PARN_DANRE
ID PARN_DANRE Reviewed; 660 AA.
AC Q7ZU92; Q6TGW3;
DT 01-MAR-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2005, sequence version 2.
DT 03-AUG-2022, entry version 110.
DE RecName: Full=Poly(A)-specific ribonuclease PARN;
DE EC=3.1.13.4;
DE AltName: Full=Polyadenylate-specific ribonuclease;
GN Name=parn; ORFNames=zgc:56067;
OS Danio rerio (Zebrafish) (Brachydanio rerio).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
OC Danionidae; Danioninae; Danio.
OX NCBI_TaxID=7955;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC TISSUE=Kidney marrow;
RX PubMed=15520368; DOI=10.1073/pnas.0407241101;
RA Song H.-D., Sun X.-J., Deng M., Zhang G.-W., Zhou Y., Wu X.-Y., Sheng Y.,
RA Chen Y., Ruan Z., Jiang C.-L., Fan H.-Y., Zon L.I., Kanki J.P., Liu T.X.,
RA Look A.T., Chen Z.;
RT "Hematopoietic gene expression profile in zebrafish kidney marrow.";
RL Proc. Natl. Acad. Sci. U.S.A. 101:16240-16245(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC STRAIN=AB;
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (APR-2003) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-560; SER-614; SER-643 AND
RP THR-649, AND IDENTIFICATION BY MASS SPECTROMETRY.
RC TISSUE=Embryo;
RX PubMed=18307296; DOI=10.1021/pr700667w;
RA Lemeer S., Pinkse M.W.H., Mohammed S., van Breukelen B., den Hertog J.,
RA Slijper M., Heck A.J.R.;
RT "Online automated in vivo zebrafish phosphoproteomics: from large-scale
RT analysis down to a single embryo.";
RL J. Proteome Res. 7:1555-1564(2008).
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 and is also used to silence certain maternal mRNAs
CC translationally during oocyte maturation and early embryonic
CC development (By similarity). {ECO:0000250}.
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 -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}. Nucleus {ECO:0000250}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q7ZU92-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q7ZU92-2; Sequence=VSP_012900;
CC -!- SIMILARITY: Belongs to the CAF1 family. {ECO:0000305}.
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DR EMBL; AY398393; AAQ97826.1; -; mRNA.
DR EMBL; BC050496; AAH50496.1; -; mRNA.
DR AlphaFoldDB; Q7ZU92; -.
DR SMR; Q7ZU92; -.
DR STRING; 7955.ENSDARP00000028687; -.
DR iPTMnet; Q7ZU92; -.
DR PaxDb; Q7ZU92; -.
DR PRIDE; Q7ZU92; -.
DR ZFIN; ZDB-GENE-040426-880; parn.
DR eggNOG; KOG1990; Eukaryota.
DR InParanoid; Q7ZU92; -.
DR PhylomeDB; Q7ZU92; -.
DR Reactome; R-DRE-429947; Deadenylation of mRNA.
DR Reactome; R-DRE-450604; KSRP (KHSRP) binds and destabilizes mRNA.
DR PRO; PR:Q7ZU92; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Unplaced.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0000175; F:3'-5'-exoribonuclease activity; IBA:GO_Central.
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; IBA:GO_Central.
DR GO; GO:0003723; F:RNA binding; ISS:UniProtKB.
DR GO; GO:0030097; P:hemopoiesis; IMP:ZFIN.
DR GO; GO:0000289; P:nuclear-transcribed mRNA poly(A) tail shortening; IBA:GO_Central.
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; 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 Alternative splicing; Cytoplasm; Exonuclease; Hydrolase; Metal-binding;
KW Nuclease; Nucleus; Phosphoprotein; Reference proteome; RNA-binding.
FT CHAIN 1..660
FT /note="Poly(A)-specific ribonuclease PARN"
FT /id="PRO_0000212854"
FT DOMAIN 177..243
FT /note="R3H"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00382"
FT REGION 606..660
FT /note="Disordered"
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 290
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:O95453"
FT BINDING 380
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:O95453"
FT SITE 324
FT /note="Interaction with poly(A)"
FT /evidence="ECO:0000250|UniProtKB:O95453"
FT MOD_RES 560
FT /note="Phosphoserine"
FT /evidence="ECO:0000269|PubMed:18307296"
FT MOD_RES 614
FT /note="Phosphoserine"
FT /evidence="ECO:0000269|PubMed:18307296"
FT MOD_RES 643
FT /note="Phosphoserine"
FT /evidence="ECO:0000269|PubMed:18307296"
FT MOD_RES 649
FT /note="Phosphothreonine"
FT /evidence="ECO:0000269|PubMed:18307296"
FT VAR_SEQ 632..644
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|Ref.2"
FT /id="VSP_012900"
FT CONFLICT 135
FT /note="N -> T (in Ref. 1; AAQ97826)"
FT /evidence="ECO:0000305"
FT CONFLICT 227
FT /note="A -> T (in Ref. 1; AAQ97826)"
FT /evidence="ECO:0000305"
FT CONFLICT 551
FT /note="W -> R (in Ref. 1; AAQ97826)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 660 AA; 75261 MW; 81D1D9DDF22A8DD0 CRC64;
MEVTRQNFKE VLPEVCNAVQ EADFISIDGE FTGISDGPSV SALTNGLDTP EERYTKLRKH
SMNFLLFQFG VCTFRYDQNQ STYITKAFNF YIFPKPFSRT SPDIKFICQS SSIDFLASQG
FDFNKVFRSG IPYLNQEEEC QLREQYEERR GQMNGAGPVS YTPPSGTGVC NVPEDQREFI
RSVEEKVEAL LKNTDQTLDL EPCTGFQRKL IYQTLNSKYS KGLHVEALET EKKERFIQIS
KVDDEERRRR EQQKQQREQE ELNDAVGFSR VIRAISKSGK LVVGHNMLLD VMHTIHQFCG
PLPEELDDFK EVAMTVFPRL LDTKLMASTQ PFKEIIHNTS LAELHKQLRQ KPFRPPTTEC
PEGLQSYDTS TEQLHEAGYD AFITGLCFIS MANYLGSFLT PPKSHISARS KLLEPFYNKL
FLMRVIDIPY LNMSGPDLQP KRDHVLYVTF PKEWKTSDLY QLFSAFGNIQ VSWVDDTSAF
VSLSQTEQVQ IAMNTSRYAE SYRIQTYAEY LQSRQKNTHS SRKWASDGWA DTSYPSVAMT
TASGYSHTDN WHQAVKRSIS PSLDEQNHGA DSSWTNYSVK KIKTEGSCTQ TYADVAGSCD
WPRLQADEGG ASVSPVAEEA ELDEFSANQS QGKRSRKHKK RKSDASETTP PALFDVPQVW
