DXO_PICST
ID DXO_PICST Reviewed; 396 AA.
AC A3LNL5;
DT 02-DEC-2020, integrated into UniProtKB/Swiss-Prot.
DT 24-JUL-2007, sequence version 2.
DT 03-AUG-2022, entry version 76.
DE RecName: Full=Decapping nuclease RAI1 {ECO:0000305};
DE Short=SsRai1 {ECO:0000303|PubMed:26101253, ECO:0000303|PubMed:28283058};
DE EC=3.6.1.- {ECO:0000269|PubMed:26101253};
DE AltName: Full=NAD-capped RNA hydrolase RAI1 {ECO:0000305};
DE Short=DeNADding enzyme RAI1 {ECO:0000305};
DE EC=3.6.1.- {ECO:0000250|UniProtKB:O13836};
GN Name=RAI1 {ECO:0000303|PubMed:26101253};
GN ORFNames=PICST_55876 {ECO:0000312|EMBL:ABN64879.2};
OS Scheffersomyces stipitis (strain ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL
OS Y-11545) (Yeast) (Pichia stipitis).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Debaryomycetaceae; Scheffersomyces.
OX NCBI_TaxID=322104;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545;
RX PubMed=17334359; DOI=10.1038/nbt1290;
RA Jeffries T.W., Grigoriev I.V., Grimwood J., Laplaza J.M., Aerts A.,
RA Salamov A., Schmutz J., Lindquist E., Dehal P., Shapiro H., Jin Y.-S.,
RA Passoth V., Richardson P.M.;
RT "Genome sequence of the lignocellulose-bioconverting and xylose-fermenting
RT yeast Pichia stipitis.";
RL Nat. Biotechnol. 25:319-326(2007).
RN [2] {ECO:0007744|PDB:5BTO}
RP X-RAY CRYSTALLOGRAPHY (1.64 ANGSTROMS), AND FUNCTION.
RX PubMed=26101253; DOI=10.1093/nar/gkv620;
RA Wang V.Y., Jiao X., Kiledjian M., Tong L.;
RT "Structural and biochemical studies of the distinct activity profiles of
RT Rai1 enzymes.";
RL Nucleic Acids Res. 43:6596-6606(2015).
RN [3] {ECO:0007744|PDB:5ULJ}
RP X-RAY CRYSTALLOGRAPHY (1.91 ANGSTROMS) OF 1-394 IN COMPLEX WITH NADP AND
RP CALCIUM, AND COFACTOR.
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 (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:26101253). 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) (By similarity).
CC {ECO:0000250|UniProtKB:O13836, ECO:0000250|UniProtKB:O70348,
CC ECO:0000250|UniProtKB:Q06349, ECO:0000269|PubMed:26101253}.
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: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:28283058};
CC Note=Divalent metal cation. {ECO:0000269|PubMed:28283058};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:P53063}.
CC -!- SIMILARITY: Belongs to the DXO/Dom3Z family. {ECO:0000305}.
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DR EMBL; CP000496; ABN64879.2; -; Genomic_DNA.
DR RefSeq; XP_001382908.2; XM_001382871.1.
DR PDB; 5BTO; X-ray; 1.64 A; A/B=1-396.
DR PDB; 5ULJ; X-ray; 1.91 A; A/B/C/D=1-394.
DR PDBsum; 5BTO; -.
DR PDBsum; 5ULJ; -.
DR AlphaFoldDB; A3LNL5; -.
DR SMR; A3LNL5; -.
DR STRING; 4924.XP_001382908.2; -.
DR EnsemblFungi; ABN64879; ABN64879; PICST_55876.
DR GeneID; 4837555; -.
DR KEGG; pic:PICST_55876; -.
DR eggNOG; KOG1982; Eukaryota.
DR HOGENOM; CLU_024877_4_1_1; -.
DR InParanoid; A3LNL5; -.
DR OMA; MAYWGYK; -.
DR OrthoDB; 1034620at2759; -.
DR Proteomes; UP000002258; Chromosome 2.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
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:0006397; P:mRNA processing; IEA:UniProtKB-KW.
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; Reference proteome; RNA-binding.
FT CHAIN 1..396
FT /note="Decapping nuclease RAI1"
FT /id="PRO_0000451696"
FT BINDING 107..109
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:28283058,
FT ECO:0007744|PDB:5ULJ"
FT BINDING 179
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000269|PubMed:28283058,
FT ECO:0007744|PDB:5ULJ"
FT BINDING 228
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:28283058,
FT ECO:0007744|PDB:5ULJ"
FT BINDING 230
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000269|PubMed:28283058,
FT ECO:0007744|PDB:5ULJ"
FT BINDING 249
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000269|PubMed:28283058,
FT ECO:0007744|PDB:5ULJ"
FT BINDING 250
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000269|PubMed:28283058,
FT ECO:0007744|PDB:5ULJ"
FT BINDING 251
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:28283058,
FT ECO:0007744|PDB:5ULJ"
FT BINDING 275
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:28283058,
FT ECO:0007744|PDB:5ULJ"
FT STRAND 2..5
FT /evidence="ECO:0007829|PDB:5BTO"
FT STRAND 20..27
FT /evidence="ECO:0007829|PDB:5BTO"
FT HELIX 37..43
FT /evidence="ECO:0007829|PDB:5BTO"
FT HELIX 52..54
FT /evidence="ECO:0007829|PDB:5BTO"
FT TURN 61..64
FT /evidence="ECO:0007829|PDB:5BTO"
FT HELIX 65..67
FT /evidence="ECO:0007829|PDB:5BTO"
FT HELIX 73..75
FT /evidence="ECO:0007829|PDB:5BTO"
FT HELIX 80..94
FT /evidence="ECO:0007829|PDB:5BTO"
FT STRAND 103..107
FT /evidence="ECO:0007829|PDB:5BTO"
FT HELIX 108..116
FT /evidence="ECO:0007829|PDB:5BTO"
FT HELIX 117..119
FT /evidence="ECO:0007829|PDB:5BTO"
FT STRAND 125..132
FT /evidence="ECO:0007829|PDB:5BTO"
FT STRAND 135..140
FT /evidence="ECO:0007829|PDB:5BTO"
FT HELIX 142..159
FT /evidence="ECO:0007829|PDB:5BTO"
FT HELIX 162..181
FT /evidence="ECO:0007829|PDB:5BTO"
FT STRAND 183..186
FT /evidence="ECO:0007829|PDB:5BTO"
FT HELIX 188..190
FT /evidence="ECO:0007829|PDB:5BTO"
FT HELIX 193..197
FT /evidence="ECO:0007829|PDB:5BTO"
FT STRAND 199..202
FT /evidence="ECO:0007829|PDB:5BTO"
FT STRAND 205..207
FT /evidence="ECO:0007829|PDB:5BTO"
FT STRAND 209..218
FT /evidence="ECO:0007829|PDB:5BTO"
FT STRAND 221..228
FT /evidence="ECO:0007829|PDB:5BTO"
FT STRAND 231..234
FT /evidence="ECO:0007829|PDB:5BTO"
FT HELIX 243..246
FT /evidence="ECO:0007829|PDB:5BTO"
FT STRAND 247..254
FT /evidence="ECO:0007829|PDB:5BTO"
FT HELIX 259..279
FT /evidence="ECO:0007829|PDB:5BTO"
FT STRAND 283..289
FT /evidence="ECO:0007829|PDB:5BTO"
FT STRAND 294..302
FT /evidence="ECO:0007829|PDB:5BTO"
FT HELIX 303..305
FT /evidence="ECO:0007829|PDB:5BTO"
FT HELIX 306..311
FT /evidence="ECO:0007829|PDB:5BTO"
FT HELIX 326..343
FT /evidence="ECO:0007829|PDB:5BTO"
FT STRAND 352..358
FT /evidence="ECO:0007829|PDB:5BTO"
FT TURN 359..362
FT /evidence="ECO:0007829|PDB:5BTO"
FT STRAND 363..368
FT /evidence="ECO:0007829|PDB:5BTO"
FT HELIX 371..378
FT /evidence="ECO:0007829|PDB:5BTO"
FT TURN 379..381
FT /evidence="ECO:0007829|PDB:5BTO"
FT HELIX 385..393
FT /evidence="ECO:0007829|PDB:5BTO"
SQ SEQUENCE 396 AA; 46084 MW; 86FA8C46A0A96B86 CRC64;
MMKTLSLQSR AKTTALKQPK EIFAFARDID GEFVYDQKIV KDENVSYYYL PDSKIDGSID
LQAGYAKFKK IPEEKNMSDM KCLLTALTKY EQEHNNGEKV NVDIITYRGL MTKLLALPYN
LNDPVDLNVL AYDGQLFINS DEEIELARRK EEDEHKQQSM TPEKYDHMKR CEFSGYKFEA
IATLPKPWAD CSRQQIDKRG KKMVNNYEQY ISVIKTGIGE AKMLLAGEVD CVWDYIPEDG
KDVLSHYMEL KTTRILESNG QVVNFEKKLF KTWAQCFLMG IRKVVYGFRD DSFFLRDVEL
YKTEEIPLLI KNNALTENKS GGKINCTTAL KWYGAVIEWL LQEIPRDDTS KAYRVSFDPS
TRTFTLRELM GNENSRLRNG EMLTSEFKQW RESIQK
