DXO_SCHPO
ID DXO_SCHPO Reviewed; 352 AA.
AC O13836;
DT 27-MAR-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 129.
DE RecName: Full=Decapping nuclease din1 {ECO:0000305};
DE EC=3.6.1.- {ECO:0000269|PubMed:19194460};
DE AltName: Full=Dhp1-interacting protein 1 {ECO:0000303|PubMed:11238999};
DE AltName: Full=NAD-capped RNA hydrolase Rai1 {ECO:0000305};
DE Short=DeNADding enzyme Rai1 {ECO:0000305};
DE Short=spRai1 {ECO:0000303|PubMed:28283058};
DE EC=3.6.1.- {ECO:0000269|PubMed:28283058};
GN Name=din1 {ECO:0000303|PubMed:11238999};
GN Synonyms=rai1 {ECO:0000303|PubMed:28283058}; ORFNames=SPAC19D5.06c;
OS Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina;
OC Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae;
OC Schizosaccharomyces.
OX NCBI_TaxID=284812;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RX PubMed=11238999; DOI=10.1093/nar/29.6.1326;
RA Shobuike T., Tatebayashi K., Tani T., Sugano S., Ikeda H.;
RT "The dhp1+ gene, encoding a putative nuclear 5'3' exoribonuclease, is
RT required for proper chromosome segregation in fission yeast.";
RL Nucleic Acids Res. 29:1326-1333(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=972 / ATCC 24843;
RX PubMed=11859360; DOI=10.1038/nature724;
RA Wood V., Gwilliam R., Rajandream M.A., Lyne M.H., Lyne R., Stewart A.,
RA Sgouros J.G., Peat N., Hayles J., Baker S.G., Basham D., Bowman S.,
RA Brooks K., Brown D., Brown S., Chillingworth T., Churcher C.M., Collins M.,
RA Connor R., Cronin A., Davis P., Feltwell T., Fraser A., Gentles S.,
RA Goble A., Hamlin N., Harris D.E., Hidalgo J., Hodgson G., Holroyd S.,
RA Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K., James K.D.,
RA Jones L., Jones M., Leather S., McDonald S., McLean J., Mooney P.,
RA Moule S., Mungall K.L., Murphy L.D., Niblett D., Odell C., Oliver K.,
RA O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E., Rutherford K.M.,
RA Rutter S., Saunders D., Seeger K., Sharp S., Skelton J., Simmonds M.N.,
RA Squares R., Squares S., Stevens K., Taylor K., Taylor R.G., Tivey A.,
RA Walsh S.V., Warren T., Whitehead S., Woodward J.R., Volckaert G., Aert R.,
RA Robben J., Grymonprez B., Weltjens I., Vanstreels E., Rieger M.,
RA Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Duesterhoeft A.,
RA Fritzc C., Holzer E., Moestl D., Hilbert H., Borzym K., Langer I., Beck A.,
RA Lehrach H., Reinhardt R., Pohl T.M., Eger P., Zimmermann W., Wedler H.,
RA Wambutt R., Purnelle B., Goffeau A., Cadieu E., Dreano S., Gloux S.,
RA Lelaure V., Mottier S., Galibert F., Aves S.J., Xiang Z., Hunt C.,
RA Moore K., Hurst S.M., Lucas M., Rochet M., Gaillardin C., Tallada V.A.,
RA Garzon A., Thode G., Daga R.R., Cruzado L., Jimenez J., Sanchez M.,
RA del Rey F., Benito J., Dominguez A., Revuelta J.L., Moreno S.,
RA Armstrong J., Forsburg S.L., Cerutti L., Lowe T., McCombie W.R.,
RA Paulsen I., Potashkin J., Shpakovski G.V., Ussery D., Barrell B.G.,
RA Nurse P.;
RT "The genome sequence of Schizosaccharomyces pombe.";
RL Nature 415:871-880(2002).
RN [3]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-218, AND IDENTIFICATION BY
RP MASS SPECTROMETRY.
RX PubMed=18257517; DOI=10.1021/pr7006335;
RA Wilson-Grady J.T., Villen J., Gygi S.P.;
RT "Phosphoproteome analysis of fission yeast.";
RL J. Proteome Res. 7:1088-1097(2008).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH RAT1, FUNCTION,
RP COFACTOR, AND METAL-BINDING SITES.
RX PubMed=19194460; DOI=10.1038/nature07731;
RA Xiang S., Cooper-Morgan A., Jiao X., Kiledjian M., Manley J.L., Tong L.;
RT "Structure and function of the 5'-->3' exoribonuclease Rat1 and its
RT activating partner Rai1.";
RL Nature 458:784-788(2009).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, AND MUTAGENESIS OF 199-GLU--ASP-201.
RX PubMed=28283058; DOI=10.1016/j.cell.2017.02.019;
RA Jiao X., Doamekpor S.K., Bird J.G., Nickels B.E., Tong L., Hart R.P.,
RA Kiledjian M.;
RT "5' end nicotinamide adenine dinucleotide cap in human cells promotes RNA
RT decay through DXO-mediated deNADding.";
RL Cell 168:1015-1027(2017).
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 (PubMed:28283058). The NAD-cap is present at the 5'-end of some RNAs
CC and snoRNAs (By similarity). In contrast to the canonical 5'-end N7
CC methylguanosine (m7G) cap, the NAD cap promotes mRNA decay (By
CC similarity). Also acts as a non-canonical decapping enzyme that removes
CC the entire cap structure of m7G capped or incompletely capped RNAs and
CC mediates their subsequent degradation (PubMed:28283058). Specifically
CC degrades pre-mRNAs with a defective m7G cap and is part of a pre-mRNA
CC capping quality control (PubMed:28283058). Has decapping activity
CC toward incomplete 5'-end m7G cap mRNAs such as unmethylated 5'-end-
CC capped RNA (cap0), while it has no activity toward 2'-O-ribose
CC methylated m7G cap (cap1) (PubMed:28283058). Also possesses RNA 5'-
CC pyrophosphohydrolase activity by hydrolyzing the 5'-end triphosphate to
CC release pyrophosphates (By similarity). {ECO:0000250|UniProtKB:O70348,
CC ECO:0000250|UniProtKB:Q06349, ECO:0000269|PubMed:28283058}.
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:0000269|PubMed:28283058};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:60881;
CC Evidence={ECO:0000269|PubMed:28283058};
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:P53063};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:66929;
CC Evidence={ECO:0000250|UniProtKB:P53063};
CC -!- COFACTOR:
CC Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC Evidence={ECO:0000269|PubMed:19194460};
CC Note=Divalent metal cation. {ECO:0000269|PubMed:19194460};
CC -!- SUBUNIT: Interacts with rat1. {ECO:0000269|PubMed:19194460}.
CC -!- INTERACTION:
CC O13836; P40848: dhp1; NbExp=2; IntAct=EBI-15755601, EBI-15755578;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:P53063}.
CC -!- SIMILARITY: Belongs to the DXO/Dom3Z family. {ECO:0000305}.
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DR EMBL; AB045607; BAB20823.1; -; mRNA.
DR EMBL; CU329670; CAB16716.1; -; Genomic_DNA.
DR PIR; T37966; T37966.
DR RefSeq; NP_594904.1; NM_001020334.2.
DR PDB; 3FQD; X-ray; 2.20 A; B=1-352.
DR PDB; 3FQG; X-ray; 2.00 A; A=1-352.
DR PDB; 6WUG; X-ray; 1.90 A; A=1-352.
DR PDB; 6WUI; X-ray; 1.90 A; A=1-352.
DR PDBsum; 3FQD; -.
DR PDBsum; 3FQG; -.
DR PDBsum; 6WUG; -.
DR PDBsum; 6WUI; -.
DR AlphaFoldDB; O13836; -.
DR SMR; O13836; -.
DR BioGRID; 278997; 7.
DR DIP; DIP-59744N; -.
DR IntAct; O13836; 1.
DR STRING; 4896.SPAC19D5.06c.1; -.
DR iPTMnet; O13836; -.
DR MaxQB; O13836; -.
DR PaxDb; O13836; -.
DR PRIDE; O13836; -.
DR EnsemblFungi; SPAC19D5.06c.1; SPAC19D5.06c.1:pep; SPAC19D5.06c.
DR GeneID; 2542540; -.
DR KEGG; spo:SPAC19D5.06c; -.
DR PomBase; SPAC19D5.06c; din1.
DR VEuPathDB; FungiDB:SPAC19D5.06c; -.
DR eggNOG; KOG1982; Eukaryota.
DR HOGENOM; CLU_024877_4_1_1; -.
DR InParanoid; O13836; -.
DR OMA; IYLCARD; -.
DR PhylomeDB; O13836; -.
DR EvolutionaryTrace; O13836; -.
DR PRO; PR:O13836; -.
DR Proteomes; UP000002485; Chromosome I.
DR GO; GO:0005829; C:cytosol; HDA:PomBase.
DR GO; GO:0090730; C:Las1 complex; ISO:PomBase.
DR GO; GO:0005634; C:nucleus; HDA:PomBase.
DR GO; GO:0140432; F:5'-hydroxyl dinucleotide hydrolase; IDA:PomBase.
DR GO; GO:0019003; F:GDP binding; IDA:PomBase.
DR GO; GO:0046872; F:metal ion 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; IDA:UniProtKB.
DR GO; GO:0034353; F:RNA pyrophosphohydrolase activity; IDA:PomBase.
DR GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
DR GO; GO:0110155; P:NAD-cap decapping; IDA:UniProtKB.
DR GO; GO:0000956; P:nuclear-transcribed mRNA catabolic process; IBA:GO_Central.
DR GO; GO:0034428; P:nuclear-transcribed mRNA catabolic process, exonucleolytic, 5'-3'; IDA:PomBase.
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 3D-structure; Hydrolase; Metal-binding; mRNA processing; Nuclease;
KW Nucleotide-binding; Nucleus; Phosphoprotein; Reference proteome;
KW RNA-binding.
FT CHAIN 1..352
FT /note="Decapping nuclease din1"
FT /id="PRO_0000079900"
FT BINDING 33
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 93..95
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 150
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000269|PubMed:19194460"
FT BINDING 182
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 199
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 201
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000269|PubMed:19194460"
FT BINDING 239
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000269|PubMed:19194460"
FT BINDING 240
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000269|PubMed:19194460"
FT BINDING 241
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 263
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT MOD_RES 218
FT /note="Phosphoserine"
FT /evidence="ECO:0000269|PubMed:18257517"
FT MUTAGEN 199..201
FT /note="EVD->AVA: Abolishes the decapping activity on NAD-
FT cap RNAs."
FT /evidence="ECO:0000269|PubMed:28283058"
FT STRAND 2..6
FT /evidence="ECO:0007829|PDB:6WUI"
FT HELIX 7..9
FT /evidence="ECO:0007829|PDB:6WUI"
FT STRAND 22..29
FT /evidence="ECO:0007829|PDB:6WUI"
FT STRAND 35..39
FT /evidence="ECO:0007829|PDB:6WUI"
FT STRAND 43..45
FT /evidence="ECO:0007829|PDB:3FQG"
FT TURN 54..61
FT /evidence="ECO:0007829|PDB:6WUI"
FT HELIX 73..81
FT /evidence="ECO:0007829|PDB:6WUI"
FT STRAND 88..93
FT /evidence="ECO:0007829|PDB:6WUI"
FT HELIX 94..102
FT /evidence="ECO:0007829|PDB:6WUI"
FT TURN 103..105
FT /evidence="ECO:0007829|PDB:6WUI"
FT STRAND 111..117
FT /evidence="ECO:0007829|PDB:6WUI"
FT TURN 119..121
FT /evidence="ECO:0007829|PDB:6WUI"
FT STRAND 124..127
FT /evidence="ECO:0007829|PDB:6WUI"
FT HELIX 134..137
FT /evidence="ECO:0007829|PDB:3FQD"
FT HELIX 141..152
FT /evidence="ECO:0007829|PDB:6WUI"
FT STRAND 154..156
FT /evidence="ECO:0007829|PDB:3FQG"
FT HELIX 159..161
FT /evidence="ECO:0007829|PDB:3FQD"
FT HELIX 164..168
FT /evidence="ECO:0007829|PDB:3FQD"
FT HELIX 170..172
FT /evidence="ECO:0007829|PDB:3FQD"
FT STRAND 180..189
FT /evidence="ECO:0007829|PDB:6WUI"
FT STRAND 192..200
FT /evidence="ECO:0007829|PDB:6WUI"
FT STRAND 202..205
FT /evidence="ECO:0007829|PDB:6WUI"
FT HELIX 234..236
FT /evidence="ECO:0007829|PDB:6WUI"
FT STRAND 237..243
FT /evidence="ECO:0007829|PDB:6WUI"
FT HELIX 251..266
FT /evidence="ECO:0007829|PDB:6WUI"
FT STRAND 271..277
FT /evidence="ECO:0007829|PDB:6WUI"
FT STRAND 281..290
FT /evidence="ECO:0007829|PDB:6WUI"
FT HELIX 293..298
FT /evidence="ECO:0007829|PDB:6WUI"
FT HELIX 299..301
FT /evidence="ECO:0007829|PDB:6WUI"
FT HELIX 309..328
FT /evidence="ECO:0007829|PDB:6WUI"
FT STRAND 335..340
FT /evidence="ECO:0007829|PDB:6WUI"
FT STRAND 345..350
FT /evidence="ECO:0007829|PDB:6WUI"
SQ SEQUENCE 352 AA; 40751 MW; 7965C8588FCEE460 CRC64;
MLREFSFYDV PPAHVPPVSE PLEIACYSLS RDRELLLDDS KLSYYYPPPL FSDLNTGFPN
RFHPPKSDPD PISIVKDVLM TKGIQMNSSF LTWRGLITKI MCAPLDPRNH WETYLVMDPT
SGIIMMEERT RSETSYANQD RMCYWGYKFE AISTLPEIWD ACSRDQIEQR DNQDVVPDEQ
YCSIVKINIG KSKLILAGEV DCIWDKKPCS AKESDVHSDD GTIEEDASNA ENPNLHYVEL
KTSKKYPLEN YGMRKKLLKY WAQSFLLGIG RIIIGFRDDN GILIEMKELF THQIPKMLRP
YFKPNDWTPN RLLVVLEHAL EWIKQTVKQH PPSTEFTLSY TGGSKLVLRQ II
