C11orf54

Chromosome 11 open reading frame 54 (C11orf54) is a protein that in humans is encoded by the C11orf54 gene.[5] 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.[6]

C11orf54
Available structures
PDBOrtholog search: PDBe RCSB
Identifiers
AliasesC11orf54, PTD012, PTOD012, chromosome 11 open reading frame 54
External IDsOMIM: 615810 MGI: 1918234 HomoloGene: 8531 GeneCards: C11orf54
Orthologs
SpeciesHumanMouse
Entrez

28970

70984

Ensembl

ENSG00000182919

ENSMUSG00000031938

UniProt

Q9H0W9

Q91V76

RefSeq (mRNA)

NM_001199484
NM_001199485
NM_133732
NM_001359258

RefSeq (protein)

NP_001186413
NP_001186414
NP_598493
NP_001346187

Location (UCSC)Chr 11: 93.74 – 93.76 MbChr 9: 15.19 – 15.22 Mb
PubMed search[3][4]
Wikidata
View/Edit HumanView/Edit Mouse

Gene

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.[6]

Gene neighborhood for C11orf54

mRNA

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.[6]

-
VariantIsoformLength (bp)Accession Number
1ester hydrolase C11orf54 isoform a2726NM_001286067.1
2ester hydrolase C11orf54 isoform a2589NM_001286068.1
3ester hydrolase C11orf54 isoform a2594NM_001286069.1
4ester hydrolase C11orf54 isoform b2444NM_014039.3
5ester hydrolase C11orf54 isoform c2442NM_001286070.1
6ester hydrolase C11orf54 isoform d2417NM_001286071.1

[6]

The amino acid sequence contains the domain of unknown function 1907. Found in this transcript is the HxHxxxxxxxxxH motif which coordinates the zinc ion involved in the hydrolase activity.[7] 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.[8]

Protein

Primary sequence

Table 2 shows the different characteristics of the protein sequence throughout humans and other orthologs.[9]

OrganismMolecular Weight (kiloDalton)Isoelectric pointHigh Bias Amino AcidsRepeats
Human35.15.9FAEFS
Mouse35.05.9HNone
13 Lined Ground Squirrel35.16.0F,HPAEF
Giant Panda35.26.5FPAEF

Secondary structure

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.[7]

Subcellular localization

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.[10]

Expression & post translational modifications

Image 1: Post-Transcriptional Modifications to C11orf54 protein

See image one.[11][12] The protein is highly expressed in the kidneys and moderately expressed in the adrenal gland, colon, liver, testis and thyroid gland.[13]

Homology

Paralogs

There are no paralogs for C11orf54.[5]

Orthologs

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.[9] The most distant orthologs are bacteria. Figure 2 shows the unrooted phylogenetic tree of a few of C11orf54’s orthologs.[5]

SpeciesCommon NameClassAccession NumberPercent IdentityDivergence (MYA median)
Microtus ochrogasterPrairie VolemammaliaXP_005346877.187.088
Chelonia mydasGreen Sea TurtlereptiliaXP_007069537.172.8320
Xenopus tropicalisBurmese PythonreptiliaXP_007434894.170.9320
Python bivittatusRed JunglefowlAveNP_001264206.173.4320
Gallus gallusCommon CuckooAveXP_009564677.172.5320
Cuculus canorusSouthern PlatyfishActinopterygiiXP_005800827.165.2432
Xiphophorus maculatusZebrafishActinopterygiiNP_997781.162.4432
Danio rerioAcorn WormEnteropneustaXP_002738479.155.6627
Saccoglossus kowalevskiiAtlantic Horseshoe CrabMerostomataXP_013785734.156.6758
Limulus polyphemusWestern Clawed FrogAmphibiaXP_012812415.155.1353
Crassostrea gigasPacific OysterBivalviaXP_011412414.150.0758
Tribolium castaneumRed Flour BeetleInsectaXP_968861.149.0758
Drosophila bipectinataFruitflyInsectaXP_017103988.146.0758
Megachile rotundataAlfalfa leafcutter beeInsectaXP_003702672.144.8758
Zymoseptoria brevisfungiDothideomycetesKJX93246.136.51150
Cladophialophora carrioniifungiDothideomycetesOCT48531.135.81150
Alternaria alternatafungiDothideomycetesXP_018384285.136.21150
Candidatus Pelagibacter ubiquebacteriaBacteriaWP_075504325.134.54090
Pelagibacteraceae bacteriumbacteriaBacteriaOCW82973.134.14090

Function

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.[7]

Interacting Proteins

Protein NameAbbreviation
Ubiquitin CUBC
Collagen, type IV, alpha 3COL4A3
Thyroid Hormone Receptor Interactor 13TRIP13
DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-likeDDX60L
Glutamine-fructose-6-phosphate transaminase 2GFPT2
Superkiller viralicidic activity 2-like (S. cerevisiae)SKIV2L
OTU domain, ubiquitin aldehyde binding 1OTUB1

[14]

References

  1. GRCh38: Ensembl release 89: ENSG00000182919 - Ensembl, May 2017
  2. GRCm38: Ensembl release 89: ENSMUSG00000031938 - Ensembl, May 2017
  3. "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  4. "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  5. "Entrez Gene: C11orf54 chromosome 11 open reading frame 54".
  6. "C11orf54". NCBI Gene. NCBI (National Center for Biotechnology Information).
  7. 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 2242484. PMID 16522806.
  8. Langton MJ, Serpell CJ, Beer PD (2016). "Anion Recognition in Water: Recent Advances from a Supramolecular and Macromolecular Perspective". Angewandte Chemie International Edition. 55 (6): 1974–87. doi:10.1002/anie.201506589. PMC 4755225. PMID 26612067.
  9. 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. S2CID 1412129.
  10. Briesemeister S, Rahnenführer J, Kohlbacher O (2010). "Going from where to why–interpretable prediction of protein subcellular localization". Bioinformatics. 26 (9): 1232–8. doi:10.1093/bioinformatics/btq115. PMC 2859129. PMID 20299325.
  11. 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.
  12. 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. doi:10.1142/9789812799623_0029. ISBN 978-981-02-4777-5. PMID 11928486.
  13. 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. S2CID 802377.
  14. 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 3531103. PMID 23203871.

Further reading

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