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Q8K1R3 (PNPT1_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Last modified May 29, 2013. Version 102. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Polyribonucleotide nucleotidyltransferase 1, mitochondrial

EC=2.7.7.8
Alternative name(s):
3'-5' RNA exonuclease OLD35
PNPase old-35
Polynucleotide phosphorylase 1
Short name=PNPase 1
Polynucleotide phosphorylase-like protein
Gene names
Name:Pnpt1
Synonyms:Pnpase
OrganismMus musculus (Mouse) [Reference proteome]
Taxonomic identifier10090 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus

Protein attributes

Sequence length783 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.7

Catalytic activity

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

Subunit structure

Homotrimer; in free form. Homooligomer. Component of the mitochondrial degradosome (mtEXO) complex which is a heteropentamer containing 2 copies of SUPV3L1 and 3 copies of PNPT1. Interacts with TCL1A; the interaction has no effect on PNPT1 exonuclease activity By similarity.

Subcellular location

Cytoplasm By similarity. Mitochondrion By similarity. Mitochondrion intermembrane space; Peripheral membrane protein Ref.6.

Disruption phenotype

Mice show alteration in the mechanisms of polycistronic mtRNAs processing in mitochondria, resulting in fewer mature mtRNAs and a reduction in electron transport chain (ETC) components formation. Ref.7

Sequence similarities

Belongs to the polyribonucleotide nucleotidyltransferase family.

Contains 1 KH domain.

Contains 1 S1 motif domain.

Sequence caution

The sequence AAO33354.1 differs from that shown. Reason: Frameshift at positions 3, 6, 20, 23, 273, 286, 300, 312, 314, 320 and 325.

Ontologies

Keywords
   Biological processTransport
mRNA processing
   Cellular componentCytoplasm
Membrane
Mitochondrion
   Coding sequence diversityAlternative splicing
   DomainTransit peptide
   LigandRNA-binding
   Molecular functionExonuclease
Hydrolase
Nuclease
Nucleotidyltransferase
Transferase
   PTMAcetylation
Phosphoprotein
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processcellular response to interferon-beta

Inferred from electronic annotation. Source: Compara

cellular response to oxidative stress

Inferred from sequence or structural similarity. Source: UniProtKB

mitochondrial RNA 3'-end processing

Inferred from sequence or structural similarity. Source: UniProtKB

mitochondrial RNA 5'-end processing

Inferred from sequence or structural similarity. Source: UniProtKB

mitochondrial mRNA catabolic process

Inferred from mutant phenotype Ref.7. Source: UniProtKB

mitochondrial mRNA polyadenylation

Inferred from sequence or structural similarity. Source: UniProtKB

mitochondrion morphogenesis

Inferred from mutant phenotype Ref.6Ref.7. Source: UniProtKB

mitotic cell cycle arrest

Inferred from sequence or structural similarity. Source: UniProtKB

negative regulation of growth

Inferred from sequence or structural similarity. Source: UniProtKB

nuclear polyadenylation-dependent mRNA catabolic process

Inferred from sequence or structural similarity. Source: UniProtKB

positive regulation of mRNA catabolic process

Inferred from sequence or structural similarity. Source: UniProtKB

positive regulation of miRNA catabolic process

Inferred from sequence or structural similarity. Source: UniProtKB

positive regulation of mitochondrial RNA catabolic process

Inferred from sequence or structural similarity. Source: UniProtKB

protein homotrimerization

Inferred from sequence or structural similarity. Source: UniProtKB

rRNA import into mitochondrion

Inferred from sequence or structural similarity. Source: UniProtKB

regulation of cellular respiration

Inferred from mutant phenotype Ref.6Ref.7. Source: UniProtKB

regulation of cellular senescence

Inferred from sequence or structural similarity. Source: UniProtKB

   Cellular_componentmitochondrial degradosome

Inferred from sequence or structural similarity. Source: UniProtKB

mitochondrial intermembrane space

Inferred from direct assay Ref.6. Source: MGI

plasma membrane

Inferred from electronic annotation. Source: Compara

   Molecular_function3'-5'-exoribonuclease activity

Inferred from sequence or structural similarity. Source: UniProtKB

miRNA binding

Inferred from sequence or structural similarity. Source: UniProtKB

poly(G) RNA binding

Inferred from sequence or structural similarity. Source: UniProtKB

poly(U) RNA binding

Inferred from sequence or structural similarity. Source: UniProtKB

polyribonucleotide nucleotidyltransferase activity

Inferred from sequence or structural similarity. Source: UniProtKB

Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q8K1R3-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
Isoform 2 (identifier: Q8K1R3-2)

The sequence of this isoform differs from the canonical sequence as follows:
     535-540: GIEDYN → ASIFPV
     541-783: Missing.
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Transit peptide1 – 4545Mitochondrion Potential
Chain46 – 783738Polyribonucleotide nucleotidyltransferase 1, mitochondrial
PRO_0000024752

Regions

Domain605 – 66460KH
Domain679 – 75072S1 motif

Amino acid modifications

Modified residue2641N6-acetyllysine By similarity
Modified residue2851N6-acetyllysine By similarity

Natural variations

Alternative sequence535 – 5406GIEDYN → ASIFPV in isoform 2.
VSP_013639
Alternative sequence541 – 783243Missing in isoform 2.
VSP_013640

Experimental info

Sequence conflict901A → P in AAO33354. Ref.2
Sequence conflict2981V → G in AAO33354. Ref.2
Sequence conflict3151K → Q in AAO33354. Ref.2
Sequence conflict4151I → V in AAO33354. Ref.2
Sequence conflict4311P → L in BAB23374. Ref.3

Secondary structure

.......... 783
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified October 1, 2002. Version 1.
Checksum: F35F6BE91AAB5626

FASTA78385,683
        10         20         30         40         50         60 
MAACRLCCLC PCLRPLGCGP LGRPGRNRAL SYLQMRALWS STGSRAVTVD LGHRKLEISS 

        70         80         90        100        110        120 
GKLARFADGC AVIQSGDTAV MVTAVSKTKA SPSQFMPLVV DYRQKAAAAG RIPTNYLRRE 

       130        140        150        160        170        180 
IGSSDREVLT SRVIDRSIRP LFPAGYFYDT QVLCNLLAVD GINEPDILAV NGASVALSLS 

       190        200        210        220        230        240 
DIPWNGPVGA VRIGMIDGEC VVNPTRREMS SSTLNLVVAG APKSQIVMLE ASAENILQQD 

       250        260        270        280        290        300 
FCHAIKVGVK YTQQIIQGIQ QLVKEIGVAK RTPQKIFTPS AEIVKYTKII AMEKLYAVFT 

       310        320        330        340        350        360 
DYEHDKVSRD EAVNKIRLDT EEHLKEKFPE VDQFEIIESF NIVAKEVFRS IILNEYKRCD 

       370        380        390        400        410        420 
GRDLTSLRNI SCEVDMFKTL HGSALFQRGQ TQVLCTVTFD SLESSIKSDQ IITAINGVKD 

       430        440        450        460        470        480 
KNFMLHYEFP PYATNETGKV TGVNRRELGH GALAEKALCP VIPKDFPFTI RVTSEVLESN 

       490        500        510        520        530        540 
GSSSMASACG GSLALMDAGV PISSAVAGVA VGLVTKTNPE KGEIEDYRLL TDILGIEDYN 

       550        560        570        580        590        600 
GDMDFKIAGT NKGITALQAD IKLPGVPIKI IMEAIQQASV AKKEILQIMN KTISKPRASR 

       610        620        630        640        650        660 
KENGPVVETV KVPLSKRAKF VGPGGYHLKK LQAETGVTIS QVDEETFSIF APTPTAMHEA 

       670        680        690        700        710        720 
RDFITEICRD DQEQQLEFGA VYTATITEIR DTGVMVKLYP NMTAVLLHNS QLDQRKIKHP 

       730        740        750        760        770        780 
TALGLEVGQE IQVKYFGRDP ADGRMRLSRK VLQSPATTAL KTLNDRSSIV MGEPVSQSSN 


SNP 

« Hide

Isoform 2 [UniParc].

Checksum: E57BFA2B602361C4
Show »

FASTA54058,923

References

« Hide 'large scale' references
[1]"Protein-protein interactions between human exosome components support the assembly of RNase PH-type subunits into a six-membered PNPase-like ring."
Raijmakers R., Vree Egberts W., van Venrooij W.J., Pruijn G.J.M.
J. Mol. Biol. 323:653-663(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
[2]"Cloning of mouse homolog of old-35."
Leszczyniecka M., Fisher P.B.
Submitted (JAN-2002) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
[3]"The transcriptional landscape of the mammalian genome."
Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J. expand/collapse author list , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
Strain: C57BL/6J.
Tissue: Liver and Lung.
[4]"Lineage-specific biology revealed by a finished genome assembly of the mouse."
Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S., She X., Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W., Kapustin Y., Meric P., Maglott D., Birtle Z., Marques A.C., Graves T., Zhou S. expand/collapse author list , Teague B., Potamousis K., Churas C., Place M., Herschleb J., Runnheim R., Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z., Lindblad-Toh K., Eichler E.E., Ponting C.P.
PLoS Biol. 7:E1000112-E1000112(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: C57BL/6J.
[5]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
Strain: FVB/N.
Tissue: Mammary gland and Mammary tumor.
[6]"Mammalian polynucleotide phosphorylase is an intermembrane space RNase that maintains mitochondrial homeostasis."
Chen H.W., Rainey R.N., Balatoni C.E., Dawson D.W., Troke J.J., Wasiak S., Hong J.S., McBride H.M., Koehler C.M., Teitell M.A., French S.W.
Mol. Cell. Biol. 26:8475-8487(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION.
[7]"PNPASE regulates RNA import into mitochondria."
Wang G., Chen H.W., Oktay Y., Zhang J., Allen E.L., Smith G.M., Fan K.C., Hong J.S., French S.W., McCaffery J.M., Lightowlers R.N., Morse H.C. III, Koehler C.M., Teitell M.A.
Cell 142:456-467(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, DISRUPTION PHENOTYPE.
[8]"Solution structure of the alpha-helical domain from mouse hypothetical PNPase."
RIKEN structural genomics initiative (RSGI)
Submitted (NOV-2004) to the PDB data bank
Cited for: STRUCTURE BY NMR OF 273-363.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AJ507387 mRNA. Translation: CAD45436.1.
AF465249 mRNA. Translation: AAO33354.1. Frameshift.
AK004563 mRNA. Translation: BAB23374.1.
AK149419 mRNA. Translation: BAE28862.1.
BX000351 Genomic DNA. Translation: CAI25081.1.
BC027228 mRNA. Translation: AAH27228.2.
BC049283 mRNA. Translation: AAH49283.1.
BC055826 mRNA. Translation: AAH55826.1.
IPIIPI00321923.
IPI00556889.
RefSeqNP_082145.1. NM_027869.1.
XP_003689309.1. XM_003689261.1.
UniGeneMm.211131.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1WHUNMR-A273-363[»]
ProteinModelPortalQ8K1R3.
SMRQ8K1R3. Positions 44-666.
ModBaseSearch...

Protein-protein interaction databases

MINTMINT-1853678.

PTM databases

PhosphoSiteQ8K1R3.

Proteomic databases

PaxDbQ8K1R3.
PRIDEQ8K1R3.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSMUST00000020756; ENSMUSP00000020756; ENSMUSG00000020464.
GeneID71701.
KEGGmmu:71701.
UCSCuc007igp.1. mouse.

Organism-specific databases

CTD87178.
MGIMGI:1918951. Pnpt1.

Phylogenomic databases

eggNOGCOG1185.
GeneTreeENSGT00390000014001.
HOGENOMHOG000218327.
HOVERGENHBG053625.
InParanoidQ8K1R3.
KOK00962.
OMARDKTLMI.
OrthoDBEOG4T4CTT.

Gene expression databases

BgeeQ8K1R3.
GenevestigatorQ8K1R3.
GermOnlineENSMUSG00000020464. Mus musculus.

Family and domain databases

Gene3D1.10.10.400. 1 hit.
2.40.50.140. 1 hit.
3.30.230.70. 2 hits.
InterProIPR001247. 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]
PANTHERPTHR11252. PTHR11252. 1 hit.
PfamPF00013. KH_1. 1 hit.
PF03726. PNPase. 1 hit.
PF01138. RNase_PH. 2 hits.
PF03725. RNase_PH_C. 2 hits.
PF00575. S1. 1 hit.
[Graphical view]
PIRSFPIRSF005499. PNPase. 1 hit.
SMARTSM00322. KH. 1 hit.
SM00316. S1. 1 hit.
[Graphical view]
SUPFAMSSF46915. 3_ExoRNase. 1 hit.
SSF55666. 3_ExoRNase. 2 hits.
SSF50249. Nucleic_acid_OB. 1 hit.
SSF54211. Ribosomal_S5_D2-typ_fold. 2 hits.
TIGRFAMsTIGR03591. polynuc_phos. 1 hit.
PROSITEPS50084. KH_TYPE_1. 1 hit.
PS50126. S1. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ8K1R3.
NextBio334263.
SOURCESearch...

Entry information

Entry namePNPT1_MOUSE
AccessionPrimary (citable) accession number: Q8K1R3
Secondary accession number(s): Q3UEP9 expand/collapse secondary AC list , Q810U7, Q812B3, Q8R2U3, Q9DC52
Entry history
Integrated into UniProtKB/Swiss-Prot: May 10, 2005
Last sequence update: October 1, 2002
Last modified: May 29, 2013
This is version 102 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

MGD cross-references

Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families