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Q8GZQ3

- PNP1_ARATH

UniProt

Q8GZQ3 - PNP1_ARATH

Protein

Polyribonucleotide nucleotidyltransferase 1, chloroplastic

Gene

PNP1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 94 (01 Oct 2014)
      Sequence version 1 (01 Mar 2003)
      Previous versions | rss
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    Functioni

    Involved in the metabolism of all major classes of plastid RNAs. Required for efficient 3'-end processing of mRNAs and 3'-end maturation of rRNA transcripts, but is not sufficient to mediate their degradation. Mediates tRNA degradation. May function as a poly(A) mRNA 3'-5' degrading phosphorylase. May be required for plastid ribosome assembly and non-coding RNA biogenesis and accumulation. Seems not required for efficient translation.4 Publications

    Catalytic activityi

    RNA(n+1) + phosphate = RNA(n) + a nucleoside diphosphate.

    GO - Molecular functioni

    1. 3'-5'-exoribonuclease activity Source: UniProtKB
    2. polyribonucleotide nucleotidyltransferase activity Source: UniProtKB
    3. RNA binding Source: UniProtKB-KW

    GO - Biological processi

    1. carotene biosynthetic process Source: TAIR
    2. cellular response to phosphate starvation Source: TAIR
    3. chlorophyll biosynthetic process Source: TAIR
    4. chloroplast RNA processing Source: UniProtKB
    5. mRNA catabolic process Source: InterPro
    6. mRNA processing Source: UniProtKB-KW
    7. negative regulation of isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway Source: TAIR
    8. RNA catabolic process Source: UniProtKB
    9. RNA phosphodiester bond hydrolysis, exonucleolytic Source: GOC
    10. rRNA processing Source: UniProtKB-KW
    11. tRNA processing Source: UniProtKB-KW
    12. xanthophyll biosynthetic process Source: TAIR

    Keywords - Molecular functioni

    Exonuclease, Hydrolase, Nuclease, Nucleotidyltransferase, Transferase

    Keywords - Biological processi

    mRNA processing, rRNA processing, tRNA processing

    Keywords - Ligandi

    RNA-binding

    Enzyme and pathway databases

    BioCyciARA:AT3G03710-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Polyribonucleotide nucleotidyltransferase 1, chloroplastic (EC:2.7.7.8)
    Short name:
    AtcpPNPase
    Alternative name(s):
    Polynucleotide phosphorylase 1
    Short name:
    PNPase 1
    Protein PIGMENT DEFECTIVE 326
    Protein RESISTANT TO INHIBITION WITH FSM 10
    Gene namesi
    Name:PNP1
    Synonyms:PDE326, RIF10
    Ordered Locus Names:At3g03710
    ORF Names:F20H23.26, T12J13.1
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    ProteomesiUP000006548: Chromosome 3

    Organism-specific databases

    TAIRiAT3G03710.

    Subcellular locationi

    Plastidchloroplast 2 Publications

    GO - Cellular componenti

    1. chloroplast Source: TAIR
    2. chloroplast stroma Source: TAIR

    Keywords - Cellular componenti

    Chloroplast, Plastid

    Pathology & Biotechi

    Disruption phenotypei

    Delayed greening and retarded growth.3 Publications

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi176 – 1761R → S: Reduces RNA-binding affinity; when associated with L-184. 1 Publication
    Mutagenesisi184 – 1841P → L: Reduces RNA-binding affinity; when associated with S-176. 1 Publication
    Mutagenesisi202 – 2021S → N: No effect on activity or DNA binding. 1 Publication
    Mutagenesisi596 – 5961G → R: Loss of activity. 1 Publication
    Mutagenesisi625 – 6251D → N: Loss of activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transit peptidei1 – 4848ChloroplastSequence AnalysisAdd
    BLAST
    Chaini49 – 922874Polyribonucleotide nucleotidyltransferase 1, chloroplasticPRO_0000420275Add
    BLAST

    Proteomic databases

    PRIDEiQ8GZQ3.

    Expressioni

    Gene expression databases

    GenevestigatoriQ8GZQ3.

    Interactioni

    Protein-protein interaction databases

    STRINGi3702.AT3G03710.1-P.

    Structurei

    3D structure databases

    ProteinModelPortaliQ8GZQ3.
    SMRiQ8GZQ3. Positions 92-865.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini692 – 75261KHAdd
    BLAST
    Domaini762 – 83170S1 motifAdd
    BLAST

    Sequence similaritiesi

    Contains 1 KH domain.Curated
    Contains 1 S1 motif domain.Curated

    Keywords - Domaini

    Transit peptide

    Phylogenomic databases

    HOGENOMiHOG000218327.
    InParanoidiQ8GZQ3.
    KOiK00962.
    OMAiHGNFKSN.
    PhylomeDBiQ8GZQ3.

    Family and domain databases

    Gene3Di1.10.10.400. 2 hits.
    2.40.50.140. 1 hit.
    3.30.1370.10. 1 hit.
    3.30.230.70. 2 hits.
    HAMAPiMF_01595. PNPase.
    InterProiIPR001247. 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.
    [Graphical view]
    PANTHERiPTHR11252. PTHR11252. 1 hit.
    PfamiPF00013. KH_1. 1 hit.
    PF01138. RNase_PH. 2 hits.
    PF03725. RNase_PH_C. 2 hits.
    PF00575. S1. 1 hit.
    [Graphical view]
    SMARTiSM00322. KH. 1 hit.
    SM00316. S1. 1 hit.
    [Graphical view]
    SUPFAMiSSF46915. SSF46915. 1 hit.
    SSF50249. SSF50249. 1 hit.
    SSF54211. SSF54211. 2 hits.
    SSF54791. SSF54791. 1 hit.
    SSF55666. SSF55666. 2 hits.
    TIGRFAMsiTIGR03591. polynuc_phos. 1 hit.
    PROSITEiPS50084. KH_TYPE_1. 1 hit.
    PS50126. S1. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    Q8GZQ3-1 [UniParc]FASTAAdd to Basket

    « Hide

    MLTSPSNALH SSTPQFWPLR RSKLCRSRNF PRFHSGERSS GGGGKLCSLS    50
    LLSGSGAGKF SVRALVRPDD TDDADSVGDG SLAFPNHVSV KIPFGNREIL 100
    VETGLMGRQA SSAVTVTDGE TIVYTSVCLA DVPSEPSDFL PLYVHYQERF 150
    SAVGRTSGGF FKREGRTKDH EVLICRLIDR PLRPTMPKGF YNETQILSWV 200
    LSYDGLHAPD ALAVTSAGIA VALSEVPNAK AIAGVRVGLI GGEFIVNPTV 250
    KEMEESQLDL FLAGTDTAIL TIEGYSNFLP EEMLLQAVKV GQDAVQATCI 300
    AIEVLAKKYG KPKMLDAIRL PPPELYKHVK ELAGEELTKA LQIKSKISRR 350
    KAISSLEEKV LTILTEKGYV IDEVAFGTIE AQPDLLEDED EDEEVVPEGE 400
    VDQGDVHIRP IPRKPIPLLF SEVDVKLVFK EVSSKLLRRR IVEGGKRSDG 450
    RTLDEIRPIN SRCGLLPRAH GSTLFTRGET QALAVVTLGD KQMAQRIDNL 500
    EGSDEYKRFY LQYTFPPSSV GEVGRIGAPS RREIGHGTLA ERALETILPS 550
    DDDFPYTIRV ESTVIESNGS SSMASVCGGC LALQDAGVPV KCSVAGIAMG 600
    MVWDTEEFGG DGSPLILSDI TGAEDASGDM DFKVAGNEDG VTAFQMDIKV 650
    GGITLEIMEK ALIQAKAGRR HILAEMAKCS PPPTLSLSKY APLILIMKVH 700
    PSKVYSLIGS GGKKVKSIIE ESGVEAIDMQ DDGTVKIMAI DVASLERAKA 750
    IISGLTMVPS VGDIYRNCEI KSMAPYGAFV EIAPGREGLC HISELSAEWL 800
    AKPEDAYKVG DRIDVKLIEV NEKGQLRLSV RALLPESETD KDSQKQQPAG 850
    DSTKDKSSQR KYVNTSSKDR AAAGASKVSS GDELVLKKKD VRRATGGSSD 900
    KTMNSNSSTN EESLVNGEAT IS 922
    Length:922
    Mass (Da):99,566
    Last modified:March 1, 2003 - v1
    Checksum:iA6FFBB738F762838
    GO

    Sequence cautioni

    The sequence AAF00646.1 differs from that shown. Reason: Erroneous gene model prediction.
    The sequence AAF03462.1 differs from that shown. Reason: Erroneous gene model prediction.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti355 – 3551S → P in CAB85703. 1 PublicationCurated
    Sequence conflicti823 – 8231K → E in CAB85703. 1 PublicationCurated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AJ252123 mRNA. Translation: CAB85703.1.
    AF450480 mRNA. Translation: AAN76771.1.
    AC009327 Genomic DNA. Translation: AAF03462.1. Sequence problems.
    AC009540 Genomic DNA. Translation: AAF00646.1. Sequence problems.
    CP002686 Genomic DNA. Translation: AEE73974.1.
    RefSeqiNP_187021.2. NM_111242.2.
    UniGeneiAt.26536.

    Genome annotation databases

    EnsemblPlantsiAT3G03710.1; AT3G03710.1; AT3G03710.
    GeneIDi821181.
    KEGGiath:AT3G03710.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AJ252123 mRNA. Translation: CAB85703.1 .
    AF450480 mRNA. Translation: AAN76771.1 .
    AC009327 Genomic DNA. Translation: AAF03462.1 . Sequence problems.
    AC009540 Genomic DNA. Translation: AAF00646.1 . Sequence problems.
    CP002686 Genomic DNA. Translation: AEE73974.1 .
    RefSeqi NP_187021.2. NM_111242.2.
    UniGenei At.26536.

    3D structure databases

    ProteinModelPortali Q8GZQ3.
    SMRi Q8GZQ3. Positions 92-865.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 3702.AT3G03710.1-P.

    Proteomic databases

    PRIDEi Q8GZQ3.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi AT3G03710.1 ; AT3G03710.1 ; AT3G03710 .
    GeneIDi 821181.
    KEGGi ath:AT3G03710.

    Organism-specific databases

    GeneFarmi 4127.
    TAIRi AT3G03710.

    Phylogenomic databases

    HOGENOMi HOG000218327.
    InParanoidi Q8GZQ3.
    KOi K00962.
    OMAi HGNFKSN.
    PhylomeDBi Q8GZQ3.

    Enzyme and pathway databases

    BioCyci ARA:AT3G03710-MONOMER.

    Gene expression databases

    Genevestigatori Q8GZQ3.

    Family and domain databases

    Gene3Di 1.10.10.400. 2 hits.
    2.40.50.140. 1 hit.
    3.30.1370.10. 1 hit.
    3.30.230.70. 2 hits.
    HAMAPi MF_01595. PNPase.
    InterProi 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.
    [Graphical view ]
    PANTHERi PTHR11252. PTHR11252. 1 hit.
    Pfami PF00013. KH_1. 1 hit.
    PF01138. RNase_PH. 2 hits.
    PF03725. RNase_PH_C. 2 hits.
    PF00575. S1. 1 hit.
    [Graphical view ]
    SMARTi SM00322. KH. 1 hit.
    SM00316. S1. 1 hit.
    [Graphical view ]
    SUPFAMi SSF46915. SSF46915. 1 hit.
    SSF50249. SSF50249. 1 hit.
    SSF54211. SSF54211. 2 hits.
    SSF54791. SSF54791. 1 hit.
    SSF55666. SSF55666. 2 hits.
    TIGRFAMsi TIGR03591. polynuc_phos. 1 hit.
    PROSITEi PS50084. KH_TYPE_1. 1 hit.
    PS50126. S1. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "PNPase activity determines the efficiency of mRNA 3'-end processing, the degradation of tRNA and the extent of polyadenylation in chloroplasts."
      Walter M., Kilian J., Kudla J.
      EMBO J. 21:6905-6914(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, SUBCELLULAR LOCATION.
      Strain: cv. Columbia.
    2. "Characterisation of a cDNA encoding polynucleotidephosphorylase from Arabidopsis thaliana."
      Mudd E.A., Sullivan J.S., Day A.
      Submitted (DEC-1999) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    3. "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana."
      Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B., Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M., Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V., Choisne N., Artiguenave F.
      , Robert C., Brottier P., Wincker P., Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H., Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H., Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A., Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H., Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J., Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B., Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D., de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E., Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G., Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X., Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M., Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B., Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J., Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C., Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y., Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K., Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Tabata S.
      Nature 408:820-822(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Columbia.
    4. The Arabidopsis Information Resource (TAIR)
      Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
      Cited for: GENOME REANNOTATION.
      Strain: cv. Columbia.
    5. "Plastid cues posttranscriptionally regulate the accumulation of key enzymes of the methylerythritol phosphate pathway in Arabidopsis."
      Sauret-Gueeto S., Botella-Pavia P., Flores-Perez U., Martinez-Garcia J.F., San Roman C., Leon P., Boronat A., Rodriguez-Concepcion M.
      Plant Physiol. 141:75-84(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: DISRUPTION PHENOTYPE.
      Strain: cv. Columbia.
    6. "A mutant impaired in the production of plastome-encoded proteins uncovers a mechanism for the homeostasis of isoprenoid biosynthetic enzymes in Arabidopsis plastids."
      Flores-Perez U., Sauret-Gueeto S., Gas E., Jarvis P., Rodriguez-Concepcion M.
      Plant Cell 20:1303-1315(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBCELLULAR LOCATION.
    7. "Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks."
      Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A., Grossmann J., Gruissem W., Baginsky S.
      Plant Physiol. 150:889-903(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    8. "Abnormal physiological and molecular mutant phenotypes link chloroplast polynucleotide phosphorylase to the phosphorus deprivation response in Arabidopsis."
      Marchive C., Yehudai-Resheff S., Germain A., Fei Z., Jiang X., Judkins J., Wu H., Fernie A.R., Fait A., Stern D.B.
      Plant Physiol. 151:905-924(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: DISRUPTION PHENOTYPE.
    9. "Unexpected diversity of chloroplast noncoding RNAs as revealed by deep sequencing of the Abidopsis transcriptome."
      Hotto A.M., Schmitz R.J., Fei Z., Ecker J.R., Stern D.B.
      G3 (Bethesda) 1:559-570(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    10. "Mutational analysis of Arabidopsis chloroplast polynucleotide phosphorylase reveals roles for both RNase PH core domains in polyadenylation, RNA 3'-end maturation and intron degradation."
      Germain A., Herlich S., Larom S., Kim S.H., Schuster G., Stern D.B.
      Plant J. 67:381-394(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, DISRUPTION PHENOTYPE, MUTAGENESIS OF ARG-176; PRO-184; SER-202; GLY-596 AND ASP-625.

    Entry informationi

    Entry nameiPNP1_ARATH
    AccessioniPrimary (citable) accession number: Q8GZQ3
    Secondary accession number(s): Q9M497, Q9S749
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 28, 2012
    Last sequence update: March 1, 2003
    Last modified: October 1, 2014
    This is version 94 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Arabidopsis thaliana
      Arabidopsis thaliana: entries and gene names
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3