CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-017998
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Polyribonucleotide nucleotidyltransferase 1, mitochondrial 
Protein Synonyms/Alias
 3'-5' RNA exonuclease OLD35; PNPase old-35; Polynucleotide phosphorylase 1; PNPase 1; Polynucleotide phosphorylase-like protein 
Gene Name
 PNPT1 
Gene Synonyms/Alias
 PNPASE 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
264QGIQQLVKETGVTKRacetylation[1]
264QGIQQLVKETGVTKRubiquitination[2]
275VTKRTPQKLFTPSPEubiquitination[3]
285TPSPEIVKYTHKLAMacetylation[1, 4, 5]
289EIVKYTHKLAMERLYacetylation[1, 4, 5]
306FTDYEHDKVSRDEAVacetylation[5]
357SIVLNEYKRCDGRDLubiquitination[3]
378SCEVDMFKTLHGSALubiquitination[3]
419ITAINGIKDKNFMLHubiquitination[2]
456GHGALAEKALYPVIPubiquitination[2, 3]
521VTKTDPEKGEIEDYRacetylation[5]
569KLPGIPIKIVMEAIQmethylation[6]
582IQQASVAKKEILQIMubiquitination[3]
591EILQIMNKTISKPRAacetylation[1]
591EILQIMNKTISKPRAubiquitination[7, 8]
630PGGYNLKKLQAETGVubiquitination[3]
Reference
 [1] 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]
 [2] Landscape of the PARKIN-dependent ubiquitylome in response to mitochondrial depolarization.
 Sarraf SA, Raman M, Guarani-Pereira V, Sowa ME, Huttlin EL, Gygi SP, Harper JW.
 Nature. 2013 Apr 18;496(7445):372-6. [PMID: 23503661]
 [3] 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]
 [4] 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]
 [5] Proteomic investigations of lysine acetylation identify diverse substrates of mitochondrial deacetylase sirt3.
 Sol EM, Wagner SA, Weinert BT, Kumar A, Kim HS, Deng CX, Choudhary C.
 PLoS One. 2012;7(12):e50545. [PMID: 23236377]
 [6] Large-scale global identification of protein lysine methylation in vivo.
 Cao XJ, Arnaudo AM, Garcia BA.
 Epigenetics. 2013 May 1;8(5):477-85. [PMID: 23644510]
 [7] 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]
 [8] 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
 RNA-binding protein implicated in numerous RNA metabolic processes. Hydrolyzes single-stranded polyribonucleotides processively in the 3'-to-5' direction. Mitochondrial intermembrane factor with RNA-processing exoribonulease activity. Component of the mitochondrial degradosome (mtEXO) complex, that degrades 3' overhang double-stranded RNA with a 3'-to-5' directionality in an ATP-dependent manner. Required for correct processing and polyadenylation of mitochondrial mRNAs. Plays a role as a cytoplasmic RNA import factor that mediates the translocation of small RNA components, like the 5S RNA, the RNA subunit of ribonuclease P and the mitochondrial RNA-processing (MRP) RNA, into the mitochondrial matrix. Plays a role in mitochondrial morphogenesis and respiration; regulates the expression of the electron transport chain (ETC) components at the mRNA and protein levels. In the cytoplasm, shows a 3'-to-5' exoribonuclease mediating mRNA degradation activity; degrades c- myc mRNA upon treatment with IFNB1/IFN-beta, resulting in a growth arrest in melanoma cells. Regulates the stability of specific mature miRNAs in melanoma cells; specifically and selectively degrades miR-221, preferentially. Plays also a role in RNA cell surveillance by cleaning up oxidized RNAs. Binds to the RNA subunit of ribonuclease P, MRP RNA and miR-221 microRNA. 
Sequence Annotation
 DOMAIN 605 664 KH.
 DOMAIN 679 750 S1 motif.
 MOD_RES 264 264 N6-acetyllysine.
 MOD_RES 285 285 N6-acetyllysine.
 MOD_RES 289 289 N6-acetyllysine.
 MOD_RES 782 782 Phosphoserine.  
Keyword
 3D-structure; Acetylation; Complete proteome; Cytoplasm; Deafness; Disease mutation; Exonuclease; Hydrolase; Membrane; Mitochondrion; mRNA processing; Non-syndromic deafness; Nuclease; Nucleotidyltransferase; Phosphoprotein; Polymorphism; Reference proteome; RNA-binding; Transferase; Transit peptide; Transport. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 783 AA 
Protein Sequence
MAACRYCCSC LRLRPLSDGP FLLPRRDRAL TQLQVRALWS SAGSRAVAVD LGNRKLEISS 60
GKLARFADGS AVVQSGDTAV MVTAVSKTKP SPSQFMPLVV DYRQKAAAAG RIPTNYLRRE 120
IGTSDKEILT SRIIDRSIRP LFPAGYFYDT QVLCNLLAVD GVNEPDVLAI NGASVALSLS 180
DIPWNGPVGA VRIGIIDGEY VVNPTRKEMS SSTLNLVVAG APKSQIVMLE ASAENILQQD 240
FCHAIKVGVK YTQQIIQGIQ QLVKETGVTK RTPQKLFTPS PEIVKYTHKL AMERLYAVFT 300
DYEHDKVSRD EAVNKIRLDT EEQLKEKFPE ADPYEIIESF NVVAKEVFRS IVLNEYKRCD 360
GRDLTSLRNV SCEVDMFKTL HGSALFQRGQ TQVLCTVTFD SLESGIKSDQ VITAINGIKD 420
KNFMLHYEFP PYATNEIGKV TGLNRRELGH GALAEKALYP VIPRDFPFTI RVTSEVLESN 480
GSSSMASACG GSLALMDSGV PISSAVAGVA IGLVTKTDPE KGEIEDYRLL TDILGIEDYN 540
GDMDFKIAGT NKGITALQAD IKLPGIPIKI VMEAIQQASV AKKEILQIMN KTISKPRASR 600
KENGPVVETV QVPLSKRAKF VGPGGYNLKK LQAETGVTIS QVDEETFSVF APTPSAMHEA 660
RDFITEICKD DQEQQLEFGA VYTATITEIR DTGVMVKLYP NMTAVLLHNT QLDQRKIKHP 720
TALGLEVGQE IQVKYFGRDP ADGRMRLSRK VLQSPATTVV RTLNDRSSIV MGEPISQSSS 780
NSQ 783 
Gene Ontology
 GO:0045025; C:mitochondrial degradosome; IDA:UniProtKB.
 GO:0005758; C:mitochondrial intermembrane space; IDA:UniProtKB.
 GO:0005886; C:plasma membrane; IDA:HPA.
 GO:0000175; F:3'-5'-exoribonuclease activity; IDA:UniProtKB.
 GO:0035198; F:miRNA binding; IDA:UniProtKB.
 GO:0034046; F:poly(G) RNA binding; IDA:UniProtKB.
 GO:0008266; F:poly(U) RNA binding; IDA:UniProtKB.
 GO:0004654; F:polyribonucleotide nucleotidyltransferase activity; IDA:UniProtKB.
 GO:0035458; P:cellular response to interferon-beta; IDA:UniProtKB.
 GO:0034599; P:cellular response to oxidative stress; IDA:UniProtKB.
 GO:0000958; P:mitochondrial mRNA catabolic process; IDA:UniProtKB.
 GO:0097222; P:mitochondrial mRNA polyadenylation; IMP:UniProtKB.
 GO:0000965; P:mitochondrial RNA 3'-end processing; IMP:UniProtKB.
 GO:0000964; P:mitochondrial RNA 5'-end processing; IMP:UniProtKB.
 GO:0070584; P:mitochondrion morphogenesis; ISS:UniProtKB.
 GO:0071850; P:mitotic cell cycle arrest; IDA:UniProtKB.
 GO:0045926; P:negative regulation of growth; IDA:UniProtKB.
 GO:0071042; P:nuclear polyadenylation-dependent mRNA catabolic process; IDA:UniProtKB.
 GO:2000627; P:positive regulation of miRNA catabolic process; IDA:UniProtKB.
 GO:0000962; P:positive regulation of mitochondrial RNA catabolic process; IDA:UniProtKB.
 GO:0061014; P:positive regulation of mRNA catabolic process; IMP:UniProtKB.
 GO:0070207; P:protein homotrimerization; IDA:UniProtKB.
 GO:0043457; P:regulation of cellular respiration; ISS:UniProtKB.
 GO:2000772; P:regulation of cellular senescence; IDA:UniProtKB.
 GO:0035928; P:rRNA import into mitochondrion; IDA:UniProtKB. 
Interpro
 IPR001247; ExoRNase_PH_dom1.
 IPR015847; ExoRNase_PH_dom2.
 IPR004087; KH_dom.
 IPR004088; KH_dom_type_1.
 IPR012340; NA-bd_OB-fold.
 IPR012162; PNPase.
 IPR027408; PNPase/RNase_PH_dom.
 IPR015848; PNPase_PH_RNA-bd_bac/org-type.
 IPR003029; Rbsml_prot_S1_RNA-bd_dom.
 IPR020568; Ribosomal_S5_D2-typ_fold.
 IPR022967; RNA-binding_domain_S1. 
Pfam
 PF00013; KH_1
 PF03726; PNPase
 PF01138; RNase_PH
 PF03725; RNase_PH_C
 PF00575; S1 
SMART
 SM00322; KH
 SM00316; S1 
PROSITE
 PS50084; KH_TYPE_1
 PS50126; S1 
PRINTS