C11orf54

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C11orf54
Available structures
PDB Ortholog search: PDBe RCSB
Identifiers
Aliases C11orf54, PTD012, PTOD012, chromosome 11 open reading frame 54
External IDs MGI: 1918234 HomoloGene: 8531 GeneCards: C11orf54
Orthologs
Species Human Mouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

NM_001199484
NM_001199485
NM_133732

RefSeq (protein)
Location (UCSC) Chr 11: 93.74 – 93.76 Mb Chr 9: 15.28 – 15.31 Mb
PubMed search [1] [2]
Wikidata
View/Edit Human View/Edit Mouse

Chromosome 11 open reading frame 54 (C11orf54) is a protein that in humans is encoded by the C11orf54 gene.[3] The "Homo sapiens" gene, C11orf54 is also known as PTD012 and PTOD12. C11orf54 exhibits hydrolase activity on p-nitrophenyl acetate and acts on ester bonds, though the overall function is still not fully understood by the scientific community. The protein is highly conserved with the most distant homolog found is in bacteria.[4]


Gene[edit]

C11orf54 is located on chromosome 11 at 11q21. Common aliases of the gene are PTD012 and PT0D12. The gene consists 13 exons and spans 23730 bp. C11orf54 is flanked by TAF1D and MED17. [4]

Alt=Gene neighborhood for C11orf54

mRNA[edit]

The protein ester hydrolase c11orf54 exists as a monomer and is composed of 315 amino acids. There are 6 isoforms for C11orf54. See table 1.[4]

-
Variant Isoform Length (bp) Accession Number
1 ester hydrolase C11orf54 isoform a 2726 NM_001286067.1
2 ester hydrolase C11orf54 isoform a 2589 NM_001286068.1
3 ester hydrolase C11orf54 isoform a 2594 NM_001286069.1
4 ester hydrolase C11orf54 isoform b 2444 NM_014039.3
5 ester hydrolase C11orf54 isoform c 2442 NM_001286070.1
6 ester hydrolase C11orf54 isoform d 2417 NM_001286071.1

[4]

The amino acid sequence contains the Domain of Uknown Function 1907. Found in this transcript is the HxHxxxxxxxxxH motif which coordinates the zinc ion involved in the hydrolase activity.[5] An LR nest motif is found at lys262 and Arg263. The LR nest motif forms hydrogen bonds between the NH groups and anions; an acetate anion is coordinated with the LR nest. [6]

Protein[edit]

Primary sequence[edit]

Table 2 shows the different characteristics of the protein sequence throughout humans and other orthologs.[7]}}</ref>

Organism Molecular Weight (kiloDalton) Isoelectric point High Bias Amino Acids Repeats
Human 35.1 5.9 F AEFS
Mouse 35.0 5.9 H None
13 Lined Ground Squirrel 35.1 6.0 F,H PAEF
Giant Panda 35.2 6.5 F PAEF

Secondary structure[edit]

The protein of C11orf54 exists as a monomer in solution. The protein assumes a globular shape of 20 beta strands and 4 alpha helices, containing 9 antiparallel beta strands forming a beta screw region. The β-screw region of C11orf54 has structural similarity to the cyclic adenosine 3′,5′-monophosphate (cAMP) binding domain of the regulatory subunit of protein kinase A. A zinc ion is bound to the HxHxxxxxxxxxH motif found in the sequence. [5]

Subcellular localization[edit]

C11orf54 is predicted to be localized 60.9% in the cytoplasm, 21.7% in the nucleus, 13.0% mitochondrial and 4.3% in the Golgi Apparatus.[8]

Expression & post translational modifications[edit]

Image 1: Post-Transcriptional Modifications to C11orf54 protein

See image one.[9][10] The protein is highly expressed in the kidneys and moderately expressed in the adrenal gland, colon, liver, testis and thyroid gland.[11]

Homology[edit]

Paralogs[edit]

There are no paralogs for C11orf54. [3]

Orthologs[edit]

The protein Ester Hydrolase C11orf54 has many orthologs (see table.) It is highly conserved (60-100% identity) in mammals, reptiles, birds, and fish. The protein is moderately conserved (30-59.99% identity) in invertebrates, amphibia, Cnidaria, Mollusca, fungi and bacteria. It is not conserved in archaea.[7] The most distant orthologs are bacteria. Figure 2 shows the unrooted phylogenetic tree of a few of C11orf54’s orthologs.[3]

Species Common Name Class Accession Number Percent Identity Divergence (MYA median)
Microtus ochrogaster Prairie Vole mammalia XP_005346877.1 87.0 88
Chelonia mydas Green Sea Turtle reptilia XP_007069537.1 72.8 320
Xenopus tropicalis Burmese Python reptilia XP_007434894.1 70.9 320
Python bivittatus Red Junglefowl Ave NP_001264206.1 73.4 320
Gallus gallus Common Cuckoo Ave XP_009564677.1 72.5 320
Cuculus canorus Southern Platyfish Actinopterygii XP_005800827.1 65.2 432
Xiphophorus maculatus Zebrafish Actinopterygii NP_997781.1 62.4 432
Danio rerio Acorn Worm Enteropneusta XP_002738479.1 55.6 627
Saccoglossus kowalevskii Atlantic Horseshoe Crab Merostomata XP_013785734.1 56.6 758
Limulus polyphemus Western Clawed Frog Amphibia XP_012812415.1 55.1 353
Crassostrea gigas Pacific Oyster Bivalvia XP_011412414.1 50.0 758
Tribolium castaneum Red Flour Beetle Insecta XP_968861.1 49.0 758
Drosophila bipectinata Fruitfly Insecta XP_017103988.1 46.0 758
Megachile rotundata Alfalfa leafcutter bee Insecta XP_003702672.1 44.8 758
Zymoseptoria brevis fungi Dothideomycetes KJX93246.1 36.5 1150
Cladophialophora carrionii fungi Dothideomycetes OCT48531.1 35.8 1150
Alternaria alternata fungi Dothideomycetes XP_018384285.1 36.2 1150
Candidatus Pelagibacter ubique bacteria Bacteria WP_075504325.1 34.5 4090
Pelagibacteraceae bacterium bacteria Bacteria OCW82973.1 34.1 4090

Function[edit]

C11orf54's coordination with a zinc ion through three histidines and an acetate anion is likely to point to a function of the protein being an enzymatic reaction as an ester hydrolase. The protein has a high turnover number when reacted with p-nitrophenyl acetate (0.042 sec−1) as compared to a 1 sec−1 turnover rate found in another enzyme (bovine carbonic anhydrase II) that reacts with p-nitrophenyl acetate. [5]

Interacting Proteins[edit]

Protein Name Abbreviation
Ubiquitin C UBC
Collagen, type IV, alpha 3 COL4A3
Thyroid Hormone Receptor Interactor 13 TRIP13
DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like DDX60L
Glutamine-fructose-6-phosphate transaminase 2 GFPT2
Superkiller viralicidic activity 2-like (S. cerevisiae) SKIV2L
OTU domain, ubiquitin aldehyde binding 1 OTUB1

[12]



References[edit]

  1. ^ "Human PubMed Reference:". 
  2. ^ "Mouse PubMed Reference:". 
  3. ^ a b c "Entrez Gene: C11orf54 chromosome 11 open reading frame 54". 
  4. ^ a b c d "C11orf54". NCBI Gene. NCBI (National Center for Biotechnology Information). 
  5. ^ a b c Manjasetty BA, Büssow K, Fieber-Erdmann M, Roske Y, Gobom J, Scheich C, Götz F, Niesen FH, Heinemann U (April 2006). "Crystal structure of Homo sapiens PTD012 reveals a zinc-containing hydrolase fold". Protein Science. 15 (4): 914–20. doi:10.1110/ps.052037006. PMC 2242484Freely accessible. PMID 16522806. 
  6. ^ Langton MJ, Serpell CJ, Beer PD (2016). "Anion Recognition in Water: Recent Advances from a Supramolecular and Macromolecular Perspective". Angewandte Chemie (International Ed. in English). 55 (6): 1974–87. doi:10.1002/anie.201506589. PMC 4755225Freely accessible. PMID 26612067. 
  7. ^ a b Subramaniam S (1998). "The Biology Workbench--a seamless database and analysis environment for the biologist". Proteins. 32 (1): 1–2. doi:10.1002/(SICI)1097-0134(19980701)32:1<1::AID-PROT1>3.0.CO;2-Q. PMID 9672036. 
  8. ^ Briesemeister S, Rahnenführer J, Kohlbacher O (2010). "Going from where to why–interpretable prediction of protein subcellular localization". Bioinformatics (Oxford, England). 26 (9): 1232–8. doi:10.1093/bioinformatics/btq115. PMID 20299325. 
  9. ^ Blom N, Gammeltoft S, Brunak S (1999). "Sequence and structure-based prediction of eukaryotic protein phosphorylation sites". Journal of Molecular Biology. 294 (5): 1351–62. doi:10.1006/jmbi.1999.3310. PMID 10600390. 
  10. ^ Gupta R, Brunak S (2002). "Prediction of glycosylation across the human proteome and the correlation to protein function". Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing: 310–22. PMID 11928486. 
  11. ^ Uhlén M, Fagerberg L, Hallström BM, Lindskog C, Oksvold P, Mardinoglu A, et al. (January 2015). "Proteomics. Tissue-based map of the human proteome". Science. 347 (6220): 1260419. doi:10.1126/science.1260419. PMID 25613900. 
  12. ^ Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, von Mering C, Jensen LJ (2013). "STRING v9.1: protein-protein interaction networks, with increased coverage and integration". Nucleic Acids Research. 41 (Database issue): D808–15. doi:10.1093/nar/gks1094. PMC 3531103Freely accessible. PMID 23203871. 

Further reading[edit]

External links[edit]