PNDC1_MOUSE
ID PNDC1_MOUSE Reviewed; 531 AA.
AC B2RXZ1;
DT 15-MAR-2017, integrated into UniProtKB/Swiss-Prot.
DT 01-JUL-2008, sequence version 1.
DT 03-AUG-2022, entry version 87.
DE RecName: Full=Poly(A)-specific ribonuclease PNLDC1 {ECO:0000305};
DE EC=3.1.13.4 {ECO:0000269|PubMed:27515512};
DE AltName: Full=PARN-like domain-containing protein 1 {ECO:0000312|MGI:MGI:2685159};
DE AltName: Full=Poly(A)-specific ribonuclease domain-containing protein 1 {ECO:0000312|MGI:MGI:2685159};
GN Name=Pnldc1 {ECO:0000312|MGI:MGI:2685159};
OS Mus musculus (Mouse).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Mus; Mus.
OX NCBI_TaxID=10090;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=C57BL/6J;
RX PubMed=19468303; DOI=10.1371/journal.pbio.1000112;
RA Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S., She X.,
RA Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W., Kapustin Y.,
RA Meric P., Maglott D., Birtle Z., Marques A.C., Graves T., Zhou S.,
RA Teague B., Potamousis K., Churas C., Place M., Herschleb J., Runnheim R.,
RA Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z., Lindblad-Toh K.,
RA Eichler E.E., Ponting C.P.;
RT "Lineage-specific biology revealed by a finished genome assembly of the
RT mouse.";
RL PLoS Biol. 7:E1000112-E1000112(2009).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Brain;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [3]
RP TISSUE SPECIFICITY.
RX PubMed=26919431; DOI=10.1016/j.cell.2016.01.008;
RA Izumi N., Shoji K., Sakaguchi Y., Honda S., Kirino Y., Suzuki T.,
RA Katsuma S., Tomari Y.;
RT "Identification and functional analysis of the pre-piRNA 3' trimmer in
RT silkworms.";
RL Cell 164:962-973(2016).
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, SUBCELLULAR LOCATION, TISSUE SPECIFICITY,
RP DEVELOPMENTAL STAGE, AND INDUCTION.
RX PubMed=27515512; DOI=10.1093/nar/gkw709;
RA Anastasakis D., Skeparnias I., Shaukat A.N., Grafanaki K., Kanellou A.,
RA Taraviras S., Papachristou D.J., Papakyriakou A., Stathopoulos C.;
RT "Mammalian PNLDC1 is a novel poly(A) specific exonuclease with discrete
RT expression during early development.";
RL Nucleic Acids Res. 44:8908-8920(2016).
CC -!- FUNCTION: 3'-exoribonuclease that has a preference for poly(A) tails of
CC mRNAs, thereby efficiently degrading poly(A) tails (PubMed:27515512).
CC Exonucleolytic degradation of the poly(A) tail is often the first step
CC in the decay of eukaryotic mRNAs and is also used to silence certain
CC maternal mRNAs translationally during oocyte maturation and early
CC embryonic development (PubMed:27515512). May act as a regulator of
CC multipotency in embryonic stem cells (PubMed:27515512). Is a critical
CC factor for proper spermatogenesis, involved in pre-piRNAs processing to
CC generate mature piRNAs (By similarity). {ECO:0000250|UniProtKB:Q8NA58,
CC ECO:0000269|PubMed:27515512}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Exonucleolytic cleavage of poly(A) to 5'-AMP.; EC=3.1.13.4;
CC Evidence={ECO:0000269|PubMed:27515512};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000250|UniProtKB:Q8NA58};
CC -!- SUBCELLULAR LOCATION: Endoplasmic reticulum membrane
CC {ECO:0000269|PubMed:27515512}; Single-pass membrane protein
CC {ECO:0000250|UniProtKB:Q8NA58}. Note=Localizes mainly in the
CC endoplasmic reticulum. {ECO:0000269|PubMed:27515512}.
CC -!- TISSUE SPECIFICITY: Specifically expressed in embryonic stem cells
CC (PubMed:27515512). Highly expressed in testis (PubMed:26919431,
CC PubMed:27515512). {ECO:0000269|PubMed:26919431,
CC ECO:0000269|PubMed:27515512}.
CC -!- DEVELOPMENTAL STAGE: Expressed during early embryo development and
CC fades during differentiation. {ECO:0000269|PubMed:27515512}.
CC -!- INDUCTION: Down-regulated in differentiated cells, due to methylation
CC of its promoter by the methyltransferase DNMT3B.
CC {ECO:0000269|PubMed:27515512}.
CC -!- SIMILARITY: Belongs to the CAF1 family. {ECO:0000305}.
CC -!- CAUTION: Preliminary results in vitro suggested that Pnldc1 might act
CC as an exonuclease that specifically cleaves precursor piRNAs (pre-
CC piRNAs) at their 3' ends (PubMed:26919431). These results however
CC require additional experimental evidences: another report showed that
CC the protein mainly localizes to the endoplasmic reticulum and
CC preferentially acts on poly(A) tails (PubMed:27515512).
CC {ECO:0000269|PubMed:26919431, ECO:0000269|PubMed:27515512}.
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DR EMBL; AL589878; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BC158033; AAI58034.1; -; mRNA.
DR CCDS; CCDS49948.1; -.
DR RefSeq; NP_001030038.1; NM_001034866.1.
DR AlphaFoldDB; B2RXZ1; -.
DR SMR; B2RXZ1; -.
DR STRING; 10090.ENSMUSP00000129377; -.
DR PhosphoSitePlus; B2RXZ1; -.
DR PaxDb; B2RXZ1; -.
DR PRIDE; B2RXZ1; -.
DR ProteomicsDB; 289464; -.
DR Antibodypedia; 64136; 74 antibodies from 18 providers.
DR Ensembl; ENSMUST00000163394; ENSMUSP00000129377; ENSMUSG00000073460.
DR GeneID; 240023; -.
DR KEGG; mmu:240023; -.
DR UCSC; uc012akg.1; mouse.
DR CTD; 154197; -.
DR MGI; MGI:2685159; Pnldc1.
DR VEuPathDB; HostDB:ENSMUSG00000073460; -.
DR eggNOG; KOG1990; Eukaryota.
DR GeneTree; ENSGT00940000153167; -.
DR HOGENOM; CLU_018030_3_0_1; -.
DR InParanoid; B2RXZ1; -.
DR OMA; HRWYLEH; -.
DR OrthoDB; 1402758at2759; -.
DR PhylomeDB; B2RXZ1; -.
DR TreeFam; TF314502; -.
DR BRENDA; 3.1.13.4; 3474.
DR BioGRID-ORCS; 240023; 1 hit in 72 CRISPR screens.
DR PRO; PR:B2RXZ1; -.
DR Proteomes; UP000000589; Chromosome 17.
DR RNAct; B2RXZ1; protein.
DR Bgee; ENSMUSG00000073460; Expressed in cleaving embryo and 88 other tissues.
DR ExpressionAtlas; B2RXZ1; baseline and differential.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005783; C:endoplasmic reticulum; IDA:UniProtKB.
DR GO; GO:0005789; C:endoplasmic reticulum membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0000175; F:3'-5'-exoribonuclease activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004535; F:poly(A)-specific ribonuclease activity; IDA:UniProtKB.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0001825; P:blastocyst formation; IMP:MGI.
DR GO; GO:0000184; P:nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; IEA:UniProtKB-KW.
DR GO; GO:0000289; P:nuclear-transcribed mRNA poly(A) tail shortening; IDA:UniProtKB.
DR GO; GO:1990511; P:piRNA biosynthetic process; ISO:MGI.
DR GO; GO:0007283; P:spermatogenesis; ISO:MGI.
DR Gene3D; 3.30.420.10; -; 2.
DR InterPro; IPR006941; RNase_CAF1.
DR InterPro; IPR012337; RNaseH-like_sf.
DR InterPro; IPR036397; RNaseH_sf.
DR Pfam; PF04857; CAF1; 1.
DR SUPFAM; SSF53098; SSF53098; 1.
PE 1: Evidence at protein level;
KW Endoplasmic reticulum; Exonuclease; Hydrolase; Magnesium; Membrane;
KW Metal-binding; Nonsense-mediated mRNA decay; Nuclease; Reference proteome;
KW RNA-binding; Transmembrane; Transmembrane helix.
FT CHAIN 1..531
FT /note="Poly(A)-specific ribonuclease PNLDC1"
FT /id="PRO_0000439351"
FT TRANSMEM 506..526
FT /note="Helical"
FT /evidence="ECO:0000255"
FT BINDING 28
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:O95453"
FT BINDING 30
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:O95453"
FT BINDING 271
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:O95453"
FT BINDING 365
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:O95453"
SQ SEQUENCE 531 AA; 61292 MW; 5D0DB6502327E239 CRC64;
MDVGADEFEQ SLPLLQELVA GADFVGLDIE FTGLRSNLSR PQQISLFDLP SEWYLKTRQS
VQQFTICQIG LSMFSSIEGE SNKYVAHSCN FFLFPTTFGI LDSEFSFQAS SVQFLNQYGF
DYNKFLKNGI PYMNEEQEKK IKHSILRGNW RVRSSLDKDQ IKVVIDKVTQ WLDLAEEGDQ
MTLPGIAGFQ AFEVQLVLRQ ALPNIWTVLK EEWVIVKKVS QPQRWYLEHA SCDQVSCWKE
QILLSARGFS VFFQMLVKAQ KPLVGHNMMM DLLHLHEKFF RPLPESYDQF KQNIHSLFPV
LIDTKNVTKD IWKELRFPRV SNLLEVYEVL SSNLNPTKDS GPVIIHARQC KKYAETKCPH
EAAYDAFLCG SVLLKVAHLL LQRVHGNGAV HEPAFPQYLD VLAPYVNQVN LIRAGVPKIN
FSGPDYPSIR PPVLILTVKR WPGVSEQQVY REFQNLCKFD VRRFTRSQFL LLTNKFKDAR
SVLKEYRNHP TLQVSLYRSW RHSPNITCLL QVCSIVTTWA MIAFLLGRPM P
