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Q8GZQ3

- PNP1_ARATH

UniProt

Q8GZQ3 - PNP1_ARATH

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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

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
Complete GO annotation...

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
Complete GO annotation...

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. S1_dom.
[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

        10         20         30         40         50
MLTSPSNALH SSTPQFWPLR RSKLCRSRNF PRFHSGERSS GGGGKLCSLS
60 70 80 90 100
LLSGSGAGKF SVRALVRPDD TDDADSVGDG SLAFPNHVSV KIPFGNREIL
110 120 130 140 150
VETGLMGRQA SSAVTVTDGE TIVYTSVCLA DVPSEPSDFL PLYVHYQERF
160 170 180 190 200
SAVGRTSGGF FKREGRTKDH EVLICRLIDR PLRPTMPKGF YNETQILSWV
210 220 230 240 250
LSYDGLHAPD ALAVTSAGIA VALSEVPNAK AIAGVRVGLI GGEFIVNPTV
260 270 280 290 300
KEMEESQLDL FLAGTDTAIL TIEGYSNFLP EEMLLQAVKV GQDAVQATCI
310 320 330 340 350
AIEVLAKKYG KPKMLDAIRL PPPELYKHVK ELAGEELTKA LQIKSKISRR
360 370 380 390 400
KAISSLEEKV LTILTEKGYV IDEVAFGTIE AQPDLLEDED EDEEVVPEGE
410 420 430 440 450
VDQGDVHIRP IPRKPIPLLF SEVDVKLVFK EVSSKLLRRR IVEGGKRSDG
460 470 480 490 500
RTLDEIRPIN SRCGLLPRAH GSTLFTRGET QALAVVTLGD KQMAQRIDNL
510 520 530 540 550
EGSDEYKRFY LQYTFPPSSV GEVGRIGAPS RREIGHGTLA ERALETILPS
560 570 580 590 600
DDDFPYTIRV ESTVIESNGS SSMASVCGGC LALQDAGVPV KCSVAGIAMG
610 620 630 640 650
MVWDTEEFGG DGSPLILSDI TGAEDASGDM DFKVAGNEDG VTAFQMDIKV
660 670 680 690 700
GGITLEIMEK ALIQAKAGRR HILAEMAKCS PPPTLSLSKY APLILIMKVH
710 720 730 740 750
PSKVYSLIGS GGKKVKSIIE ESGVEAIDMQ DDGTVKIMAI DVASLERAKA
760 770 780 790 800
IISGLTMVPS VGDIYRNCEI KSMAPYGAFV EIAPGREGLC HISELSAEWL
810 820 830 840 850
AKPEDAYKVG DRIDVKLIEV NEKGQLRLSV RALLPESETD KDSQKQQPAG
860 870 880 890 900
DSTKDKSSQR KYVNTSSKDR AAAGASKVSS GDELVLKKKD VRRATGGSSD
910 920
KTMNSNSSTN EESLVNGEAT IS
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. S1_dom.
[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

« Hide 'large scale' publications
  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 29, 2014
This is version 95 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