DXO_CAEEL
ID DXO_CAEEL Reviewed; 393 AA.
AC Q10660;
DT 01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1996, sequence version 1.
DT 03-AUG-2022, entry version 103.
DE RecName: Full=Decapping nuclease dom-3 {ECO:0000305};
DE EC=3.6.1.- {ECO:0000250|UniProtKB:O70348};
DE AltName: Full=Dom-3 homolog Z {ECO:0000305};
DE AltName: Full=NAD-capped RNA hydrolase dom-3 {ECO:0000305};
DE Short=DeNADding enzyme dom-3 {ECO:0000305};
DE EC=3.6.1.- {ECO:0000250|UniProtKB:O70348};
GN Name=dom-3 {ECO:0000312|WormBase:F54C1.2}; ORFNames=F54C1.2;
OS Caenorhabditis elegans.
OC Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida;
OC Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae;
OC Caenorhabditis.
OX NCBI_TaxID=6239;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], AND DEVELOPMENTAL STAGE.
RC STRAIN=Bristol N2;
RX PubMed=8601481; DOI=10.1093/genetics/141.4.1383;
RA Paulsen J.E., Capowski E.E., Strome S.;
RT "Phenotypic and molecular analysis of mes-3, a maternal-effect gene
RT required for proliferation and viability of the germ line in C. elegans.";
RL Genetics 141:1383-1398(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Bristol N2;
RX PubMed=9851916; DOI=10.1126/science.282.5396.2012;
RG The C. elegans sequencing consortium;
RT "Genome sequence of the nematode C. elegans: a platform for investigating
RT biology.";
RL Science 282:2012-2018(1998).
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. {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 (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:O77932};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:66929;
CC Evidence={ECO:0000250|UniProtKB:O77932};
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 -!- DEVELOPMENTAL STAGE: Present at all stages. Levels increase from L1 to
CC adult stages. {ECO:0000269|PubMed:8601481}.
CC -!- SIMILARITY: Belongs to the DXO/Dom3Z family. {ECO:0000305}.
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DR EMBL; U34893; AAB01720.1; -; mRNA.
DR EMBL; FO080890; CCD67543.1; -; Genomic_DNA.
DR PIR; S60465; S60465.
DR RefSeq; NP_491496.1; NM_059095.5.
DR AlphaFoldDB; Q10660; -.
DR SMR; Q10660; -.
DR STRING; 6239.F54C1.2.2; -.
DR EPD; Q10660; -.
DR PaxDb; Q10660; -.
DR PeptideAtlas; Q10660; -.
DR EnsemblMetazoa; F54C1.2.1; F54C1.2.1; WBGene00001050.
DR GeneID; 172124; -.
DR KEGG; cel:CELE_F54C1.2; -.
DR UCSC; F54C1.2.1; c. elegans.
DR CTD; 172124; -.
DR WormBase; F54C1.2; CE11044; WBGene00001050; dom-3.
DR eggNOG; KOG1982; Eukaryota.
DR GeneTree; ENSGT00390000006425; -.
DR HOGENOM; CLU_024877_1_2_1; -.
DR InParanoid; Q10660; -.
DR OMA; IYLCARD; -.
DR OrthoDB; 1034620at2759; -.
DR PhylomeDB; Q10660; -.
DR PRO; PR:Q10660; -.
DR Proteomes; UP000001940; Chromosome I.
DR Bgee; WBGene00001050; Expressed in adult organism and 3 other tissues.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004518; F:nuclease activity; IEA:UniProtKB-KW.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0110152; F:RNA NAD-cap (NAD-forming) hydrolase activity; IEA:RHEA.
DR GO; GO:0034353; F:RNA pyrophosphohydrolase activity; IBA:GO_Central.
DR GO; GO:0110155; P:NAD-cap decapping; IBA:GO_Central.
DR GO; GO:0000956; P:nuclear-transcribed mRNA catabolic process; IBA:GO_Central.
DR GO; GO:0090305; P:nucleic acid phosphodiester bond hydrolysis; IBA:GO_Central.
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 Hydrolase; Magnesium; Metal-binding; Nuclease; Nucleotide-binding;
KW Reference proteome; RNA-binding.
FT CHAIN 1..393
FT /note="Decapping nuclease dom-3"
FT /id="PRO_0000079976"
FT REGION 1..37
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..19
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 74
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 113
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 144..146
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 205
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 205
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 257
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 257
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 259
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 259
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 269
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 270
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 271
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 293
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
SQ SEQUENCE 393 AA; 45858 MW; E56798CEB803409A CRC64;
MSHYGGNPRG NSSHQFGRKD FQQSDSKHIP KITGQPLPNE VQIPFDNMIY ETRNPPKFEK
QAKFISEYCI NYDRKLQLGR MRAKKFHDKL PPNNLSLDLG KGFETFDPKE GDEKIIMLLE
WINQMAPEGG RLKKVIHEAD VVCWRGLITK ICSTIYNKEE GWRIDAIKRK GVIFLCEEKT
EQAKNRDLNQ TDLDKRMSYW GHKFEQYVTL DDDAEQPDTS SPVTTKEEYA VVFRNDLQTD
QRLNPEKRSI GIFYSGEVDC LDRHGNMLEL KTQKGELGHG FYKYSKSFKW WLQSSLVNVD
HIIVGLRTQE GHVKSLTSLR TREIPQRASW NFRAGFEFLS TIFTYILNCL EKDGDACVIE
YRSEMGIHKG IQMRRVPVDE FDFVPNEFLE KFC
