DXO_ASHGO
ID DXO_ASHGO Reviewed; 376 AA.
AC Q753P9;
DT 02-DEC-2020, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 93.
DE RecName: Full=Decapping nuclease RAI1 {ECO:0000305};
DE Short=AgRai1 {ECO:0000303|PubMed:26101253};
DE EC=3.6.1.- {ECO:0000269|PubMed:26101253};
DE AltName: Full=5'-3' exoribonuclease RAI1 {ECO:0000305};
DE EC=3.1.13.- {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=AGOS_AFR263C {ECO:0000312|EMBL:AAS53634.1};
OS Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
OS (Yeast) (Eremothecium gossypii).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Eremothecium.
OX NCBI_TaxID=284811;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056;
RX PubMed=15001715; DOI=10.1126/science.1095781;
RA Dietrich F.S., Voegeli S., Brachat S., Lerch A., Gates K., Steiner S.,
RA Mohr C., Poehlmann R., Luedi P., Choi S., Wing R.A., Flavier A.,
RA Gaffney T.D., Philippsen P.;
RT "The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces
RT cerevisiae genome.";
RL Science 304:304-307(2004).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056;
RX PubMed=23749448; DOI=10.1534/g3.112.002881;
RA Dietrich F.S., Voegeli S., Kuo S., Philippsen P.;
RT "Genomes of Ashbya fungi isolated from insects reveal four mating-type
RT loci, numerous translocations, lack of transposons, and distinct gene
RT duplications.";
RL G3 (Bethesda) 3:1225-1239(2013).
RN [3] {ECO:0007744|PDB:5BTB, ECO:0007744|PDB:5BTE}
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) IN COMPLEX WITH MANGANESE, FUNCTION,
RP AND COFACTOR.
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).
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 (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:26101253). Specifically
CC degrades pre-mRNAs with a defective m7G cap and is part of a pre-mRNA
CC capping quality control (PubMed:26101253). 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) (By similarity). Also has 5'-3' exonuclease
CC activity (PubMed:26101253). Also possesses RNA 5'-pyrophosphohydrolase
CC activity by hydrolyzing the 5'-end triphosphate to release
CC pyrophosphates (PubMed:26101253). {ECO:0000250|UniProtKB:O13836,
CC ECO:0000250|UniProtKB:O70348, ECO:0000250|UniProtKB:Q06349,
CC 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:26101253};
CC Note=Divalent metal cation. {ECO:0000269|PubMed:26101253};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:P53063}.
CC -!- SIMILARITY: Belongs to the DXO/Dom3Z family. {ECO:0000305}.
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DR EMBL; AE016819; AAS53634.1; -; Genomic_DNA.
DR RefSeq; NP_985810.1; NM_211165.1.
DR PDB; 5BTB; X-ray; 1.80 A; A=1-376.
DR PDB; 5BTE; X-ray; 2.40 A; A/B=1-376.
DR PDBsum; 5BTB; -.
DR PDBsum; 5BTE; -.
DR AlphaFoldDB; Q753P9; -.
DR SMR; Q753P9; -.
DR STRING; 33169.AAS53634; -.
DR EnsemblFungi; AAS53634; AAS53634; AGOS_AFR263C.
DR GeneID; 4622073; -.
DR KEGG; ago:AGOS_AFR263C; -.
DR eggNOG; KOG1982; Eukaryota.
DR HOGENOM; CLU_024877_4_1_1; -.
DR InParanoid; Q753P9; -.
DR OMA; MAYWGYK; -.
DR Proteomes; UP000000591; Chromosome VI.
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:0006397; P:mRNA processing; IEA:UniProtKB-KW.
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 3D-structure; Exonuclease; Hydrolase; Metal-binding; mRNA processing;
KW Nuclease; Nucleotide-binding; Nucleus; Reference proteome; RNA-binding.
FT CHAIN 1..376
FT /note="Decapping nuclease RAI1"
FT /id="PRO_0000451694"
FT BINDING 105..107
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 166
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250|UniProtKB:A3LNL5"
FT BINDING 215
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 217
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000269|PubMed:26101253,
FT ECO:0007744|PDB:5BTE"
FT BINDING 235
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000269|PubMed:26101253,
FT ECO:0007744|PDB:5BTE"
FT BINDING 236
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000269|PubMed:26101253,
FT ECO:0007744|PDB:5BTE"
FT BINDING 237
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 261
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT STRAND 6..8
FT /evidence="ECO:0007829|PDB:5BTB"
FT STRAND 22..30
FT /evidence="ECO:0007829|PDB:5BTB"
FT TURN 31..33
FT /evidence="ECO:0007829|PDB:5BTB"
FT STRAND 34..37
FT /evidence="ECO:0007829|PDB:5BTB"
FT HELIX 50..54
FT /evidence="ECO:0007829|PDB:5BTB"
FT TURN 59..65
FT /evidence="ECO:0007829|PDB:5BTB"
FT HELIX 69..72
FT /evidence="ECO:0007829|PDB:5BTB"
FT HELIX 81..94
FT /evidence="ECO:0007829|PDB:5BTB"
FT STRAND 101..105
FT /evidence="ECO:0007829|PDB:5BTB"
FT HELIX 106..114
FT /evidence="ECO:0007829|PDB:5BTB"
FT TURN 115..118
FT /evidence="ECO:0007829|PDB:5BTB"
FT HELIX 121..123
FT /evidence="ECO:0007829|PDB:5BTB"
FT STRAND 125..131
FT /evidence="ECO:0007829|PDB:5BTB"
FT STRAND 134..140
FT /evidence="ECO:0007829|PDB:5BTB"
FT HELIX 154..169
FT /evidence="ECO:0007829|PDB:5BTB"
FT STRAND 170..173
FT /evidence="ECO:0007829|PDB:5BTB"
FT HELIX 175..177
FT /evidence="ECO:0007829|PDB:5BTB"
FT HELIX 180..183
FT /evidence="ECO:0007829|PDB:5BTB"
FT HELIX 186..188
FT /evidence="ECO:0007829|PDB:5BTB"
FT STRAND 196..205
FT /evidence="ECO:0007829|PDB:5BTB"
FT STRAND 208..215
FT /evidence="ECO:0007829|PDB:5BTB"
FT STRAND 218..221
FT /evidence="ECO:0007829|PDB:5BTB"
FT HELIX 230..232
FT /evidence="ECO:0007829|PDB:5BTB"
FT STRAND 233..240
FT /evidence="ECO:0007829|PDB:5BTB"
FT HELIX 245..263
FT /evidence="ECO:0007829|PDB:5BTB"
FT TURN 264..266
FT /evidence="ECO:0007829|PDB:5BTB"
FT STRAND 269..275
FT /evidence="ECO:0007829|PDB:5BTB"
FT STRAND 280..288
FT /evidence="ECO:0007829|PDB:5BTB"
FT HELIX 291..295
FT /evidence="ECO:0007829|PDB:5BTB"
FT HELIX 304..319
FT /evidence="ECO:0007829|PDB:5BTB"
FT HELIX 326..328
FT /evidence="ECO:0007829|PDB:5BTB"
FT STRAND 332..338
FT /evidence="ECO:0007829|PDB:5BTB"
FT STRAND 341..347
FT /evidence="ECO:0007829|PDB:5BTB"
FT HELIX 350..354
FT /evidence="ECO:0007829|PDB:5BTB"
FT STRAND 355..359
FT /evidence="ECO:0007829|PDB:5BTB"
FT HELIX 361..370
FT /evidence="ECO:0007829|PDB:5BTB"
SQ SEQUENCE 376 AA; 43048 MW; AF55E4889A866AF8 CRC64;
MVFESELLLQ RRLATTALKQ PKELGYYSTN VGGELKVMDE SNLSYYYLPD ADIEKHIDLS
AGARKFQDEQ AEAEDDTGSL HGLLQTLMEY ERRKSKKVNA DIIAFRGQVK RLIHCAFGGH
ATDVDMYVMS FDGQLFIRAA RKKLEFPTSP RESWAYLAYY SGYKFERMAL LDRPVAETPR
EVLESRGKQV VRNGPQYKTV VRTGVGEHKL VLGAEVDGIF DFREPTGDNL KHYVELKVAK
KVQTLKDATN FEQKLFSVWL QCFLVGINRV IIGFRDEKFV LKSVEEFSTS EIPLLLKSTG
LRNACVDAIK WYGALTKWLC ELPRGPEDDF KLYRLSCSRG ALHLRQLHDE DLANGDDIIP
GWFREWRRSL SKSHGS
