PARN_XENLA
ID PARN_XENLA Reviewed; 631 AA.
AC Q90ZA1; Q6GN38; Q6NTN9;
DT 01-MAR-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 99.
DE RecName: Full=Poly(A)-specific ribonuclease PARN;
DE EC=3.1.13.4;
DE AltName: Full=Deadenylating nuclease;
DE AltName: Full=Deadenylation nuclease;
DE AltName: Full=Polyadenylate-specific ribonuclease;
DE AltName: Full=parn-A;
GN Name=parn;
OS Xenopus laevis (African clawed frog).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia;
OC Batrachia; Anura; Pipoidea; Pipidae; Xenopodinae; Xenopus; Xenopus.
OX NCBI_TaxID=8355;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, SUBCELLULAR LOCATION, CLEAVAGE,
RP TISSUE SPECIFICITY, AND DEVELOPMENTAL STAGE.
RC TISSUE=Kidney;
RX PubMed=11424938; DOI=10.1017/s1355838201010020;
RA Copeland P.R., Wormington M.;
RT "The mechanism and regulation of deadenylation: identification and
RT characterization of Xenopus PARN.";
RL RNA 7:875-886(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Embryo, and Ovary;
RG NIH - Xenopus Gene Collection (XGC) project;
RL Submitted (APR-2004) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP PROTEIN SEQUENCE OF 237-242; 326-334; 421-425 AND 505-513, AND FUNCTION.
RX PubMed=9736620; DOI=10.1093/emboj/17.18.5427;
RA Koerner C.G., Wormington M., Muckenthaler M., Schneider S., Dehlin E.,
RA Wahle E.;
RT "The deadenylating nuclease (DAN) is involved in poly(A) tail removal
RT during the meiotic maturation of Xenopus oocytes.";
RL EMBO J. 17:5427-5437(1998).
RN [4]
RP TISSUE SPECIFICITY.
RX PubMed=12573214; DOI=10.1016/s0960-9822(03)00014-9;
RA Baggs J.E., Green C.B.;
RT "Nocturnin, a deadenylase in Xenopus laevis retina: a mechanism for
RT posttranscriptional control of circadian-related mRNA.";
RL Curr. Biol. 13:189-198(2003).
RN [5]
RP INTERACTION WITH PAPD4.
RX PubMed=17052452; DOI=10.1016/j.molcel.2006.08.016;
RA Kim J.H., Richter J.D.;
RT "Opposing polymerase-deadenylase activities regulate cytoplasmic
RT polyadenylation.";
RL Mol. Cell 24:173-183(2006).
CC -!- FUNCTION: 3'-exoribonuclease that has a preference for poly(A) tails of
CC mRNAs, thereby efficiently degrading poly(A) tails. Exonucleolytic
CC degradation of the poly(A) tail is often the first step in the decay of
CC eukaryotic mRNAs. Required during meiotic maturation to silence certain
CC maternal mRNAs translationally. Does not require an adenosine residue
CC at the 3' end, however, the addition of 25 non-adenylate residues at
CC the 3' terminus, or a 3' terminal phosphate is inhibitory. Involved in
CC dormant mRNAs regulation during oocyte maturation by counteracting
CC polyadenylation mediated by papd4/gld2nt in immature eggs. During
CC maturation it is excluded from the ribonucleoprotein complex, allowing
CC poly(A) elongation by papd4/gld2nt and activation of mRNAs.
CC {ECO:0000269|PubMed:11424938, ECO:0000269|PubMed:9736620}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Exonucleolytic cleavage of poly(A) to 5'-AMP.; EC=3.1.13.4;
CC -!- COFACTOR:
CC Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC Evidence={ECO:0000250|UniProtKB:O95453};
CC -!- SUBUNIT: Component of a complex at least composed of cpeb1, cpsf1,
CC papd4/gld2, pabpc1/ePAB, parn and sympk.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:11424938}. Nucleus
CC {ECO:0000269|PubMed:11424938}.
CC -!- TISSUE SPECIFICITY: In retina, it is constitutively present in most
CC retinal cells, including the photoreceptors.
CC {ECO:0000269|PubMed:11424938, ECO:0000269|PubMed:12573214}.
CC -!- DEVELOPMENTAL STAGE: Expressed throughout early development.
CC {ECO:0000269|PubMed:11424938}.
CC -!- PTM: A 62 kDa form, which is produced by proteolytic cleavage, also
CC exists. {ECO:0000269|PubMed:11424938}.
CC -!- SIMILARITY: Belongs to the CAF1 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAH73682.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305};
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DR EMBL; AF309688; AAK64218.1; -; mRNA.
DR EMBL; BC068919; AAH68919.1; -; mRNA.
DR EMBL; BC073682; AAH73682.1; ALT_SEQ; mRNA.
DR RefSeq; NP_001081143.1; NM_001087674.1.
DR AlphaFoldDB; Q90ZA1; -.
DR SMR; Q90ZA1; -.
DR IntAct; Q90ZA1; 2.
DR MaxQB; Q90ZA1; -.
DR DNASU; 394409; -.
DR GeneID; 394409; -.
DR KEGG; xla:394409; -.
DR CTD; 394409; -.
DR Xenbase; XB-GENE-1003109; parn.L.
DR OMA; VGLTICH; -.
DR OrthoDB; 1402758at2759; -.
DR BRENDA; 3.1.13.4; 6725.
DR Proteomes; UP000186698; Chromosome 9_10L.
DR Bgee; 394409; Expressed in blastula and 19 other tissues.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0043169; F:cation binding; ISS:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004535; F:poly(A)-specific ribonuclease activity; IEA:UniProtKB-EC.
DR GO; GO:0003723; F:RNA binding; ISS:UniProtKB.
DR GO; GO:0051321; P:meiotic cell cycle; IEA:UniProtKB-KW.
DR GO; GO:0006402; P:mRNA catabolic process; IEA:InterPro.
DR CDD; cd02637; R3H_PARN; 1.
DR Gene3D; 3.30.420.10; -; 2.
DR Gene3D; 3.30.70.330; -; 1.
DR InterPro; IPR012677; Nucleotide-bd_a/b_plait_sf.
DR InterPro; IPR034042; PARN_R3H.
DR InterPro; IPR014789; PolyA-riboNase_RNA-binding.
DR InterPro; IPR001374; R3H_dom.
DR InterPro; IPR036867; R3H_dom_sf.
DR InterPro; IPR035979; RBD_domain_sf.
DR InterPro; IPR006941; RNase_CAF1.
DR InterPro; IPR012337; RNaseH-like_sf.
DR InterPro; IPR036397; RNaseH_sf.
DR Pfam; PF04857; CAF1; 1.
DR Pfam; PF01424; R3H; 1.
DR Pfam; PF08675; RNA_bind; 1.
DR SUPFAM; SSF53098; SSF53098; 1.
DR SUPFAM; SSF54928; SSF54928; 1.
DR SUPFAM; SSF82708; SSF82708; 1.
DR PROSITE; PS51061; R3H; 1.
PE 1: Evidence at protein level;
KW Cytoplasm; Direct protein sequencing; Exonuclease; Hydrolase; Meiosis;
KW Metal-binding; Nuclease; Nucleus; Reference proteome; RNA-binding.
FT CHAIN 1..631
FT /note="Poly(A)-specific ribonuclease PARN"
FT /id="PRO_0000212855"
FT DOMAIN 178..244
FT /note="R3H"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00382"
FT REGION 147..173
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 568..631
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 151..173
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 28
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:O95453"
FT BINDING 30
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:O95453"
FT BINDING 291
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:O95453"
FT BINDING 381
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:O95453"
FT SITE 325
FT /note="Interaction with poly(A)"
FT /evidence="ECO:0000250|UniProtKB:O95453"
FT CONFLICT 330
FT /note="T -> P (in Ref. 3; AA sequence)"
FT /evidence="ECO:0000305"
FT CONFLICT 375
FT /note="L -> P (in Ref. 2; AAH68919)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 631 AA; 72846 MW; B213916954E51C64 CRC64;
MEITRSNFKD TLPKVYKAIE EADFLAIDGE FSGISDGPSV STLTNGFDTP EERYTKLKKH
SMEFLLFQFG LCTFNYDNTE AKYLMKSFNF YIFPKPFNRN SPDKKFVCQS SSIDFLANQG
FDFNKVFRNG IPYLNQEEER VLRDQYEDRR SQSNGASTMS YISPNSSKTP VSIPDEQKGF
IDKVVERVED FLKNEQKSMN VEPCTGYQRK LIYQTLNWKY PRGIHVETVE SEKKERYIVI
SKVDEEERKR MEQQKQAKER EELDDAVGFS RIIQAISSSG KLVVGHNMLL DVMHTIHQFF
CQLPDELNEF KEVTNCVFPR VLDTKLMAST NPFKEIIYNT SLAELEKRLK EAPFKPPKVD
SAEGFQSYNT ASEQLHEAGY DAYITGLCFI SMANYLGSFL SPPKDYVSCR SKIVRPFFNK
LFLMRIMDIP YLNLEGPDLQ PKRDNVLHVT FPKEWKTSDL YQLFSAFGNI QVSWIDDTSA
FVSLSQPEQV QIAVNTSKYA ESYRIQTYAE YIEKKNDESQ TKRKWAEDGW KDLERKRLKT
QYNSYIPQNP VFYGNCFAPS FAVKRSMSPI QEEAASDDTE EVHTHENDPS NPGATEQGKK
PKNHKRQKID SAPPETSDGG SSVLFEVPDT W
