Poly(A)-specific ribonuclease

Poly(A)-specific ribonuclease

PDB rendering based on 1whv.

Available structures

Ortholog search: PDBe, RCSB

List of PDB id codes
2A1R, 2A1S, 3CTR

Identifiers

PARN ; DAN

External IDs

OMIM: 604212 MGI: 1921358 HomoloGene: 31098 GeneCards: PARN Gene

Gene ontology
Molecular function	• nucleotide binding • mRNA 3'-UTR binding • nuclease activity • poly(A)-specific ribonuclease activity • protein binding • protein kinase binding • poly(A) RNA binding • metal ion binding
Cellular component	• nucleus • nucleolus • cytoplasm • cytosol
Biological process	• nuclear-transcribed mRNA catabolic process, nonsense-mediated decay • nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay • nuclear-transcribed mRNA poly(A) tail shortening • female gamete generation • RNA modification • gene expression • RNA metabolic process • mRNA metabolic process • nucleic acid phosphodiester bond hydrolysis • RNA phosphodiester bond hydrolysis, exonucleolytic
Sources: Amigo / QuickGO

RNA expression pattern

More reference expression data

Orthologs

Species

Human

Mouse

ENSG00000140694

ENSMUSG00000022685

RefSeq (mRNA)

RefSeq (protein)

Location (UCSC)

Chr 16:
14.53 – 14.73 Mb

Chr 16:
13.54 – 13.67 Mb

PubMed search

Poly(A)-specific ribonuclease (PARN), also known as polyadenylate-specific ribonuclease or deadenylating nuclease (DAN), is an enzyme that in humans is encoded by the PARN gene.^[1]^[2]

Function

Exonucleolytic degradation of the poly(A) tail is often the first step in the decay of eukaryotic mRNAs. The amino acid sequence of poly(A)-specific ribonuclease shows homology to the RNase D family of 3'-exonucleases. The protein appears to be localized in both the nucleus and the cytoplasm. It is not stably associated with polysomes or ribosomal subunits.^[2]

References

↑ Buiting K, Korner C, Ulrich B, Wahle E, Horsthemke B (May 2000). "The human gene for the poly(A)-specific ribonuclease (PARN) maps to 16p13 and has a truncated copy in the Prader-Willi/Angelman syndrome region on 15q11→q13". Cytogenet Cell Genet 87 (1–2): 125–31. doi:10.1159/000015378. PMID 10640832.
↑ 2.0 2.1 "Entrez Gene: PARN poly(A)-specific ribonuclease (deadenylation nuclease)".

Further reading

Körner CG, Wahle E (1997). "Poly(A) tail shortening by a mammalian poly(A)-specific 3'-exoribonuclease". J. Biol. Chem. 272 (16): 10448–56. doi:10.1074/jbc.272.16.10448. PMID 9099687.
Körner CG, Wormington M, Muckenthaler M et al. (1998). "The deadenylating nuclease (DAN) is involved in poly(A) tail removal during the meiotic maturation of Xenopus oocytes". EMBO J. 17 (18): 5427–37. doi:10.1093/emboj/17.18.5427. PMC 1170868. PMID 9736620.
Dehlin E, Wormington M, Körner CG, Wahle E (2000). "Cap-dependent deadenylation of mRNA". EMBO J. 19 (5): 1079–86. doi:10.1093/emboj/19.5.1079. PMC 305646. PMID 10698948.
Martinez J, Ren YG, Thuresson AC et al. (2000). "A 54-kDa fragment of the Poly(A)-specific ribonuclease is an oligomeric, processive, and cap-interacting Poly(A)-specific 3' exonuclease". J. Biol. Chem. 275 (31): 24222–30. doi:10.1074/jbc.M001705200. PMID 10801819.
Gao M, Fritz DT, Ford LP, Wilusz J (2000). "Interaction between a Poly(A)-Specific Ribonuclease and the 5′ Cap Influences mRNA Deadenylation Rates In Vitro". Mol. Cell 5 (3): 479–88. doi:10.1016/S1097-2765(00)80442-6. PMC 2811581. PMID 10882133.
Gao M, Wilusz CJ, Peltz SW, Wilusz J (2001). "A novel mRNA-decapping activity in HeLa cytoplasmic extracts is regulated by AU-rich elements". EMBO J. 20 (5): 1134–43. doi:10.1093/emboj/20.5.1134. PMC 145468. PMID 11230136.
Martînez J, Ren YG, Nilsson P et al. (2001). "The mRNA cap structure stimulates rate of poly(A) removal and amplifies processivity of degradation". J. Biol. Chem. 276 (30): 27923–9. doi:10.1074/jbc.M102270200. PMID 11359775.
Copeland PR, Wormington M (2001). "The mechanism and regulation of deadenylation: identification and characterization of Xenopus PARN". RNA 7 (6): 875–86. doi:10.1017/S1355838201010020. PMC 1370141. PMID 11424938.
Chen CY, Gherzi R, Ong SE et al. (2002). "AU binding proteins recruit the exosome to degrade ARE-containing mRNAs". Cell 107 (4): 451–64. doi:10.1016/S0092-8674(01)00578-5. PMID 11719186.
Ren YG, Martínez J, Virtanen A (2002). "Identification of the active site of poly(A)-specific ribonuclease by site-directed mutagenesis and Fe(2+)-mediated cleavage". J. Biol. Chem. 277 (8): 5982–7. doi:10.1074/jbc.M111515200. PMID 11742007.
Andersen JS, Lyon CE, Fox AH et al. (2002). "Directed proteomic analysis of the human nucleolus". Curr. Biol. 12 (1): 1–11. doi:10.1016/S0960-9822(01)00650-9. PMID 11790298.
Scherl A, Couté Y, Déon C et al. (2003). "Functional Proteomic Analysis of Human Nucleolus". Mol. Biol. Cell 13 (11): 4100–9. doi:10.1091/mbc.E02-05-0271. PMC 133617. PMID 12429849.
Strausberg RL, Feingold EA, Grouse LH et al. (2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A. 99 (26): 16899–903. doi:10.1073/pnas.242603899. PMC 139241. PMID 12477932.
Lai WS, Kennington EA, Blackshear PJ (2003). "Tristetraprolin and Its Family Members Can Promote the Cell-Free Deadenylation of AU-Rich Element-Containing mRNAs by Poly(A) Ribonuclease". Mol. Cell. Biol. 23 (11): 3798–812. doi:10.1128/MCB.23.11.3798-3812.2003. PMC 155217. PMID 12748283.
Lejeune F, Li X, Maquat LE (2003). "Nonsense-mediated mRNA decay in mammalian cells involves decapping, deadenylating, and exonucleolytic activities". Mol. Cell 12 (3): 675–87. doi:10.1016/S1097-2765(03)00349-6. PMID 14527413.
Ota T, Suzuki Y, Nishikawa T et al. (2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40–5. doi:10.1038/ng1285. PMID 14702039.
Gherzi R, Lee KY, Briata P et al. (2004). "A KH domain RNA binding protein, KSRP, promotes ARE-directed mRNA turnover by recruiting the degradation machinery". Mol. Cell 14 (5): 571–83. doi:10.1016/j.molcel.2004.05.002. PMID 15175153.
Lehner B, Sanderson CM (2004). "A Protein Interaction Framework for Human mRNA Degradation". Genome Res. 14 (7): 1315–23. doi:10.1101/gr.2122004. PMC 442147. PMID 15231747.
Ren YG, Kirsebom LA, Virtanen A (2005). "Coordination of divalent metal ions in the active site of poly(A)-specific ribonuclease". J. Biol. Chem. 279 (47): 48702–6. doi:10.1074/jbc.M403858200. PMID 15358788.

PDB gallery

1whv: Solution structure of the RNA binding domain from hypothetical protein BAB23382

2a1r: Crystal structure of PARN nuclease domain

2a1s: Crystal structure of native PARN nuclease domain