ID   PNP2_ARATH              Reviewed;         991 AA.
AC   Q9S7G6;
DT   28-NOV-2012, integrated into UniProtKB/Swiss-Prot.
DT   01-MAY-2000, sequence version 1.
DT   03-AUG-2022, entry version 151.
DE   RecName: Full=Polyribonucleotide nucleotidyltransferase 2, mitochondrial;
DE            Short=AtmtPNPase {ECO:0000303|PubMed:15037609};
DE            EC=2.7.7.8 {ECO:0000269|PubMed:15037609, ECO:0000269|PubMed:16537927};
DE   AltName: Full=Polynucleotide phosphorylase 2;
DE            Short=PNPase 2;
DE   Flags: Precursor;
GN   Name=PNP2; OrderedLocusNames=At5g14580; ORFNames=T15N1.70;
OS   Arabidopsis thaliana (Mouse-ear cress).
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC   rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX   NCBI_TaxID=3702;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA], FUNCTION, CATALYTIC ACTIVITY, AND
RP   SUBCELLULAR LOCATION.
RC   STRAIN=cv. Columbia;
RX   PubMed=15037609; DOI=10.1074/jbc.m401182200;
RA   Perrin R., Meyer E.H., Zaepfel M., Kim Y.-J., Mache R.,
RA   Grienenberger J.-M., Gualberto J.M., Gagliardi D.;
RT   "Two exoribonucleases act sequentially to process mature 3'-ends of atp9
RT   mRNAs in Arabidopsis mitochondria.";
RL   J. Biol. Chem. 279:25440-25446(2004).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Columbia;
RX   PubMed=11130714; DOI=10.1038/35048507;
RA   Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
RA   Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M.,
RA   Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.,
RA   Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M.,
RA   Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L.,
RA   O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D.,
RA   Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M.,
RA   Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L.,
RA   Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B.,
RA   Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P.,
RA   Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M.,
RA   Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D.,
RA   Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
RA   Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
RA   Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
RA   Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A.,
RA   McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U.,
RA   Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W.,
RA   Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M.,
RA   Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S.,
RA   Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G.,
RA   Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W.,
RA   Bevan M., Fransz P.F.;
RT   "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.";
RL   Nature 408:823-826(2000).
RN   [3]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Columbia;
RX   PubMed=27862469; DOI=10.1111/tpj.13415;
RA   Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA   Town C.D.;
RT   "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT   genome.";
RL   Plant J. 89:789-804(2017).
RN   [4]
RP   FUNCTION, AND CATALYTIC ACTIVITY.
RX   PubMed=16537927; DOI=10.1128/mcb.26.7.2869-2876.2006;
RA   Holec S., Lange H., Kuehn K., Alioua M., Boerner T., Gagliardi D.;
RT   "Relaxed transcription in Arabidopsis mitochondria is counterbalanced by
RT   RNA stability control mediated by polyadenylation and polynucleotide
RT   phosphorylase.";
RL   Mol. Cell. Biol. 26:2869-2876(2006).
CC   -!- FUNCTION: Involved in the 3'-end maturation of mitochondrial mRNAs,
CC       rRNAs and tRNAs. Functions as a poly(A) mRNA 3'-5' degrading
CC       phosphorylase and is required for the degradation of highly expressed
CC       transcripts of non-coding regions. {ECO:0000269|PubMed:15037609,
CC       ECO:0000269|PubMed:16537927}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=phosphate + RNA(n+1) = a ribonucleoside 5'-diphosphate +
CC         RNA(n); Xref=Rhea:RHEA:22096, Rhea:RHEA-COMP:14527, Rhea:RHEA-
CC         COMP:17342, ChEBI:CHEBI:43474, ChEBI:CHEBI:57930, ChEBI:CHEBI:140395;
CC         EC=2.7.7.8; Evidence={ECO:0000269|PubMed:15037609,
CC         ECO:0000269|PubMed:16537927};
CC   -!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:15037609}.
CC   -!- MISCELLANEOUS: Plants silencing PNP2 stop growing after two to three
CC       weeks. {ECO:0000305|PubMed:15037609}.
CC   -!- SIMILARITY: Belongs to the polyribonucleotide nucleotidyltransferase
CC       family. {ECO:0000305}.
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DR   EMBL; Y14685; CAB43864.1; -; mRNA.
DR   EMBL; Y14686; CAB43865.1; -; Genomic_DNA.
DR   EMBL; AL163792; CAB87625.1; -; Genomic_DNA.
DR   EMBL; CP002688; AED92050.1; -; Genomic_DNA.
DR   PIR; T48631; T48631.
DR   RefSeq; NP_196962.1; NM_121462.4.
DR   AlphaFoldDB; Q9S7G6; -.
DR   SMR; Q9S7G6; -.
DR   STRING; 3702.AT5G14580.1; -.
DR   PaxDb; Q9S7G6; -.
DR   PRIDE; Q9S7G6; -.
DR   ProteomicsDB; 249435; -.
DR   EnsemblPlants; AT5G14580.1; AT5G14580.1; AT5G14580.
DR   GeneID; 831309; -.
DR   Gramene; AT5G14580.1; AT5G14580.1; AT5G14580.
DR   KEGG; ath:AT5G14580; -.
DR   Araport; AT5G14580; -.
DR   TAIR; locus:2222662; AT5G14580.
DR   eggNOG; KOG1067; Eukaryota.
DR   HOGENOM; CLU_004217_4_1_1; -.
DR   InParanoid; Q9S7G6; -.
DR   OMA; RAFNDGS; -.
DR   OrthoDB; 236073at2759; -.
DR   PhylomeDB; Q9S7G6; -.
DR   PRO; PR:Q9S7G6; -.
DR   Proteomes; UP000006548; Chromosome 5.
DR   ExpressionAtlas; Q9S7G6; baseline and differential.
DR   Genevisible; Q9S7G6; AT.
DR   GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR   GO; GO:0005739; C:mitochondrion; IBA:GO_Central.
DR   GO; GO:0000175; F:3'-5'-exoribonuclease activity; IMP:UniProtKB.
DR   GO; GO:0004654; F:polyribonucleotide nucleotidyltransferase activity; IMP:UniProtKB.
DR   GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0000958; P:mitochondrial mRNA catabolic process; IBA:GO_Central.
DR   GO; GO:0000965; P:mitochondrial RNA 3'-end processing; IBA:GO_Central.
DR   GO; GO:0000957; P:mitochondrial RNA catabolic process; IMP:UniProtKB.
DR   GO; GO:0000963; P:mitochondrial RNA processing; IMP:UniProtKB.
DR   GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
DR   GO; GO:0006401; P:RNA catabolic process; IBA:GO_Central.
DR   GO; GO:0006364; P:rRNA processing; IEA:UniProtKB-KW.
DR   GO; GO:0008033; P:tRNA processing; IEA:UniProtKB-KW.
DR   Gene3D; 2.40.50.140; -; 1.
DR   Gene3D; 3.30.1370.10; -; 1.
DR   Gene3D; 3.30.230.70; -; 2.
DR   HAMAP; MF_01595; PNPase; 1.
DR   InterPro; IPR001247; ExoRNase_PH_dom1.
DR   InterPro; IPR015847; ExoRNase_PH_dom2.
DR   InterPro; IPR036345; ExoRNase_PH_dom2_sf.
DR   InterPro; IPR036612; KH_dom_type_1_sf.
DR   InterPro; IPR012340; NA-bd_OB-fold.
DR   InterPro; IPR012162; PNPase.
DR   InterPro; IPR027408; PNPase/RNase_PH_dom_sf.
DR   InterPro; IPR015848; PNPase_PH_RNA-bd_bac/org-type.
DR   InterPro; IPR020568; Ribosomal_S5_D2-typ_fold.
DR   InterPro; IPR022967; S1_dom.
DR   InterPro; IPR003029; S1_domain.
DR   PANTHER; PTHR11252; PTHR11252; 1.
DR   Pfam; PF03726; PNPase; 1.
DR   Pfam; PF01138; RNase_PH; 2.
DR   Pfam; PF03725; RNase_PH_C; 1.
DR   Pfam; PF00575; S1; 1.
DR   SMART; SM00316; S1; 2.
DR   SUPFAM; SSF50249; SSF50249; 1.
DR   SUPFAM; SSF54211; SSF54211; 2.
DR   SUPFAM; SSF54791; SSF54791; 1.
DR   SUPFAM; SSF55666; SSF55666; 2.
DR   TIGRFAMs; TIGR03591; polynuc_phos; 1.
DR   PROSITE; PS50126; S1; 1.
PE   1: Evidence at protein level;
KW   Exonuclease; Hydrolase; Mitochondrion; mRNA processing; Nuclease;
KW   Nucleotidyltransferase; Reference proteome; Repeat; RNA-binding;
KW   rRNA processing; Transferase; Transit peptide; tRNA processing.
FT   TRANSIT         1..39
FT                   /note="Mitochondrion"
FT                   /evidence="ECO:0000255"
FT   CHAIN           40..991
FT                   /note="Polyribonucleotide nucleotidyltransferase 2,
FT                   mitochondrial"
FT                   /id="PRO_5001028364"
FT   DOMAIN          609..667
FT                   /note="KH"
FT   DOMAIN          678..746
FT                   /note="S1 motif 1"
FT   DOMAIN          925..987
FT                   /note="S1 motif 2"
FT   REGION          813..865
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        817..840
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ   SEQUENCE   991 AA;  107772 MW;  9557E25980C6D1A5 CRC64;
     MSSIVNRASS ASLPNFLAWR ALGFRTICSG RLGFAPSVPD SPVSAGTKIL ESFKEEFEVG
     SRVVSFETGK IARFANGSVV LGMDETKVLS TVTCAKTDSP RDFLPLTVDY QEKQYAQGLI
     PNTYMRREGA PKERELLCGR LIDRPIRPLF PTGFYHEVQI MASVLSSDGK QDPDILAANA
     SSAALMLSDV PWGGPIGVIR IGRICGQFVV NPTMDELSSS DLNLIYACTR DKTMMIDVQS
     REISEKDLAA ALRLAHPEAV KYLDPQIRLA EKAGKQKKEY KLSMLSDKTL EKVADLAATR
     IESVFTDPSY GKFERGEALD NIGKDVRKVF EEEGDQESLS ILPKAVDTVR KKVVRSRMIS
     DGFRVDGRHV DEVRPIYCES HYLPALHGSA LFSRGDTQVL CTVTLGAPAE AQSLDSLVGP
     PKKRFMLHYS FPPYCTNEVG KRGGLNRREV GHGTLAEKAL LAVLPPEEAF PYTIRINSEV
     MSSDGSTSMA SVCGGSMALM DAGIPLRAHV AGVSVGLITD VDPSSGEIKD YRIVTDILGL
     EDHLGDMDFK IAGTRDGVTA IQLDIKPAGI PLDIVCESLE NAREARLQIL DHMERNINSP
     RGQDGAYSPR LATLKYSNDS LRTLIGPMGV LKRKIEVETG ARLSIDNGTL TIVAKNQDVM
     EKAQEQVDFI IGRELVVGGV YKGTVSSIKE YGAFVEFPGG QQGLLHMSEL SHEPVSKVSD
     VLDIGQCITT MCIETDVRGN IKLSRKALLP KPKRKPASDA GKDPVMKESS TVYIENSSVG
     EIVASMPSIV TPLQKSRLSV PAVVIRTAVE CNEAEKSSPV NDNDKPRRAA TSKPDRKPKS
     TASKLIATQK EEEALESIAP EETSAECGEI LKQDGKLKSV SPKNNSTASN LVSFSKAKKS
     TMKENLSENK AEESASVSTR KLKIGTEMTA TVDHVRALGL VLDLGGEIRG MYIFQGDKDK
     FKKGDTLRVK CTSFNTKGVP VMALVDEEGE E