DXO1_YEAST
ID DXO1_YEAST Reviewed; 442 AA.
AC Q06349; D6VT01;
DT 17-OCT-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 128.
DE RecName: Full=Decapping and exoribonuclease protein 1 {ECO:0000305};
DE EC=3.6.1.- {ECO:0000269|PubMed:22961381};
DE AltName: Full=5'-3' exoribonuclease DXO1 {ECO:0000305};
DE EC=3.1.13.- {ECO:0000269|PubMed:22961381};
DE AltName: Full=NAD-capped RNA hydrolase DXO1 {ECO:0000305};
DE Short=DeNADding enzyme DXO1 {ECO:0000305};
DE EC=3.6.1.- {ECO:0000250|UniProtKB:O13836};
GN Name=DXO1; OrderedLocusNames=YDR370C;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169867;
RA Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G.,
RA Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C.,
RA Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F.,
RA Delaveau T., del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M.,
RA Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T.,
RA Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C.,
RA Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S.,
RA Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L.,
RA Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H.,
RA Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M.,
RA Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M.,
RA Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A.,
RA Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G.,
RA Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E.,
RA Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S.,
RA Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D.,
RA Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V.,
RA Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E.,
RA Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M.,
RA Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D.,
RA Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X.,
RA Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A.,
RA Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R.,
RA Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T.,
RA Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L.,
RA Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E.,
RA Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L.,
RA Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M.,
RA Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K.,
RA Mewes H.-W., Zollner A., Zaccaria P.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.";
RL Nature 387:75-78(1997).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [3]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
RN [4]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [5]
RP FUNCTION.
RX PubMed=22961381; DOI=10.1038/nsmb.2381;
RA Chang J.H., Jiao X., Chiba K., Oh C., Martin C.E., Kiledjian M., Tong L.;
RT "Dxo1 is a new type of eukaryotic enzyme with both decapping and 5'-3'
RT exoribonuclease activity.";
RL Nat. Struct. Mol. Biol. 19:1011-1017(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 (By similarity). The NAD-cap is present at the 5'-end of some RNAs and
CC snoRNAs. In contrast to the canonical 5'-end N7 methylguanosine (m7G)
CC cap, the NAD cap promotes mRNA decay (By similarity). Also acts as a
CC non-canonical decapping enzyme that removes the entire cap structure of
CC m7G capped or incompletely capped RNAs (PubMed:22961381). Has decapping
CC activity toward incomplete 5'-end m7G cap mRNAs such as unmethylated
CC 5'-end-capped RNA (cap0), while it has no activity toward 2'-O-ribose
CC methylated m7G cap (cap1) (PubMed:22961381). Also has 5'-3' exonuclease
CC activity (PubMed:22961381). {ECO:0000250|UniProtKB:O13836,
CC ECO:0000250|UniProtKB:O70348, ECO:0000269|PubMed:22961381}.
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:O13836};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:60881;
CC Evidence={ECO:0000250|UniProtKB:O13836};
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:Q6CPU0};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:66929;
CC Evidence={ECO:0000250|UniProtKB:Q6CPU0};
CC -!- COFACTOR:
CC Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC Evidence={ECO:0000250|UniProtKB:Q5AAT0};
CC Note=Divalent metal cation. {ECO:0000250|UniProtKB:Q5AAT0};
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}.
CC -!- MISCELLANEOUS: Present with 1040 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the DXO/Dom3Z family. {ECO:0000305}.
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DR EMBL; U28373; AAB64806.1; -; Genomic_DNA.
DR EMBL; BK006938; DAA12211.1; -; Genomic_DNA.
DR PIR; S61165; S61165.
DR RefSeq; NP_010658.3; NM_001180678.3.
DR AlphaFoldDB; Q06349; -.
DR SMR; Q06349; -.
DR BioGRID; 32429; 12.
DR DIP; DIP-5250N; -.
DR IntAct; Q06349; 1.
DR STRING; 4932.YDR370C; -.
DR MaxQB; Q06349; -.
DR PaxDb; Q06349; -.
DR PRIDE; Q06349; -.
DR EnsemblFungi; YDR370C_mRNA; YDR370C; YDR370C.
DR GeneID; 851976; -.
DR KEGG; sce:YDR370C; -.
DR SGD; S000002778; DXO1.
DR VEuPathDB; FungiDB:YDR370C; -.
DR eggNOG; ENOG502RWNP; Eukaryota.
DR HOGENOM; CLU_696510_0_0_1; -.
DR InParanoid; Q06349; -.
DR OMA; CIRSICK; -.
DR BioCyc; YEAST:G3O-29920-MON; -.
DR PRO; PR:Q06349; -.
DR Proteomes; UP000002311; Chromosome IV.
DR RNAct; Q06349; protein.
DR GO; GO:0005737; C:cytoplasm; HDA:SGD.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0004527; F:exonuclease activity; IEA:UniProtKB-KW.
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: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 1: Evidence at protein level;
KW Cytoplasm; Exonuclease; Hydrolase; Metal-binding; Nuclease;
KW Nucleotide-binding; Reference proteome; RNA-binding.
FT CHAIN 1..442
FT /note="Decapping and exoribonuclease protein 1"
FT /id="PRO_0000253847"
FT REGION 31..56
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 101
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 255
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250|UniProtKB:O13836"
FT BINDING 293
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 295
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250|UniProtKB:O13836"
FT BINDING 306
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250|UniProtKB:O13836"
FT BINDING 307
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250|UniProtKB:O13836"
FT BINDING 308
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 330
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
SQ SEQUENCE 442 AA; 50492 MW; 504F7C6AA40B50E4 CRC64;
MSTEQDAVLG LAKDLEGINL LTVPNLERGH QSKLCKEKTT SDSSSSRKPS QQRDNYRKRR
PKLICIPYTS FLHTGMHNFL TKPPRDIFHE SKEVALFTNG RAYTILRKDL IPNLKESIAE
LYESSLLEAK KRKVPYLGHD LFANIDEFVP MTISELDSVS PCFSYIENWI LDNPGKDFKI
GKKFTVVTTR HHIVDLTMHL FNRRNRQTSL IVTYMGAGLL SFCRNVKKDS QMSKEGIYSN
DPNMKKICYS GFEFENWVTE NSKVADLTGS KCPIFSLVES KLSEEIGLLI RCEMDAFNPV
SETNTELKCF APLSMHNSNH RRKLLKTWVQ TGLLPNSDIM IGLRDSHSGQ LLDIQWYSRD
LLCKKFNHPG LPTNKKELNY NAQIAVEWCH YCIEAICKLV EANISDYSST KPESFEIGID
TNNAIVITKL KTTPRNVELF GM
