Poly(A)-specific ribonuclease

PDB rendering based on 1whv.

Available structures

Ortholog search: PDBe, RCSB

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

Identifiers

Symbols

PARN ; DAN; DKCB6; PFBMFT4

External IDs

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

EC number

3.1.13.4

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 • nucleic acid phosphodiester bond hydrolysis • RNA phosphodiester bond hydrolysis, exonucleolytic
Sources: Amigo / QuickGO

RNA expression pattern

More reference expression data

Orthologs

Species

Human

Mouse

RefSeq (mRNA)

RefSeq (protein)

Location (UCSC)

Chr 16:
14.44 – 14.63 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.
1 2 "Entrez Gene: PARN poly(A)-specific ribonuclease (deadenylation nuclease)".

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

Hydrolase: esterases (EC 3.1)

3.1.1: Carboxylic
ester hydrolases

Lipase

Phospholipase
- A1
- A2
- B

3.1.2: Thioesterase

3.1.3: Phosphatase

3.1.4: Phosphodiesterase

3.1.6: Sulfatase

Nuclease (includes
deoxyribonuclease and
ribonuclease)

3.1.11-16: Exonuclease

Exodeoxyribonuclease	RecBCD

Exoribonuclease	Oligonucleotidase

3.1.21-31: Endonuclease

Endodeoxyribonuclease	Deoxyribonuclease I Deoxyribonuclease II Deoxyribonuclease IV Restriction enzyme UvrABC endonuclease

Endoribonuclease	RNase III RNase H 1 2A 2B 2C RNase P RNase A 1 2 3 4/5 RNase T1 RNA-induced silencing complex

either deoxy- or ribo-	Aspergillus nuclease S1 Micrococcal nuclease

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Poly(A)-specific ribonuclease

Function

References

Further reading