many orthologs across eukaryotes.

Properties and Structure[edit | edit source]

General Properties[2][edit | edit source]

  • DUF829 makes up 87% of TMEM53's length
  • Contains a transmembrane domain but lacks a signal peptide
  • Molecular weight 31.6 kilodaltons
  • Isoelectric point 8.56
  • Leucine-rich (14.4% of amino acids are leucines)
  • Predicted to be localized to the nucleus [1]

Secondary Structure[edit | edit source]

The secondary structure of TMEM53 is predicted to consist of alternating pairs of alpha helices and beta sheets.[2]

Alternative Splicing[edit | edit source]

TMEM53 has 3 exons. Twelve alternative splice forms have been identified using 26 alternative exons.[3] The following table includes the predicted post-translational modifications for each isoform.[4]

AceView Splice Form[3] # Amino Acids % ID with RefSeq # of Clones Found DUF829 CK2 sites PKC sites Tyr sites Pumilio site N-Myristoylation sites Extras (not comparable to RefSeq)
a 277 RefSeq 64 X 2 3 1 1 2
b 247 88.8% 6 X 2 2 1 1 2
c 204 64.4% 1 X 2 1 1 1 2 Microbody C-terminal targeting signal
d 204 73.6% 10 X 2 2 1 1 1
e 223 57.5% 2 X 1 4 3
f 143 21.4% 1 X 1 3 3 Amidation site, Asn glycosylation site, cAMP-dependent phosphorylation site
g 142 n/a 1 1 3 1
h 137 45.1% 2 X 1 3 2 Protein prenyltransferase repeat
i 129 32.1% 1 X 4 2
j 139 27.2% 21 X 2 3
k 110 n/a 1 1 4 3 Amidation site, Asn glycosylation site, cAMP-dependent phosphorylation site
l 106 n/a 5 3

Function[edit | edit source]

The function of TMEM53 is not fully understood. It contains a domain of unknown function, DUF829, which is approximately 240 amino acids long. This domain has not been found in proteins other than TMEM53 and its orthologs.

Expression[edit | edit source]

Based on human and mouse EST profiles and a human tissue GEO profile, TMEM53 appears to be expressed ubiquitously at low levels in both normal and cancerous tissues.[5][6][7]

More specific expression patterns have also been observed:

  • Expressed in mice at higher levels in dorsal root ganglia than in the spinal cord[8]
  • Expressed at lower levels in brain tissue with Huntington's disease than in normal brain tissue[9]
  • Expressed at very low levels in the mouse brain, with the areas of highest detectable expression being the hypothalamus, pons, midbrain, and amygdala[10]

Homology[edit | edit source]

Transmembrane protein 53 has no paralogs. It does, however, have orthologs extending throughout eukaryotes, from primates to amoeba. The following table presents a selection of orthologs found using searches in BLAST[11] and BLAT.[12] It is not a comprehensive list, but rather a small selection meant to display the diversity of species in which orthologs are found.

Scientific Name Common Name Accession Number Sequence Length Percent Identity Percent Similarity
Homo sapiens Human NP_078863 277 aa - -
Macaca mulatta Rhesus monkey XP_001093396.1 204 aa 97% 98%
Canis lupus familiaris Dog XP_539639.2 278 aa 88% 92%
Mus musculus Mouse NP_081113.1 276 aa 86% 91%
Monodelphis domestica Opossum XP_001376124.1 405 aa 69% 82%
Gallus gallus Chicken XP_422420.1 276 aa 56% 70%
Xenopus laevis Frog NP_001086490.1 285 aa 54% 69%
Danio rerio Zebrafish NP_001002637.1 281 aa 47% 66%
Ciona intestinalis Sea squirt XP_002127410.1 290 aa 37% 51%
Drosophila melanogaster Fruit fly NP_610178.2 368 aa 35% 56%
Apis mellifera Honey bee XP_392954.1 326 aa 32% 52%
Strongylocentrotus purpuratus Purple sea urchin XP_788598.1 287 aa 32% 52%
Oryza sativa Rice EEC81354.1 412 aa 31% 45%
Nematostella vectensis Sea anemone XP_001628968.1 242 aa 29% 52%
Populus trichocarpa Black cottonwood XP_002306371.1 443 aa 29% 45%
Aspergillus nidulans Fungus XP_657927.1 285 aa 27% 44%
Dictyostelium discoideum Amoeba XP_644630.1 354 aa 27% 44%

Based on ClustalW[2] multiple sequence alignments of 38 orthologs, including the ones above, 11 amino acids are completely conserved throughout all species with this protein.

Predicted Post-Translational Modification[edit | edit source]

Using bioinformatic analysis tools like MyHits Motif Scan[4] and various tools at ExPASy[13] and comparing to multiple sequence alignments, highly conserved potential sites of post-translational modification were identified. The following is not a comprehensive list of predicted modification sites; it includes only the ones that use highly conserved amino acids.

  • CK2 phosphorylation sites 140-143, 217-220
  • Tyrosine phosphorylation sites 209-216, 263
  • PKC phosphorylation site 19-21 conserved in mammals
  • N-myristoylation site 27-32 conserved in mammals
  • N-myristoylation site 153-158 conserved in vertebrates

T216, the tyrosine for a tyrosine phosphorylation site, and S217, the serine for a predicted CK2 phosphorylation site, are completely conserved throughout the protein's evolutionary history.[2] This suggests high likelihood that these sites are real and important for the protein's function.

References[edit | edit source]

  1. ↑ 1.0 1.1 Schirmer EC, Florens L, Guan T, Yates JR, Gerace L (September 2003). "Nuclear membrane proteins with potential disease links found by subtractive proteomics". Science. 301 (5638): 1380–2. doi:10.1126/science.1088176. PMID 12958361.
  2. ↑ 2.0 2.1 2.2 2.3 SDSC Biology Workbench 2.0
  3. ↑ 3.0 3.1 NCBI AceView: TMEM53
  4. ↑ 4.0 4.1 MyHits Motif Scan
  5. ↑ EST Profile Viewer- Human
  6. ↑ EST Profile Viewer- Mouse
  7. ↑ Su AI, Wiltshire T, Batalov S, Lapp H, et al. (April 2004). "A gene atlas of the mouse and human protein-encoding transcriptomes". Proceedings of the National Academy of Sciences, USA. 101 (16): 6062–7. doi:10.1073/pnas.0400782101. PMC 395923. PMID 15075390.
  8. ↑ LeDoux MS, Xu L, Xiao J, Ferrell B, et al. (Aug 2006). "Murine central and peripheral nervous system transcriptomes: comparative expression". Brain Res. 1107 (1): 24–41. doi:10.1016/j.brainres.2006.05.101. PMID 16824496.
  9. ↑ Apostol BL, Illes K, Pallos J, Bodai L, et al. (Jan 2006). "Mutant huntingtin alters MAPK signaling pathways in PC12 and striatal cells: ERK1/2 protects against mutant huntingtin-associated toxicity". Human Molecular Genetics. 15 (2): 273–85. doi:10.1093/hmg/ddi443. PMID 16330479.
  10. ↑ Allen Brain Atlas
  11. ↑ NCBI BLAST: Basic Local Alignment Search Tool
  12. ↑ BLAT Search Genome[permanent dead link]
  13. ↑ ExPASy Proteomics Server
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