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Protein

Polyribonucleotide nucleotidyltransferase 1, mitochondrial

Gene

Pnpt1

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

RNA-binding protein implicated in numerous RNA metabolic processes. Catalyzes the phosphorolysis of 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.1 Publication

Catalytic activityi

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

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionExonuclease, Hydrolase, Nuclease, Nucleotidyltransferase, RNA-binding, Transferase
Biological processmRNA processing, Transport

Names & Taxonomyi

Protein namesi
Recommended 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 namesi
Name:Pnpt1
Synonyms:Pnpase
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 11

Organism-specific databases

MGIiMGI:1918951 Pnpt1

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Membrane, Mitochondrion

Pathology & Biotechi

Disruption phenotypei

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.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transit peptidei1 – 45MitochondrionSequence analysisAdd BLAST45
ChainiPRO_000002475246 – 783Polyribonucleotide nucleotidyltransferase 1, mitochondrialAdd BLAST738

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei250N6-acetyllysineCombined sources1
Modified residuei264N6-acetyllysineBy similarity1
Modified residuei285N6-acetyllysineBy similarity1
Modified residuei552N6-succinyllysineCombined sources1
Modified residuei754PhosphoserineBy similarity1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiQ8K1R3
PaxDbiQ8K1R3
PeptideAtlasiQ8K1R3
PRIDEiQ8K1R3

PTM databases

iPTMnetiQ8K1R3
PhosphoSitePlusiQ8K1R3
SwissPalmiQ8K1R3

Expressioni

Gene expression databases

BgeeiENSMUSG00000020464
GenevisibleiQ8K1R3 MM

Interactioni

Subunit structurei

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).By similarity

Protein-protein interaction databases

IntActiQ8K1R3, 1 interactor
STRINGi10090.ENSMUSP00000020756

Structurei

Secondary structure

1783
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi281 – 299Combined sources19
Helixi307 – 324Combined sources18
Turni325 – 327Combined sources3
Beta strandi329 – 331Combined sources3
Helixi333 – 352Combined sources20

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1WHUNMR-A273-363[»]
ProteinModelPortaliQ8K1R3
SMRiQ8K1R3
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ8K1R3

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini605 – 664KHPROSITE-ProRule annotationAdd BLAST60
Domaini679 – 750S1 motifPROSITE-ProRule annotationAdd BLAST72

Sequence similaritiesi

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiKOG1067 Eukaryota
COG1185 LUCA
GeneTreeiENSGT00390000014001
HOGENOMiHOG000218327
HOVERGENiHBG053625
InParanoidiQ8K1R3
KOiK00962
OMAiRYMHNYN
OrthoDBiEOG091G03MA
PhylomeDBiQ8K1R3
TreeFamiTF315264

Family and domain databases

Gene3Di3.30.1370.10, 1 hit
3.30.230.70, 2 hits
InterProiView protein in InterPro
IPR001247 ExoRNase_PH_dom1
IPR015847 ExoRNase_PH_dom2
IPR036345 ExoRNase_PH_dom2_sf
IPR004087 KH_dom
IPR004088 KH_dom_type_1
IPR036612 KH_dom_type_1_sf
IPR012340 NA-bd_OB-fold
IPR012162 PNPase
IPR027408 PNPase/RNase_PH_dom_sf
IPR015848 PNPase_PH_RNA-bd_bac/org-type
IPR036456 PNPase_PH_RNA-bd_sf
IPR020568 Ribosomal_S5_D2-typ_fold
IPR022967 S1_dom
IPR003029 S1_domain
PANTHERiPTHR11252 PTHR11252, 1 hit
PfamiView protein in Pfam
PF00013 KH_1, 1 hit
PF03726 PNPase, 1 hit
PF01138 RNase_PH, 2 hits
PF03725 RNase_PH_C, 1 hit
PF00575 S1, 1 hit
PIRSFiPIRSF005499 PNPase, 1 hit
SMARTiView protein in SMART
SM00322 KH, 1 hit
SM00316 S1, 1 hit
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
PROSITEiView protein in PROSITE
PS50084 KH_TYPE_1, 1 hit
PS50126 S1, 1 hit

Sequences (2)i

Sequence statusi: Complete.

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

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q8K1R3-1) [UniParc]FASTAAdd to basket

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.

« Hide

        10         20         30         40         50
MAACRLCCLC PCLRPLGCGP LGRPGRNRAL SYLQMRALWS STGSRAVTVD
60 70 80 90 100
LGHRKLEISS GKLARFADGC AVIQSGDTAV MVTAVSKTKA SPSQFMPLVV
110 120 130 140 150
DYRQKAAAAG RIPTNYLRRE IGSSDREVLT SRVIDRSIRP LFPAGYFYDT
160 170 180 190 200
QVLCNLLAVD GINEPDILAV NGASVALSLS DIPWNGPVGA VRIGMIDGEC
210 220 230 240 250
VVNPTRREMS SSTLNLVVAG APKSQIVMLE ASAENILQQD FCHAIKVGVK
260 270 280 290 300
YTQQIIQGIQ QLVKEIGVAK RTPQKIFTPS AEIVKYTKII AMEKLYAVFT
310 320 330 340 350
DYEHDKVSRD EAVNKIRLDT EEHLKEKFPE VDQFEIIESF NIVAKEVFRS
360 370 380 390 400
IILNEYKRCD GRDLTSLRNI SCEVDMFKTL HGSALFQRGQ TQVLCTVTFD
410 420 430 440 450
SLESSIKSDQ IITAINGVKD KNFMLHYEFP PYATNETGKV TGVNRRELGH
460 470 480 490 500
GALAEKALCP VIPKDFPFTI RVTSEVLESN GSSSMASACG GSLALMDAGV
510 520 530 540 550
PISSAVAGVA VGLVTKTNPE KGEIEDYRLL TDILGIEDYN GDMDFKIAGT
560 570 580 590 600
NKGITALQAD IKLPGVPIKI IMEAIQQASV AKKEILQIMN KTISKPRASR
610 620 630 640 650
KENGPVVETV KVPLSKRAKF VGPGGYHLKK LQAETGVTIS QVDEETFSIF
660 670 680 690 700
APTPTAMHEA RDFITEICRD DQEQQLEFGA VYTATITEIR DTGVMVKLYP
710 720 730 740 750
NMTAVLLHNS QLDQRKIKHP TALGLEVGQE IQVKYFGRDP ADGRMRLSRK
760 770 780
VLQSPATTAL KTLNDRSSIV MGEPVSQSSN SNP
Length:783
Mass (Da):85,683
Last modified:October 1, 2002 - v1
Checksum:iF35F6BE91AAB5626
GO
Isoform 2 (identifier: Q8K1R3-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     535-540: GIEDYN → ASIFPV
     541-783: Missing.

Note: No experimental confirmation available.
Show »
Length:540
Mass (Da):58,923
Checksum:iE57BFA2B602361C4
GO

Sequence cautioni

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

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti90A → P in AAO33354 (Ref. 2) Curated1
Sequence conflicti298V → G in AAO33354 (Ref. 2) Curated1
Sequence conflicti315K → Q in AAO33354 (Ref. 2) Curated1
Sequence conflicti415I → V in AAO33354 (Ref. 2) Curated1
Sequence conflicti431P → L in BAB23374 (PubMed:16141072).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_013639535 – 540GIEDYN → ASIFPV in isoform 2. 1 Publication6
Alternative sequenceiVSP_013640541 – 783Missing in isoform 2. 1 PublicationAdd BLAST243

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ507387 mRNA Translation: CAD45436.1
AF465249 mRNA Translation: AAO33354.1 Frameshift.
AK004563 mRNA Translation: BAB23374.1
AK149419 mRNA Translation: BAE28862.1
BX000351 Genomic DNA No translation available.
BC027228 mRNA Translation: AAH27228.2
BC049283 mRNA Translation: AAH49283.1
BC055826 mRNA Translation: AAH55826.1
CCDSiCCDS24490.1 [Q8K1R3-1]
RefSeqiNP_082145.1, NM_027869.1 [Q8K1R3-1]
XP_011242053.1, XM_011243751.2 [Q8K1R3-1]
UniGeneiMm.211131

Genome annotation databases

EnsembliENSMUST00000020756; ENSMUSP00000020756; ENSMUSG00000020464 [Q8K1R3-1]
GeneIDi71701
KEGGimmu:71701
UCSCiuc007igp.1 mouse [Q8K1R3-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiPNPT1_MOUSE
AccessioniPrimary (citable) accession number: Q8K1R3
Secondary accession number(s): Q3UEP9
, Q810U7, Q812B3, Q8R2U3, Q9DC52
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 10, 2005
Last sequence update: October 1, 2002
Last modified: May 23, 2018
This is version 142 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

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