Biology:Coiled-coil domain-containing protein 135

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Short description: Protein found in humans


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


Coiled-coil domain-containing protein 135, also known as CCDC135, is a protein that in humans is encoded by the CCDC135 gene.[1][2]

Gene

CCDC90B is located on chromosome 16 in humans. It is neighbored by:[3]

  • GPR97, G protein-coupled receptor 97.
  • GPR56, encodes a member of the G protein coupled receptor family (G protein-coupled receptor 56). The gene is implicated in the regulation of brain cortical patterning. The protein binds specifically to transglutaminase 2 in the extracellular space.
  • KATNB1, katanin p80 subunit B 1. An accessory protein that helps targets the enzyme to the centrosome.
  • KIFC3, kinesin family member C3 isoform 3. KIFC3 belongs to the large superfamily of kinesins, molecular motors that use the energy of ATP hydrolysis to translocate cargoes along microtubules.

Protein

Structure

This protein is characterized by the presence of two domains.[4]

  • Nuclear localization sequence with a Score of 4 in the amino acids 265–279. The amino acid sequence for this region is:

KKQQEIRAQEKKRLR

  • Transglutaminase-like family with an E Value of 0.0018 in the amino acids 149–308. The amino acid sequence for this region is:

CAQFVSDFLTMVPLPDPLKPPSHLYSSTTVLKYQKGNCFDFSTLLCSMLIGSGYDAYCVNGYGSLDLCHMDLTREVCPLTVKPKETIKKEEK VLPKKYTIKPPRDLCSRFEQEQEVKKQQEIRAQEKKRLREEEERLMEAEKAKPDALHGLRVHSWVLVL

The protein has 17 predicted alpha helices sites, a characteristic of coiled-coil proteins, and 1 predicted beta-pleated sheet. The following image shows the predicted regions of alpha helices and beta pleated sheets by two programs STRAP[5] and Quickphyre:[6] Note: the consensus secondary structures are shown. This was carried out by constructing a multiple sequence alignment of the proteins with their secondary structures (as shown below). The predicted regions were then cross checked with the Quickphyre Program.

Secondary Structure CCDC135.gif

Homology

A sequence annotation of CCDC135.

LRRC57 is exceedingly well conserved, as shown in the sequence annotation to the right. The sequence annotation was created using 20 orthologs shown in the table below and was prepared using ClustalX2[7] and ClustalW (a tool at Biology Workbench).[8]

The following table provides a few details on orthologs of the human version of CCDC135. These orthologs were gathered from BLAT.[9] and BLAST searches[10]

Species Organism common name NCBI accession Sequence identity Sequence similarity Length (AAs) Gene common name
Homo sapiens Human NP_115645.4 100% 100% 874 Homo sapiens coiled-coil domain containing 135 (CCDC135)
Macaca mulatta Rhesus monkey XP_001100628.1 96% 98% 830 Predicted: similar to chromosome 16 open reading frame 50
Bos taurus Cow NP_001033120.1 86% 93% 872 coiled-coil domain-containing protein 135
Canis familiaris Dog XP_544386.2 85% 92% 903 Predicted: similar to chromosome 16 open reading frame 50
Equus caballus Horse XP_001915581 81% 87% 831 Predicted: similar to Coiled-coil domain containing 135
Rattus norvegicus Rat NP_001099639 84% 91% 874 hypothetical protein LOC291853
Mus musculus Mouse NP_001036180 82% 90% 876 coiled-coil domain containing 135
Ornithorhynchus anatinus Platypus XP_001508368.1 71% 85% 860 Predicted: similar to Coiled-coil domain containing 135
Monodelphis domestica Opossum XP_001363193.1 70% 84% 866 Predicted: hypothetical protein isoform 1
Gallus gallus Chicken XP_425101.2 57% 72% 868 Predicted: hypothetical protein
Taeniopygia guttata Zebra finch XP_002195392.1 50% 67% 731 Predicted: hypothetical protein
Xenopus troicalis Frog NP_001072331.1 56% 71% 856 coiled-coil domain containing 135
Danio rerio Zebrafish XP_683491 46% 66% 721 Predicted: similar to Coiled-coil domain-containing protein 135
Tetraodon nigroviridis Tetraodon CAG07272 42% 59% 526 unnamed protein product
Nematostella vectensis Sea anemone XP_001632291 53% 70% 817 predicted protein
Branchiostoma floridae Lancelet XP_002610594 51% 71% 850 hypothetical protein BRAFLDRAFT_275841
Ciona intestinalis Sea squirt XP_002123665 49% 69% 837 Predicted: similar to coiled-coil domain containing 135
Anopheles gambiae Mosquito XP_312247.4 32% 49% 662 AGAP002677-PA
Nasonia vitripennis Wasp XP_001607094 34% 55% 868 Predicted: hypothetical protein
Drosophila melanogaster Fruit fly NP_001036757.1 28% 47% 897 CG34110

Predicted properties

Chloroplast transit peptides: None
Signal pepties: Yes [4]
Nuclear Localization Sequence: KKQQEIRAQEKKRLR
C-mannosylation sites: None (However, 14 sites with scores lower than the threshold were predicted.[12])
Mitochondrial targeting: None
N-glycosylation sites: Yes
Sequence gi|223941912 at positions 100 and 493 with potentials of 0.7200 and 0.6031 receptively.

Cellular location

CCDC135 is predicted to be a Cytosol/Nuclear protein[13] with no transmembrane spans or segments. It is predicted to contain at least 56 specific phosphorylation sites[14] which include: 20 Protein Kinase C Phosphorylation sites, 11 Casein Kinase II Phosphorylation sites, and 8 cAMP/cGMP Dependent Phosphorylation sites. The amino acid sequence is also predicted to contain 10 sumoylation[15] sites at positions K236, K236, K45, K773, K499, K679, K249, K167, K540, K445, and K292.

Function

The function of CCDC135 is not yet well understood but it is thought to be involved in teratospermia.[dubious – discuss][citation needed]

References

  1. ↑ "Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs". Genome Res. 11 (3): 422–35. March 2001. doi:10.1101/gr.GR1547R. PMID 11230166. 
  2. ↑ "Entrez Gene: coiled-coil domain containing 135". https://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=84229. 
  3. ↑ "Human hg38 chr16%3A56276931-56332628 UCSC Genome Browser v420". http://genome.ucsc.edu/cgi-bin/hgTracks?insideX=115&revCmplDisp=0&hgsid=157359316&hgt.out1=1.5x&position=chr16%3A56276931-56332628&hgtgroup_map_close=0&hgtgroup_phenDis_close=1&hgtgroup_genes_close=0&hgtgroup_rna_close=0&hgtgroup_expression_close=1&hgtgroup_regulation_close=0&hgtgroup_compGeno_close=0&hgtgroup_varRep_close=1&hgtgroup_encodeGenes_close=1&hgtgroup_encodeTxLevels_close=1&hgtgroup_encodeChip_close=1&hgtgroup_encodeChrom_close=1&hgtgroup_encodeCompAndVar_close=1. 
  4. ↑ 4.0 4.1 "Kegg T01001: 84229". http://www.genome.jp/dbget-bin/www_bget?hsa:84229. 
  5. ↑ "Multiple sequence alignment: Strap". http://www.bioinformatics.org/strap/. 
  6. ↑ "Redirecting to Phyre2". http://www.sbg.bio.ic.ac.uk/~phyre/. 
  7. ↑ "Clustal Home Page". http://www.clustal.org/. 
  8. ↑ "Home". http://workbench.sdsc.edu/. 
  9. ↑ "BLAT Search Genome". http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=Human&db=hg18&hgsid=122786349. 
  10. ↑ "BLAST". http://blast.ncbi.nlm.nih.gov/Blast.cgi. 
  11. ↑ "ExPASy". SIB Switzerland. 2009-01-05. http://www.expasy.ch/. 
  12. ↑ "NetCGlyc 1.0 Server". http://www.cbs.dtu.dk/services/NetCGlyc/. 
  13. ↑ "PSORT II Prediction". http://psort.ims.u-tokyo.ac.jp/form2.html. 
  14. ↑ "NetPhosK 1.0 Server". http://www.cbs.dtu.dk/services/NetPhosK/. 
  15. ↑ "SUMOplot™ Analysis Program | Abcepta". http://www.abgent.com/tools/sumoplot. 



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