ZC3H12B

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External IDsGeneCards: [1]
Orthologs
SpeciesHumanMouse
Entrez
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RefSeq (mRNA)

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RefSeq (protein)

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ZC3H12B, also known as CXorf32 or MCPIP2, is a protein encoded by gene ZC3H12B located on chromosome Xq12 in humans.

Gene

The ZC3H12B gene is composed of 19,709 base pairs (bp) and contains 5 exons. It is located on the X chromosome at q12 on the plus strand.

ZC3H12B contains a ribonuclease domain, as well as a CCCH-type zinc finger domain. Ribonucleases (RNases) degrade RNA and are involved in the RNA maturation process. They are also a line of defense against viral RNA (D'Alessio and Riordan 1997). CCCH-type zinc fingers are associated with mRNA destabilization. CCCH-type zinc fingers have been shown to turn over mRNA without the removal of the PolyA tail (Lai and Blackshear 2001). ZC3H12B and its paralogs ZC3H12A, ZC3H12C and ZC3H12D all contain CCCH-type zinc finger domains, which have been associated with cell cycle and growth phase transitions in eukaryotes (InterPro).

Promoter

Genomatix ElDorado program predicted a 601 bp promoter upstream of the ZC3H12B gene with multiple transcription factor binding sites including nuclear factor of activated T-cells and ribonucleoprotein associated zinc finger protein MOK-2 (also known as ZNF239).

mRNA

ZC3H12B contains 7273 bp mRNA. There is only one predicted transcript by Aceview. No folding patterns have been predicted (Mfold). There are for introns excised from ZC3H12B.

Protein

ZC3H12B is a probable ribonuclease containing CCCH-type zinc finger domain and ribonuclease domains. The 836 amino acid protein has a predicted molecular weight of 94.2 kdal. It does not contain a signal peptide or a transmembrane region. PSORTII predicted 65.2% probability of nuclear location. CCCH-type zinc fingers and ribonucleases are presumably located in the nucleus for RNA cleaving and specifically, RNA hairpin cleaving (Boysen and Hearn 2008).

Structural characteristics

The protein secondary structure is a mixture of alpha helices and beta strands. The two domains identified so far are the ribonuclease and CCCH-type zinc finger domains.

Shown below is a conserved domain of ZC3H12B paralog, Mcpip1 (or ZC3H12A). In a BLAST structure comparison, there was an 82% identity match with 24% query coverage, with a predicted e-value of 2e-118. 82% identity match is enough to make comparisons of ZC3H12B and Mcpip1 (ZC3H12A) zinc finger conserved domain, which are both predicted to be composed of beta strands and alpha helices.

Post-translational modification

Phobius program predicted non-cytoplasmic protein location. NetPhos 2.0. predicted 63 phosphorylation sites in ZC3H12B, which are marked on the conceptual translation. YinOYang1.2. predicted three 0-Beta-GlcNAc attachment sites, which are competing with phosphorylation sites. 0-Beta-GlcNAc is presumably the only type of glycosylation occurring in the nucleus and/or cytoplasm of cells. There is a notable link between antigen activation by lymphocytes and dynamic 0-B-Glycosylation in nuclear proteins (Hart and Akimoto). NetNGlyc predicted glycosylation sites; however, these sites were excluded because the protein is likely nuclear and would not undergo this form of glycosylation. There were no predicted acetylation sites at the N-terminus of the protein. This is unusual because approximately 85% of human proteins are acetylated at the N terminus for synthesis, stabilization and localization of proteins (Van Damm et al.). No positive, negative or mixed charge clusters present. No hydrophobic segments detected (SAPS SDSC Biology Workbench). MitoProtII did not detect any mitochondria export signals. These post-translational tests suggest the protein is located in the nucleus and undergoes dynamic phosphorylation and 0-Beta-GlcNAc modifications.

Evolution

Select domains of ZC3H12B are conserved in most vertebrates, arthropods and annelids. There are not conserved domains in domains bacteria or archaea. There were not significantly conserved domains in yeasts, plants or protists.

Paralogs

There are three paralogs of ZC3H12B which are in the same CCCH-type zinc finger family, all which maintain greater than 50% identity to ZC3H12B based on BLAST analysis (NCBI).

Name Species NCBI accession number Length (AA) Protein identity
ZC3H12B Homo sapiens NM_001010888.3 836aa 100%
ZC3H12A Homo sapiens NM_025079.2 599aa 68%
ZC3H12C Homo sapiens NM_033390.1 883aa 53%
ZC3H12D Homo sapiens NM_207360.2 527aa 61%

Orthologs

ZC3H12B is conserved in mammals, birds, insects and nematodes (BLAST). See the table below for the summary of orthologs of ZC3H12B in humans.

Species Species common name Divergence (MYA) NCBI accession number (protein) Length (amino acids) Protein identity Similarity
Homo sapiens Human n/a NP_001010888.3 836aa 100% 100%
Pan paniscus Chimpanzee 6.3 XP_003816967.1 836aa 99% 99%
Pongo abelii Orangutan 15.7 XP_002831786.1 836aa 99% 99%
Macaca mulatta Rhesus monkey 29 XP_002806307.1 836aa 99% 99%
Callithrix jacchus Marmoset 42.6 XP_002762992.2 836aa 98% 98%
Mus musculus Mouse 92.3 NP_001030079.2 835aa 91% 94%
Sus scrofa Pig 94.2 XP_003360389.1 836aa 93% 96%
Gallus gallus Chicken 296 XP_003641177.1 837aa 77% 85%
Chrysemys picta bellii Painted turtle 296 XP_005279572.1 838aa 78% 86%
Oryzias latipes Medaka 400.1 XP_004076599.1 845aa 67% 77%
Gadus morhua Atlantic cod 400.1 AFK76491.1 842aa 29% 44%
Danio rerio Zebrafish 400.1 XP_001342172.3 982aa 68% 77%
Petromyzon marinus Lamprey 535.7 ABO21295.1 222aa 44% 58%
Branchiostoma floridae Lancelet 713.2 XP_002598834.1 492aa 66% 79%
Ciona intestinalis Vase tunicate 722.5 XP_002125834.1 863aa 54% 66%
Strongylocentrotus purpuratus Purple sea urchin 742.9 XP_787030.3 974aa 58% 72%
Aplysiomorpha californica Sea hare 782.7 XP_005113312.1 1269aa 51% 69%
Drosophila grimshawi Hawaii fruit fly 782.7 XP_001994140.1 548aa 51% 69%
Anopheles gambiae Mosquito 782.7 XP_321880 637aa 59% 75%
Apis mellifera Honey bee 782.7 XP_397264 652aa 58% 73%
Caenorhabditis elegans Round worm (nematode) 937.5 NP_491985.4 634aa 46% 64%

Expression and function

Microarrays in normal tissue expression profiling showed increased expression of the gene in the pancreas, prostate, brain, spinal cord and thymus (GEO). Unlike its paralogs, it is not expressed in macrophage-activated tissues, which indicates the paralogous relationship to the inflammatory response (Liang et al. 2008). ZC3H12B is expressed transiently in brain, thymus and testis tissues (EST).

Interaction

Predicted interactions by Ingenuity Systems showed no drug targeting molecules in pathway and no known drug targets. The listed top functions and diseases were cancer, organismal injury and abnormalities, reproductive system disease. Several miRNA interactions were predicted. The predicted miRNA targets have yet to be matched to the ZC3H12B sequence and it is unclear whether there is an interaction between the two. Tests such as Forster Resonance Energy Transfer (FRET), co-immunooprecipitation, two-hybrid screening, hydropathic complementarity, cluster-microarray and ChiP could be used in the future to test for new protein/chromatin interactions with ZC3H12B.

Clinical significance

Deletions of the Xq12 locus has resulted in several disorders such as androgen insensitivity, susceptibility to prostate cancer, spinal and bulbar muscular atrophy of Kennedy and mental retardation; however, no link has been found between these diseases and ZC3H12B (NCBI).

References

Further reading

  • Liang J, Wang J, Azfer A, Song W, Tromp G, Kolattukudy PE, Fu M (March 2008). "A novel CCCH-zinc finger protein family regulates proinflammatory activation of macrophages". The Journal of Biological Chemistry. 283 (10): 6337–46. doi:10.1074/jbc.m707861200. PMID 18178554.
  • Van Damme P, Hole K, Pimenta-Marques A, Helsens K, Vandekerckhove J, Martinho RG, Gevaert K, Arnesen T (July 2011). "NatF contributes to an evolutionary shift in protein N-terminal acetylation and is important for normal chromosome segregation". PLoS Genetics. 7 (7): e1002169. doi:10.1371/journal.pgen.1002169. PMC 3131286. PMID 21750686.

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