DXO_RAT
ID DXO_RAT Reviewed; 397 AA.
AC Q6MG77;
DT 19-SEP-2006, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 99.
DE RecName: Full=Decapping and exoribonuclease protein {ECO:0000250|UniProtKB:O77932};
DE Short=DXO {ECO:0000250|UniProtKB:O77932};
DE EC=3.6.1.- {ECO:0000250|UniProtKB:O70348};
DE AltName: Full=5'-3' exoribonuclease DXO {ECO:0000305};
DE EC=3.1.13.- {ECO:0000250|UniProtKB:O70348};
DE AltName: Full=Dom-3 homolog Z {ECO:0000250|UniProtKB:O77932};
DE AltName: Full=NAD-capped RNA hydrolase DXO {ECO:0000305};
DE Short=DeNADding enzyme DXO {ECO:0000305};
DE EC=3.6.1.- {ECO:0000250|UniProtKB:O70348};
GN Name=Dxo {ECO:0000312|RGD:1303267};
GN Synonyms=Dom3z {ECO:0000250|UniProtKB:O77932};
OS Rattus norvegicus (Rat).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Rattus.
OX NCBI_TaxID=10116;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Brown Norway;
RX PubMed=15060004; DOI=10.1101/gr.1987704;
RA Hurt P., Walter L., Sudbrak R., Klages S., Mueller I., Shiina T., Inoko H.,
RA Lehrach H., Guenther E., Reinhardt R., Himmelbauer H.;
RT "The genomic sequence and comparative analysis of the rat major
RT histocompatibility complex.";
RL Genome Res. 14:631-639(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Testis;
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 PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-392 AND SER-394, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22673903; DOI=10.1038/ncomms1871;
RA Lundby A., Secher A., Lage K., Nordsborg N.B., Dmytriyev A., Lundby C.,
RA Olsen J.V.;
RT "Quantitative maps of protein phosphorylation sites across 14 different rat
RT organs and tissues.";
RL Nat. Commun. 3:876-876(2012).
CC -!- FUNCTION: Decapping enzyme for NAD-capped RNAs: specifically hydrolyzes
CC the nicotinamide adenine dinucleotide (NAD) cap from a subset of RNAs
CC by removing the entire NAD moiety from the 5'-end of an NAD-capped RNA.
CC The NAD-cap is present at the 5'-end of some RNAs and snoRNAs. In
CC contrast to the canonical 5'-end N7 methylguanosine (m7G) cap, the NAD
CC cap promotes mRNA decay (By similarity). Preferentially acts on NAD-
CC capped transcripts in response to environmental stress (By similarity).
CC Also acts as a non-canonical decapping enzyme that removes the entire
CC cap structure of m7G capped or incompletely capped RNAs and mediates
CC their subsequent degradation. Specifically degrades pre-mRNAs with a
CC defective 5'-end m7G cap and is part of a pre-mRNA capping quality
CC control. Has decapping activity toward incomplete 5'-end m7G cap mRNAs
CC such as unmethylated 5'-end-capped RNA (cap0), while it has no activity
CC toward 2'-O-ribose methylated m7G cap (cap1). In contrast to canonical
CC decapping enzymes DCP2 and NUDT16, which cleave the cap within the
CC triphosphate linkage, the decapping activity releases the entire cap
CC structure GpppN and a 5'-end monophosphate RNA. Also has 5'-3'
CC exoribonuclease activities: The 5'-end monophosphate RNA is then
CC degraded by the 5'-3' exoribonuclease activity, enabling this enzyme to
CC decap and degrade incompletely capped mRNAs. Also possesses RNA 5'-
CC pyrophosphohydrolase activity by hydrolyzing the 5'-end triphosphate to
CC release pyrophosphates (By similarity). Exhibits decapping activity
CC towards FAD-capped RNAs (By similarity). Exhibits decapping activity
CC towards dpCoA-capped RNAs in vitro (By similarity).
CC {ECO:0000250|UniProtKB:O70348, ECO:0000250|UniProtKB:O77932}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 5'-end NAD(+)-phospho-ribonucleoside in mRNA + H2O = a 5'-
CC end phospho-ribonucleoside in mRNA + H(+) + NAD(+);
CC Xref=Rhea:RHEA:60880, Rhea:RHEA-COMP:15692, Rhea:RHEA-COMP:15698,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:57540,
CC ChEBI:CHEBI:138282, ChEBI:CHEBI:144029;
CC Evidence={ECO:0000250|UniProtKB:O70348};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:60881;
CC Evidence={ECO:0000250|UniProtKB:O70348};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 5'-end NAD(+)-phospho-ribonucleoside in snoRNA + H2O = a 5'-
CC end phospho-ribonucleoside in snoRNA + H(+) + NAD(+);
CC Xref=Rhea:RHEA:60892, Rhea:RHEA-COMP:15699, Rhea:RHEA-COMP:15700,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:57540,
CC ChEBI:CHEBI:138282, ChEBI:CHEBI:144029;
CC Evidence={ECO:0000250|UniProtKB:O70348};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:60893;
CC Evidence={ECO:0000250|UniProtKB:O70348};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside-
CC ribonucleotide in mRNA + H2O = a (N(7)-methyl 5'-triphospho-
CC guanosine)-nucleoside + a 5'-end phospho-ribonucleoside in mRNA +
CC H(+); Xref=Rhea:RHEA:66928, Rhea:RHEA-COMP:15692, Rhea:RHEA-
CC COMP:17313, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:138282,
CC ChEBI:CHEBI:172876, ChEBI:CHEBI:172877;
CC Evidence={ECO:0000250|UniProtKB:O70348};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:66929;
CC Evidence={ECO:0000250|UniProtKB:O70348};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 5'-end FAD-phospho-ribonucleoside in mRNA + H2O = a 5'-end
CC phospho-ribonucleoside in mRNA + FAD + H(+); Xref=Rhea:RHEA:67492,
CC Rhea:RHEA-COMP:15692, Rhea:RHEA-COMP:17275, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57692, ChEBI:CHEBI:138282,
CC ChEBI:CHEBI:172372; Evidence={ECO:0000250|UniProtKB:O70348};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:67493;
CC Evidence={ECO:0000250|UniProtKB:O70348};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 5'-end CoA-ribonucleoside in mRNA + H2O = 3'-dephospho-CoA +
CC a 5'-end phospho-ribonucleoside in mRNA + H(+); Xref=Rhea:RHEA:67496,
CC Rhea:RHEA-COMP:15692, Rhea:RHEA-COMP:17276, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57328, ChEBI:CHEBI:138282,
CC ChEBI:CHEBI:172371; Evidence={ECO:0000250|UniProtKB:O70348};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:67497;
CC Evidence={ECO:0000250|UniProtKB:O70348};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000250|UniProtKB:O70348};
CC Note=Binds 2 magnesium ions. {ECO:0000250|UniProtKB:O70348};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:O77932}.
CC -!- SIMILARITY: Belongs to the DXO/Dom3Z family. {ECO:0000305}.
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DR EMBL; BX883045; CAE83969.1; -; Genomic_DNA.
DR EMBL; BC082083; AAH82083.1; -; mRNA.
DR RefSeq; NP_997662.1; NM_212497.2.
DR AlphaFoldDB; Q6MG77; -.
DR SMR; Q6MG77; -.
DR STRING; 10116.ENSRNOP00000000483; -.
DR iPTMnet; Q6MG77; -.
DR PhosphoSitePlus; Q6MG77; -.
DR PaxDb; Q6MG77; -.
DR Ensembl; ENSRNOT00000000483; ENSRNOP00000000483; ENSRNOG00000000422.
DR GeneID; 361799; -.
DR KEGG; rno:361799; -.
DR UCSC; RGD:1303267; rat.
DR CTD; 1797; -.
DR RGD; 1303267; Dxo.
DR eggNOG; KOG1982; Eukaryota.
DR GeneTree; ENSGT00390000006425; -.
DR HOGENOM; CLU_024877_1_2_1; -.
DR InParanoid; Q6MG77; -.
DR OMA; MAYWGYK; -.
DR OrthoDB; 1034620at2759; -.
DR PhylomeDB; Q6MG77; -.
DR TreeFam; TF322812; -.
DR PRO; PR:Q6MG77; -.
DR Proteomes; UP000002494; Chromosome 20.
DR Bgee; ENSRNOG00000000422; Expressed in pancreas and 19 other tissues.
DR Genevisible; Q6MG77; RN.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0005654; C:nucleoplasm; IEA:Ensembl.
DR GO; GO:0005634; C:nucleus; ISS:UniProtKB.
DR GO; GO:0005886; C:plasma membrane; IEA:Ensembl.
DR GO; GO:0008409; F:5'-3' exonuclease activity; ISS:UniProtKB.
DR GO; GO:0000287; F:magnesium ion binding; ISS:UniProtKB.
DR GO; GO:0003729; F:mRNA binding; ISS:UniProtKB.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR GO; GO:0110152; F:RNA NAD-cap (NAD-forming) hydrolase activity; ISS:UniProtKB.
DR GO; GO:0034353; F:RNA pyrophosphohydrolase activity; ISS:UniProtKB.
DR GO; GO:0006402; P:mRNA catabolic process; ISS:UniProtKB.
DR GO; GO:0110155; P:NAD-cap decapping; ISS:UniProtKB.
DR GO; GO:0071028; P:nuclear mRNA surveillance; ISS:UniProtKB.
DR GO; GO:0000956; P:nuclear-transcribed mRNA catabolic process; IBA:GO_Central.
DR GO; GO:0090305; P:nucleic acid phosphodiester bond hydrolysis; ISS:UniProtKB.
DR GO; GO:0050779; P:RNA destabilization; ISS:UniProtKB.
DR InterPro; IPR013961; RAI1.
DR InterPro; IPR039039; RAI1-like_fam.
DR PANTHER; PTHR12395; PTHR12395; 1.
DR Pfam; PF08652; RAI1; 1.
PE 1: Evidence at protein level;
KW Exonuclease; Hydrolase; Magnesium; Metal-binding; Nuclease;
KW Nucleotide-binding; Nucleus; Phosphoprotein; Reference proteome;
KW RNA-binding.
FT CHAIN 1..397
FT /note="Decapping and exoribonuclease protein"
FT /id="PRO_0000249824"
FT BINDING 58
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 101
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 131..133
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 192
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 192
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 217
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 234
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 234
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 236
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 236
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 253
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 254
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 255
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 280
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT MOD_RES 392
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:22673903"
FT MOD_RES 394
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:22673903"
SQ SEQUENCE 397 AA; 45299 MW; 29572F58C6138ACF CRC64;
MEPRGTKRKA EKTEVAKTWN KLPRSLPSLR TQPSLYSGPF PFYRRPSELG CFSLDAQRQY
HGDARALRYY SPPPINGPGP DFDLRDGYPD RYQPRDEEVR ERLDHLLRWV LEHRNQLEGG
PGWLAGATVT WRGHLTKLLT TPYERQEGWQ LAASRFQGTL YLSEVETPAA RAQRLARPPL
LRELMYMGYK FEQYMCADKP GGSPDPSGEV NTNVAFCSVL RSRLGNHPLL FSGEVDCLNP
QAPCTQPPSC YVELKTSKEM HSPGQWRSFY RHKLLKWWAQ SFLPGVPYVV AGFRNPEGFV
CSLKTFPTME MFENVRNDQE GWNPSVCMNF CAAFLSFAQS TVVQDDPRLV HLFSWEPGGP
VTVSVHRDAP YAFLPSWYVE AMTQDLPSLS KTPSPKD
