DXO_XENLA
ID DXO_XENLA Reviewed; 401 AA.
AC Q5HZT0;
DT 19-SEP-2006, integrated into UniProtKB/Swiss-Prot.
DT 15-FEB-2005, sequence version 1.
DT 03-AUG-2022, entry version 55.
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:0000250|UniProtKB:O77932};
GN Synonyms=dom3z {ECO:0000250|UniProtKB:O77932};
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 [LARGE SCALE MRNA].
RC TISSUE=Egg;
RG NIH - Xenopus Gene Collection (XGC) project;
RL Submitted (JAN-2005) to the EMBL/GenBank/DDBJ databases.
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. Also acts as a non-canonical decapping enzyme
CC that removes the entire cap structure of m7G capped or incompletely
CC capped RNAs and mediates their subsequent degradation. Specifically
CC degrades pre-mRNAs with a defective 5'-end m7G cap and is part of a
CC pre-mRNA capping quality control. Has decapping activity toward
CC incomplete 5'-end m7G cap mRNAs such as unmethylated 5'-end-capped RNA
CC (cap0), while it has no activity toward 2'-O-ribose methylated m7G cap
CC (cap1). Also has 5'-3' exoribonuclease activities: The 5'-end
CC monophosphate RNA is then degraded by the 5'-3' exoribonuclease
CC activity, enabling this enzyme to decap and degrade incompletely capped
CC mRNAs. Also possesses RNA 5'-pyrophosphohydrolase activity by
CC hydrolyzing the 5'-end triphosphate to release pyrophosphates. Exhibits
CC decapping activity towards FAD-capped RNAs (By similarity). Exhibits
CC decapping activity towards dpCoA-capped RNAs in vitro (By similarity).
CC {ECO:0000250|UniProtKB:O70348}.
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; BC088900; AAH88900.1; -; mRNA.
DR RefSeq; NP_001088937.1; NM_001095468.1.
DR AlphaFoldDB; Q5HZT0; -.
DR SMR; Q5HZT0; -.
DR DNASU; 496313; -.
DR GeneID; 496313; -.
DR KEGG; xla:496313; -.
DR CTD; 496313; -.
DR Xenbase; XB-GENE-6252096; dxo.L.
DR OrthoDB; 1034620at2759; -.
DR Proteomes; UP000186698; Chromosome 8L.
DR Bgee; 496313; Expressed in neurula embryo and 19 other tissues.
DR GO; GO:0005634; C:nucleus; ISS:UniProtKB.
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: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 2: Evidence at transcript level;
KW Exonuclease; Hydrolase; Magnesium; Metal-binding; Nuclease;
KW Nucleotide-binding; Nucleus; Reference proteome; RNA-binding.
FT CHAIN 1..401
FT /note="Decapping and exoribonuclease protein"
FT /id="PRO_0000249825"
FT REGION 1..27
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..18
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 69
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 114
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 149..151
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 210
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 210
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 235
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 252
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 252
FT /ligand="substrate"
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 254
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 271
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 272
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 273
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 298
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
SQ SEQUENCE 401 AA; 46194 MW; 4854BEE12D427D59 CRC64;
MEGNKSMQRE KIDRPMKRGP EQNSLSPPLA KCPFMSCSSL KTLHSLYQGS FPFYRLPSEV
GHFSLDENRQ YHQDNRKLRY YSPPVGIREK GSPGWNVMDG YESHYVRRNE DEKEGLLHIL
TWLEKNRGVL GAHVEGGSKR PIDRDFVTWR GHLTKILCTP YETQEGWLLA VTLFKGTFYI
SEQETEAAQK KRKERSLEQE RLMYSGYKFE SYICADSPDR QPSQSAVVNT NEGFCSVLLA
RLTSHSLLIS GEVDCTDPSA KKSIPPTCYI ELKSSAQIRN PHQQRSFNRY KLLKWWCQSF
LLGIPIIVAG FRSPEGRIVS LETFKTSDIP HLVRGERNSW DPAVCMNFCN KFLSHIKSVV
TRDDPRLVYL FAWEPGCDVT FTVHTDPEYT ILPSWYVNSV N
