CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-001602
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Poly(A)-specific ribonuclease PARN 
Protein Synonyms/Alias
 Deadenylating nuclease; Deadenylation nuclease; Polyadenylate-specific ribonuclease 
Gene Name
 PARN 
Gene Synonyms/Alias
 DAN 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
168YVSPNTSKCPVTIPEubiquitination[1]
220IYQTLSWKYPKGIHVacetylation[2]
243ERYIVISKVDEEERKacetylation[3]
250KVDEEERKRREQQKHacetylation[3]
259REQQKHAKEQEELNDubiquitination[1]
326FPRLLDTKLMASTQPubiquitination[1, 4, 5, 6, 7]
413IHVSARSKLIEPFFNubiquitination[1]
421LIEPFFNKLFLMRVMubiquitination[1]
499KIAVNTSKYAESYRIacetylation[2]
499KIAVNTSKYAESYRIubiquitination[1]
Reference
 [1] Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments.
 Udeshi ND, Svinkina T, Mertins P, Kuhn E, Mani DR, Qiao JW, Carr SA.
 Mol Cell Proteomics. 2013 Mar;12(3):825-31. [PMID: 23266961]
 [2] Lysine acetylation targets protein complexes and co-regulates major cellular functions.
 Choudhary C, Kumar C, Gnad F, Nielsen ML, Rehman M, Walther TC, Olsen JV, Mann M.
 Science. 2009 Aug 14;325(5942):834-40. [PMID: 19608861]
 [3] Regulation of cellular metabolism by protein lysine acetylation.
 Zhao S, Xu W, Jiang W, Yu W, Lin Y, Zhang T, Yao J, Zhou L, Zeng Y, Li H, Li Y, Shi J, An W, Hancock SM, He F, Qin L, Chin J, Yang P, Chen X, Lei Q, Xiong Y, Guan KL.
 Science. 2010 Feb 19;327(5968):1000-4. [PMID: 20167786]
 [4] A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles.
 Wagner SA, Beli P, Weinert BT, Nielsen ML, Cox J, Mann M, Choudhary C.
 Mol Cell Proteomics. 2011 Oct;10(10):M111.013284. [PMID: 21890473]
 [5] Systematic and quantitative assessment of the ubiquitin-modified proteome.
 Kim W, Bennett EJ, Huttlin EL, Guo A, Li J, Possemato A, Sowa ME, Rad R, Rush J, Comb MJ, Harper JW, Gygi SP.
 Mol Cell. 2011 Oct 21;44(2):325-40. [PMID: 21906983]
 [6] Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass.
 Povlsen LK, Beli P, Wagner SA, Poulsen SL, Sylvestersen KB, Poulsen JW, Nielsen ML, Bekker-Jensen S, Mailand N, Choudhary C.
 Nat Cell Biol. 2012 Oct;14(10):1089-98. [PMID: 23000965]
 [7] hCKSAAP_UbSite: improved prediction of human ubiquitination sites by exploiting amino acid pattern and properties.
 Chen Z, Zhou Y, Song J, Zhang Z.
 Biochim Biophys Acta. 2013 Aug;1834(8):1461-7. [PMID: 23603789] 
Functional Description
 3'-exoribonuclease that has a preference for poly(A) tails of mRNAs, thereby efficiently degrading poly(A) tails. Exonucleolytic degradation of the poly(A) tail is often the first step in the decay of eukaryotic mRNAs and is also used to silence certain maternal mRNAs translationally during oocyte maturation and early embryonic development. Interacts with both the 3'-end poly(A) tail and the 5'-end cap structure during degradation, the interaction with the cap structure being required for an efficient degradation of poly(A) tails. Involved in nonsense-mediated mRNA decay, a critical process of selective degradation of mRNAs that contain premature stop codons. Also involved in degradation of inherently unstable mRNAs that contain AU-rich elements (AREs) in their 3'-UTR, possibly via its interaction with KHSRP. Probably mediates the removal of poly(A) tails of AREs mRNAs, which constitutes the first step of destabilization. 
Sequence Annotation
 DOMAIN 178 245 R3H.
 METAL 28 28 Divalent metal cation; catalytic
 METAL 30 30 Divalent metal cation; catalytic
 METAL 292 292 Divalent metal cation; catalytic
 METAL 382 382 Divalent metal cation; catalytic
 MOD_RES 163 163 Phosphoserine.
 MOD_RES 220 220 N6-acetyllysine.
 MOD_RES 499 499 N6-acetyllysine.
 MOD_RES 557 557 Phosphoserine; by MAPKAPK2.
 MOD_RES 587 587 Phosphoserine (By similarity).
 MOD_RES 619 619 Phosphoserine.
 MOD_RES 623 623 Phosphoserine.
 MOD_RES 628 628 Phosphoserine.
 MOD_RES 631 631 Phosphothreonine.  
Keyword
 3D-structure; Acetylation; Alternative splicing; Complete proteome; Cytoplasm; Exonuclease; Hydrolase; Magnesium; Metal-binding; Nonsense-mediated mRNA decay; Nuclease; Nucleus; Phosphoprotein; Reference proteome; RNA-binding. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 639 AA 
Protein Sequence
MEIIRSNFKS NLHKVYQAIE EADFFAIDGE FSGISDGPSV SALTNGFDTP EERYQKLKKH 60
SMDFLLFQFG LCTFKYDYTD SKYITKSFNF YVFPKPFNRS SPDVKFVCQS SSIDFLASQG 120
FDFNKVFRNG IPYLNQEEER QLREQYDEKR SQANGAGALS YVSPNTSKCP VTIPEDQKKF 180
IDQVVEKIED LLQSEENKNL DLEPCTGFQR KLIYQTLSWK YPKGIHVETL ETEKKERYIV 240
ISKVDEEERK RREQQKHAKE QEELNDAVGF SRVIHAIANS GKLVIGHNML LDVMHTVHQF 300
YCPLPADLSE FKEMTTCVFP RLLDTKLMAS TQPFKDIINN TSLAELEKRL KETPFNPPKV 360
ESAEGFPSYD TASEQLHEAG YDAYITGLCF ISMANYLGSF LSPPKIHVSA RSKLIEPFFN 420
KLFLMRVMDI PYLNLEGPDL QPKRDHVLHV TFPKEWKTSD LYQLFSAFGN IQISWIDDTS 480
AFVSLSQPEQ VKIAVNTSKY AESYRIQTYA EYMGRKQEEK QIKRKWTEDS WKEADSKRLN 540
PQCIPYTLQN HYYRNNSFTA PSTVGKRNLS PSQEEAGLED GVSGEISDTE LEQTDSCAEP 600
LSEGRKKAKK LKRMKKELSP AGSISKNSPA TLFEVPDTW 639 
Gene Ontology
 GO:0005829; C:cytosol; TAS:Reactome.
 GO:0005730; C:nucleolus; IEA:UniProtKB-SubCell.
 GO:0005634; C:nucleus; TAS:ProtInc.
 GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
 GO:0003730; F:mRNA 3'-UTR binding; TAS:ProtInc.
 GO:0000166; F:nucleotide binding; IEA:InterPro.
 GO:0004535; F:poly(A)-specific ribonuclease activity; TAS:Reactome.
 GO:0007292; P:female gamete generation; TAS:ProtInc.
 GO:0000184; P:nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; IMP:UniProtKB.
 GO:0000289; P:nuclear-transcribed mRNA poly(A) tail shortening; TAS:Reactome.
 GO:0009451; P:RNA modification; TAS:ProtInc. 
Interpro
 IPR012677; Nucleotide-bd_a/b_plait.
 IPR014789; PolyA-riboNase_RNA_binding.
 IPR001374; R3H_ss-bd.
 IPR006941; RNase_CAF1.
 IPR012337; RNaseH-like_dom. 
Pfam
 PF04857; CAF1
 PF01424; R3H
 PF08675; RNA_bind 
SMART
  
PROSITE
 PS51061; R3H 
PRINTS