PNP1_ARATH
ID PNP1_ARATH Reviewed; 922 AA.
AC Q8GZQ3; Q9M497; Q9S749;
DT 28-NOV-2012, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2003, sequence version 1.
DT 25-MAY-2022, entry version 139.
DE RecName: Full=Polyribonucleotide nucleotidyltransferase 1, chloroplastic;
DE Short=AtcpPNPase;
DE EC=2.7.7.8;
DE AltName: Full=Polynucleotide phosphorylase 1;
DE Short=PNPase 1;
DE AltName: Full=Protein PIGMENT DEFECTIVE 326;
DE AltName: Full=Protein RESISTANT TO INHIBITION WITH FSM 10;
DE Flags: Precursor;
GN Name=PNP1; Synonyms=PDE326, RIF10; OrderedLocusNames=At3g03710;
GN ORFNames=F20H23.26, T12J13.1;
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 [MRNA], FUNCTION, AND SUBCELLULAR LOCATION.
RC STRAIN=cv. Columbia;
RX PubMed=12486011; DOI=10.1093/emboj/cdf686;
RA Walter M., Kilian J., Kudla J.;
RT "PNPase activity determines the efficiency of mRNA 3'-end processing, the
RT degradation of tRNA and the extent of polyadenylation in chloroplasts.";
RL EMBO J. 21:6905-6914(2002).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA].
RA Mudd E.A., Sullivan J.S., Day A.;
RT "Characterisation of a cDNA encoding polynucleotidephosphorylase from
RT Arabidopsis thaliana.";
RL Submitted (DEC-1999) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(2000).
RN [4]
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 [5]
RP DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=16531478; DOI=10.1104/pp.106.079855;
RA Sauret-Gueeto S., Botella-Pavia P., Flores-Perez U., Martinez-Garcia J.F.,
RA San Roman C., Leon P., Boronat A., Rodriguez-Concepcion M.;
RT "Plastid cues posttranscriptionally regulate the accumulation of key
RT enzymes of the methylerythritol phosphate pathway in Arabidopsis.";
RL Plant Physiol. 141:75-84(2006).
RN [6]
RP FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=18469163; DOI=10.1105/tpc.108.058768;
RA Flores-Perez U., Sauret-Gueeto S., Gas E., Jarvis P.,
RA Rodriguez-Concepcion M.;
RT "A mutant impaired in the production of plastome-encoded proteins uncovers
RT a mechanism for the homeostasis of isoprenoid biosynthetic enzymes in
RT Arabidopsis plastids.";
RL Plant Cell 20:1303-1315(2008).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19376835; DOI=10.1104/pp.109.138677;
RA Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A.,
RA Grossmann J., Gruissem W., Baginsky S.;
RT "Large-scale Arabidopsis phosphoproteome profiling reveals novel
RT chloroplast kinase substrates and phosphorylation networks.";
RL Plant Physiol. 150:889-903(2009).
RN [8]
RP DISRUPTION PHENOTYPE.
RX PubMed=19710229; DOI=10.1104/pp.109.145144;
RA Marchive C., Yehudai-Resheff S., Germain A., Fei Z., Jiang X., Judkins J.,
RA Wu H., Fernie A.R., Fait A., Stern D.B.;
RT "Abnormal physiological and molecular mutant phenotypes link chloroplast
RT polynucleotide phosphorylase to the phosphorus deprivation response in
RT Arabidopsis.";
RL Plant Physiol. 151:905-924(2009).
RN [9]
RP FUNCTION.
RX PubMed=22384367; DOI=10.1534/g3.111.000752;
RA Hotto A.M., Schmitz R.J., Fei Z., Ecker J.R., Stern D.B.;
RT "Unexpected diversity of chloroplast noncoding RNAs as revealed by deep
RT sequencing of the Arabidopsis transcriptome.";
RL G3 (Bethesda) 1:559-570(2011).
RN [10]
RP FUNCTION, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF ARG-176; PRO-184;
RP SER-202; GLY-596 AND ASP-625.
RX PubMed=21466602; DOI=10.1111/j.1365-313x.2011.04601.x;
RA Germain A., Herlich S., Larom S., Kim S.H., Schuster G., Stern D.B.;
RT "Mutational analysis of Arabidopsis chloroplast polynucleotide
RT phosphorylase reveals roles for both RNase PH core domains in
RT polyadenylation, RNA 3'-end maturation and intron degradation.";
RL Plant J. 67:381-394(2011).
CC -!- FUNCTION: Involved in the metabolism of all major classes of plastid
CC RNAs. Required for efficient 3'-end processing of mRNAs and 3'-end
CC maturation of rRNA transcripts, but is not sufficient to mediate their
CC degradation. Mediates tRNA degradation. May function as a poly(A) mRNA
CC 3'-5' degrading phosphorylase. May be required for plastid ribosome
CC assembly and non-coding RNA biogenesis and accumulation. Seems not
CC required for efficient translation. {ECO:0000269|PubMed:12486011,
CC ECO:0000269|PubMed:18469163, ECO:0000269|PubMed:21466602,
CC ECO:0000269|PubMed:22384367}.
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;
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:12486011, ECO:0000269|PubMed:18469163}.
CC -!- DISRUPTION PHENOTYPE: Delayed greening and retarded growth.
CC {ECO:0000269|PubMed:16531478, ECO:0000269|PubMed:19710229,
CC ECO:0000269|PubMed:21466602}.
CC -!- SIMILARITY: Belongs to the polyribonucleotide nucleotidyltransferase
CC family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF00646.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=AAF03462.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AJ252123; CAB85703.1; -; mRNA.
DR EMBL; AF450480; AAN76771.1; -; mRNA.
DR EMBL; AC009327; AAF03462.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AC009540; AAF00646.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002686; AEE73974.1; -; Genomic_DNA.
DR RefSeq; NP_187021.2; NM_111242.3.
DR AlphaFoldDB; Q8GZQ3; -.
DR SMR; Q8GZQ3; -.
DR BioGRID; 6514; 4.
DR STRING; 3702.AT3G03710.1; -.
DR iPTMnet; Q8GZQ3; -.
DR PaxDb; Q8GZQ3; -.
DR PRIDE; Q8GZQ3; -.
DR ProteomicsDB; 250561; -.
DR EnsemblPlants; AT3G03710.1; AT3G03710.1; AT3G03710.
DR GeneID; 821181; -.
DR Gramene; AT3G03710.1; AT3G03710.1; AT3G03710.
DR KEGG; ath:AT3G03710; -.
DR Araport; AT3G03710; -.
DR TAIR; locus:2079429; AT3G03710.
DR eggNOG; KOG1067; Eukaryota.
DR HOGENOM; CLU_004217_2_2_1; -.
DR InParanoid; Q8GZQ3; -.
DR OMA; LHILDVM; -.
DR OrthoDB; 236073at2759; -.
DR PhylomeDB; Q8GZQ3; -.
DR PRO; PR:Q8GZQ3; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q8GZQ3; baseline and differential.
DR Genevisible; Q8GZQ3; AT.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0005739; C:mitochondrion; IBA:GO_Central.
DR GO; GO:0000175; F:3'-5'-exoribonuclease activity; IMP:UniProtKB.
DR GO; GO:0003729; F:mRNA binding; IDA:TAIR.
DR GO; GO:0004654; F:polyribonucleotide nucleotidyltransferase activity; IMP:UniProtKB.
DR GO; GO:0016120; P:carotene biosynthetic process; IMP:TAIR.
DR GO; GO:0016036; P:cellular response to phosphate starvation; IMP:TAIR.
DR GO; GO:0015995; P:chlorophyll biosynthetic process; IMP:TAIR.
DR GO; GO:0031425; P:chloroplast RNA processing; IMP:UniProtKB.
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:0006397; P:mRNA processing; IEA:UniProtKB-KW.
DR GO; GO:0010323; P:negative regulation of isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway; IMP:TAIR.
DR GO; GO:0006401; P:RNA catabolic process; IMP:UniProtKB.
DR GO; GO:0006364; P:rRNA processing; IEA:UniProtKB-KW.
DR GO; GO:0008033; P:tRNA processing; IEA:UniProtKB-KW.
DR GO; GO:0016123; P:xanthophyll biosynthetic process; IMP:TAIR.
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; IPR004087; KH_dom.
DR InterPro; IPR004088; KH_dom_type_1.
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; IPR036456; PNPase_PH_RNA-bd_sf.
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; PF00013; KH_1; 1.
DR Pfam; PF01138; RNase_PH; 2.
DR Pfam; PF03725; RNase_PH_C; 2.
DR Pfam; PF00575; S1; 1.
DR SMART; SM00322; KH; 1.
DR SMART; SM00316; S1; 1.
DR SUPFAM; SSF46915; SSF46915; 1.
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; PS50084; KH_TYPE_1; 1.
DR PROSITE; PS50126; S1; 1.
PE 1: Evidence at protein level;
KW Chloroplast; Exonuclease; Hydrolase; mRNA processing; Nuclease;
KW Nucleotidyltransferase; Plastid; Reference proteome; RNA-binding;
KW rRNA processing; Transferase; Transit peptide; tRNA processing.
FT TRANSIT 1..48
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 49..922
FT /note="Polyribonucleotide nucleotidyltransferase 1,
FT chloroplastic"
FT /id="PRO_0000420275"
FT DOMAIN 692..752
FT /note="KH"
FT DOMAIN 762..831
FT /note="S1 motif"
FT REGION 833..922
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 834..863
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 882..896
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 897..922
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MUTAGEN 176
FT /note="R->S: Reduces RNA-binding affinity; when associated
FT with L-184."
FT /evidence="ECO:0000269|PubMed:21466602"
FT MUTAGEN 184
FT /note="P->L: Reduces RNA-binding affinity; when associated
FT with S-176."
FT /evidence="ECO:0000269|PubMed:21466602"
FT MUTAGEN 202
FT /note="S->N: No effect on activity or DNA binding."
FT /evidence="ECO:0000269|PubMed:21466602"
FT MUTAGEN 596
FT /note="G->R: Loss of activity."
FT /evidence="ECO:0000269|PubMed:21466602"
FT MUTAGEN 625
FT /note="D->N: Loss of activity."
FT /evidence="ECO:0000269|PubMed:21466602"
FT CONFLICT 355
FT /note="S -> P (in Ref. 2; CAB85703)"
FT /evidence="ECO:0000305"
FT CONFLICT 823
FT /note="K -> E (in Ref. 2; CAB85703)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 922 AA; 99566 MW; A6FFBB738F762838 CRC64;
MLTSPSNALH SSTPQFWPLR RSKLCRSRNF PRFHSGERSS GGGGKLCSLS LLSGSGAGKF
SVRALVRPDD TDDADSVGDG SLAFPNHVSV KIPFGNREIL VETGLMGRQA SSAVTVTDGE
TIVYTSVCLA DVPSEPSDFL PLYVHYQERF SAVGRTSGGF FKREGRTKDH EVLICRLIDR
PLRPTMPKGF YNETQILSWV LSYDGLHAPD ALAVTSAGIA VALSEVPNAK AIAGVRVGLI
GGEFIVNPTV KEMEESQLDL FLAGTDTAIL TIEGYSNFLP EEMLLQAVKV GQDAVQATCI
AIEVLAKKYG KPKMLDAIRL PPPELYKHVK ELAGEELTKA LQIKSKISRR KAISSLEEKV
LTILTEKGYV IDEVAFGTIE AQPDLLEDED EDEEVVPEGE VDQGDVHIRP IPRKPIPLLF
SEVDVKLVFK EVSSKLLRRR IVEGGKRSDG RTLDEIRPIN SRCGLLPRAH GSTLFTRGET
QALAVVTLGD KQMAQRIDNL EGSDEYKRFY LQYTFPPSSV GEVGRIGAPS RREIGHGTLA
ERALETILPS DDDFPYTIRV ESTVIESNGS SSMASVCGGC LALQDAGVPV KCSVAGIAMG
MVWDTEEFGG DGSPLILSDI TGAEDASGDM DFKVAGNEDG VTAFQMDIKV GGITLEIMEK
ALIQAKAGRR HILAEMAKCS PPPTLSLSKY APLILIMKVH PSKVYSLIGS GGKKVKSIIE
ESGVEAIDMQ DDGTVKIMAI DVASLERAKA IISGLTMVPS VGDIYRNCEI KSMAPYGAFV
EIAPGREGLC HISELSAEWL AKPEDAYKVG DRIDVKLIEV NEKGQLRLSV RALLPESETD
KDSQKQQPAG DSTKDKSSQR KYVNTSSKDR AAAGASKVSS GDELVLKKKD VRRATGGSSD
KTMNSNSSTN EESLVNGEAT IS
