DXO_DROME
ID DXO_DROME Reviewed; 375 AA.
AC Q9VXA8;
DT 05-APR-2011, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 120.
DE RecName: Full=Decapping nuclease DXO homolog {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 CG9125 {ECO:0000305};
DE Short=DeNADding enzyme CG9125 {ECO:0000305};
DE EC=3.6.1.- {ECO:0000250|UniProtKB:O70348};
GN ORFNames=CG9125;
OS Drosophila melanogaster (Fruit fly).
OC Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota;
OC Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea;
OC Drosophilidae; Drosophila; Sophophora.
OX NCBI_TaxID=7227;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=19126864; DOI=10.1093/molbev/msn297;
RA Parsch J., Zhang Z., Baines J.F.;
RT "The influence of demography and weak selection on the McDonald-Kreitman
RT test: an empirical study in Drosophila.";
RL Mol. Biol. Evol. 26:691-698(2009).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Berkeley;
RX PubMed=10731132; DOI=10.1126/science.287.5461.2185;
RA Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D.,
RA Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F.,
RA George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N.,
RA Sutton G.G., Wortman J.R., Yandell M.D., Zhang Q., Chen L.X., Brandon R.C.,
RA Rogers Y.-H.C., Blazej R.G., Champe M., Pfeiffer B.D., Wan K.H., Doyle C.,
RA Baxter E.G., Helt G., Nelson C.R., Miklos G.L.G., Abril J.F., Agbayani A.,
RA An H.-J., Andrews-Pfannkoch C., Baldwin D., Ballew R.M., Basu A.,
RA Baxendale J., Bayraktaroglu L., Beasley E.M., Beeson K.Y., Benos P.V.,
RA Berman B.P., Bhandari D., Bolshakov S., Borkova D., Botchan M.R., Bouck J.,
RA Brokstein P., Brottier P., Burtis K.C., Busam D.A., Butler H., Cadieu E.,
RA Center A., Chandra I., Cherry J.M., Cawley S., Dahlke C., Davenport L.B.,
RA Davies P., de Pablos B., Delcher A., Deng Z., Mays A.D., Dew I.,
RA Dietz S.M., Dodson K., Doup L.E., Downes M., Dugan-Rocha S., Dunkov B.C.,
RA Dunn P., Durbin K.J., Evangelista C.C., Ferraz C., Ferriera S.,
RA Fleischmann W., Fosler C., Gabrielian A.E., Garg N.S., Gelbart W.M.,
RA Glasser K., Glodek A., Gong F., Gorrell J.H., Gu Z., Guan P., Harris M.,
RA Harris N.L., Harvey D.A., Heiman T.J., Hernandez J.R., Houck J., Hostin D.,
RA Houston K.A., Howland T.J., Wei M.-H., Ibegwam C., Jalali M., Kalush F.,
RA Karpen G.H., Ke Z., Kennison J.A., Ketchum K.A., Kimmel B.E., Kodira C.D.,
RA Kraft C.L., Kravitz S., Kulp D., Lai Z., Lasko P., Lei Y., Levitsky A.A.,
RA Li J.H., Li Z., Liang Y., Lin X., Liu X., Mattei B., McIntosh T.C.,
RA McLeod M.P., McPherson D., Merkulov G., Milshina N.V., Mobarry C.,
RA Morris J., Moshrefi A., Mount S.M., Moy M., Murphy B., Murphy L.,
RA Muzny D.M., Nelson D.L., Nelson D.R., Nelson K.A., Nixon K., Nusskern D.R.,
RA Pacleb J.M., Palazzolo M., Pittman G.S., Pan S., Pollard J., Puri V.,
RA Reese M.G., Reinert K., Remington K., Saunders R.D.C., Scheeler F.,
RA Shen H., Shue B.C., Siden-Kiamos I., Simpson M., Skupski M.P., Smith T.J.,
RA Spier E., Spradling A.C., Stapleton M., Strong R., Sun E., Svirskas R.,
RA Tector C., Turner R., Venter E., Wang A.H., Wang X., Wang Z.-Y.,
RA Wassarman D.A., Weinstock G.M., Weissenbach J., Williams S.M., Woodage T.,
RA Worley K.C., Wu D., Yang S., Yao Q.A., Ye J., Yeh R.-F., Zaveri J.S.,
RA Zhan M., Zhang G., Zhao Q., Zheng L., Zheng X.H., Zhong F.N., Zhong W.,
RA Zhou X., Zhu S.C., Zhu X., Smith H.O., Gibbs R.A., Myers E.W., Rubin G.M.,
RA Venter J.C.;
RT "The genome sequence of Drosophila melanogaster.";
RL Science 287:2185-2195(2000).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=Berkeley;
RX PubMed=12537572; DOI=10.1186/gb-2002-3-12-research0083;
RA Misra S., Crosby M.A., Mungall C.J., Matthews B.B., Campbell K.S.,
RA Hradecky P., Huang Y., Kaminker J.S., Millburn G.H., Prochnik S.E.,
RA Smith C.D., Tupy J.L., Whitfield E.J., Bayraktaroglu L., Berman B.P.,
RA Bettencourt B.R., Celniker S.E., de Grey A.D.N.J., Drysdale R.A.,
RA Harris N.L., Richter J., Russo S., Schroeder A.J., Shu S.Q., Stapleton M.,
RA Yamada C., Ashburner M., Gelbart W.M., Rubin G.M., Lewis S.E.;
RT "Annotation of the Drosophila melanogaster euchromatic genome: a systematic
RT review.";
RL Genome Biol. 3:RESEARCH0083.1-RESEARCH0083.22(2002).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=Berkeley;
RA Stapleton M., Carlson J.W., Chavez C., Frise E., George R.A., Pacleb J.M.,
RA Park S., Wan K.H., Yu C., Celniker S.E.;
RL Submitted (AUG-2010) 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. {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 -!- SIMILARITY: Belongs to the DXO/Dom3Z family. {ECO:0000305}.
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DR EMBL; FM246164; CAR94090.1; -; Genomic_DNA.
DR EMBL; AE014298; AAF48669.1; -; Genomic_DNA.
DR EMBL; BT125074; ADK95192.1; -; mRNA.
DR RefSeq; NP_996492.1; NM_206769.3.
DR AlphaFoldDB; Q9VXA8; -.
DR SMR; Q9VXA8; -.
DR BioGRID; 77731; 1.
DR STRING; 7227.FBpp0074126; -.
DR PaxDb; Q9VXA8; -.
DR DNASU; 2768882; -.
DR EnsemblMetazoa; FBtr0074352; FBpp0074126; FBgn0030793.
DR GeneID; 2768882; -.
DR KEGG; dme:Dmel_CG9125; -.
DR UCSC; CG9125-RA; d. melanogaster.
DR CTD; 10743; -.
DR FlyBase; FBgn0030793; CG9125.
DR VEuPathDB; VectorBase:FBgn0030793; -.
DR eggNOG; KOG1982; Eukaryota.
DR GeneTree; ENSGT00390000006425; -.
DR HOGENOM; CLU_024877_1_1_1; -.
DR InParanoid; Q9VXA8; -.
DR OMA; IYLCARD; -.
DR OrthoDB; 1034620at2759; -.
DR PhylomeDB; Q9VXA8; -.
DR BioGRID-ORCS; 2768882; 0 hits in 1 CRISPR screen.
DR ChiTaRS; CG9125; fly.
DR GenomeRNAi; 2768882; -.
DR PRO; PR:Q9VXA8; -.
DR Proteomes; UP000000803; Chromosome X.
DR Bgee; FBgn0030793; Expressed in embryonic/larval hemocyte (Drosophila) and 23 other tissues.
DR ExpressionAtlas; Q9VXA8; baseline and differential.
DR Genevisible; Q9VXA8; DM.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; ISS:FlyBase.
DR GO; GO:0008409; F:5'-3' exonuclease activity; ISS:FlyBase.
DR GO; GO:0004534; F:5'-3' exoribonuclease activity; IDA:FlyBase.
DR GO; GO:0046872; F:metal ion binding; 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; IDA:FlyBase.
DR GO; GO:0006402; P:mRNA catabolic process; ISS:FlyBase.
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..375
FT /note="Decapping nuclease DXO homolog"
FT /id="PRO_0000406136"
FT BINDING 43
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 120..122
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 180
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 180
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 222
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 222
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 224
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 224
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 247
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 248
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 249
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 274
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
SQ SEQUENCE 375 AA; 42903 MW; 9D1A91182B3A85BD CRC64;
MAENAGFISV PWGQHKLGAM YNTPFPSISR PKCIGVCSIN ASREFVDDAS CASYLAGQPW
PPLPFDLNGG IEDVIRKPVE NGKRDLEIML TYIKQHQKEL LRQSSSDARN LRLDSDFVTL
RGILRQIMCL QYDNRSFRVK ATLLNGNVYM CKEETPEQQL ENANMSRAQR VMCSWGFKFE
QYLTSAQAQG KPVTNVPVNE AEEFMGVYRT NLAGILMLYG AELDCVDSKE PVDFKDCRVL
DSLKFVELKT SVFNMNPHQI RTFKSFKSAN WWSQSFLVGI TTLYVGLRDT KGMLQRIDEI
DVATLARNKP WSASAMAWYL EQFLRNLKKL LVNINDPFAV VQVTFLNKHA SYEVLRGPEH
QILPNWYRDL LKTRS
