DXO_CANAL
ID DXO_CANAL Reviewed; 391 AA.
AC Q5AAT0; A0A1D8PDX0;
DT 19-SEP-2006, integrated into UniProtKB/Swiss-Prot.
DT 12-APR-2017, sequence version 4.
DT 03-AUG-2022, entry version 88.
DE RecName: Full=Decapping nuclease RAI1 {ECO:0000305};
DE Short=CaRai1 {ECO:0000303|PubMed:26101253};
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 OrderedLocusNames=CAALFM_C106800WA; ORFNames=CaO19.13610, CaO19.6230;
OS Candida albicans (strain SC5314 / ATCC MYA-2876) (Yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Debaryomycetaceae; Candida/Lodderomyces clade; Candida.
OX NCBI_TaxID=237561;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=SC5314 / ATCC MYA-2876;
RX PubMed=15123810; DOI=10.1073/pnas.0401648101;
RA Jones T., Federspiel N.A., Chibana H., Dungan J., Kalman S., Magee B.B.,
RA Newport G., Thorstenson Y.R., Agabian N., Magee P.T., Davis R.W.,
RA Scherer S.;
RT "The diploid genome sequence of Candida albicans.";
RL Proc. Natl. Acad. Sci. U.S.A. 101:7329-7334(2004).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=SC5314 / ATCC MYA-2876;
RX PubMed=17419877; DOI=10.1186/gb-2007-8-4-r52;
RA van het Hoog M., Rast T.J., Martchenko M., Grindle S., Dignard D.,
RA Hogues H., Cuomo C., Berriman M., Scherer S., Magee B.B., Whiteway M.,
RA Chibana H., Nantel A., Magee P.T.;
RT "Assembly of the Candida albicans genome into sixteen supercontigs aligned
RT on the eight chromosomes.";
RL Genome Biol. 8:RESEARCH52.1-RESEARCH52.12(2007).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], AND GENOME REANNOTATION.
RC STRAIN=SC5314 / ATCC MYA-2876;
RX PubMed=24025428; DOI=10.1186/gb-2013-14-9-r97;
RA Muzzey D., Schwartz K., Weissman J.S., Sherlock G.;
RT "Assembly of a phased diploid Candida albicans genome facilitates allele-
RT specific measurements and provides a simple model for repeat and indel
RT structure.";
RL Genome Biol. 14:RESEARCH97.1-RESEARCH97.14(2013).
RN [4] {ECO:0007744|PDB:5BTH, ECO:0007744|PDB:5BUD}
RP X-RAY CRYSTALLOGRAPHY (1.99 ANGSTROMS) IN COMPLEX WITH MANGANESE, AND
RP 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. 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: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; CP017623; AOW26335.1; -; Genomic_DNA.
DR RefSeq; XP_718819.2; XM_713726.2.
DR PDB; 5BTH; X-ray; 2.20 A; A=1-391.
DR PDB; 5BUD; X-ray; 1.99 A; A/B=1-391.
DR PDBsum; 5BTH; -.
DR PDBsum; 5BUD; -.
DR AlphaFoldDB; Q5AAT0; -.
DR SMR; Q5AAT0; -.
DR STRING; 237561.Q5AAT0; -.
DR GeneID; 3639496; -.
DR KEGG; cal:CAALFM_C106800WA; -.
DR CGD; CAL0000178137; orf19.13610.
DR VEuPathDB; FungiDB:C1_06800W_A; -.
DR eggNOG; KOG1982; Eukaryota.
DR HOGENOM; CLU_024877_4_1_1; -.
DR InParanoid; Q5AAT0; -.
DR OrthoDB; 1034620at2759; -.
DR PRO; PR:Q5AAT0; -.
DR Proteomes; UP000000559; Chromosome 1.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
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:0110152; F:RNA NAD-cap (NAD-forming) hydrolase activity; IEA:RHEA.
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; Hydrolase; Metal-binding; mRNA processing; Nuclease;
KW Nucleotide-binding; Nucleus; Reference proteome; RNA-binding.
FT CHAIN 1..391
FT /note="Decapping nuclease RAI1"
FT /id="PRO_0000249828"
FT BINDING 174
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000269|PubMed:26101253,
FT ECO:0007744|PDB:5BTH, ECO:0007744|PDB:5BUD"
FT BINDING 223
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 225
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000269|PubMed:26101253,
FT ECO:0007744|PDB:5BTH, ECO:0007744|PDB:5BUD"
FT BINDING 244
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000269|PubMed:26101253,
FT ECO:0007744|PDB:5BTH, ECO:0007744|PDB:5BUD"
FT BINDING 245
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000269|PubMed:26101253,
FT ECO:0007744|PDB:5BTH, ECO:0007744|PDB:5BUD"
FT BINDING 246
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 270
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT STRAND 2..4
FT /evidence="ECO:0007829|PDB:5BTH"
FT STRAND 20..27
FT /evidence="ECO:0007829|PDB:5BUD"
FT HELIX 38..41
FT /evidence="ECO:0007829|PDB:5BUD"
FT HELIX 49..53
FT /evidence="ECO:0007829|PDB:5BUD"
FT TURN 58..61
FT /evidence="ECO:0007829|PDB:5BUD"
FT HELIX 62..64
FT /evidence="ECO:0007829|PDB:5BUD"
FT HELIX 70..72
FT /evidence="ECO:0007829|PDB:5BUD"
FT HELIX 77..91
FT /evidence="ECO:0007829|PDB:5BUD"
FT STRAND 98..102
FT /evidence="ECO:0007829|PDB:5BUD"
FT HELIX 103..111
FT /evidence="ECO:0007829|PDB:5BUD"
FT HELIX 112..114
FT /evidence="ECO:0007829|PDB:5BUD"
FT STRAND 120..127
FT /evidence="ECO:0007829|PDB:5BUD"
FT STRAND 130..135
FT /evidence="ECO:0007829|PDB:5BUD"
FT HELIX 137..154
FT /evidence="ECO:0007829|PDB:5BUD"
FT HELIX 157..177
FT /evidence="ECO:0007829|PDB:5BUD"
FT STRAND 178..181
FT /evidence="ECO:0007829|PDB:5BUD"
FT HELIX 183..185
FT /evidence="ECO:0007829|PDB:5BUD"
FT HELIX 188..192
FT /evidence="ECO:0007829|PDB:5BUD"
FT HELIX 193..196
FT /evidence="ECO:0007829|PDB:5BUD"
FT STRAND 204..213
FT /evidence="ECO:0007829|PDB:5BUD"
FT STRAND 216..224
FT /evidence="ECO:0007829|PDB:5BUD"
FT STRAND 226..229
FT /evidence="ECO:0007829|PDB:5BUD"
FT HELIX 235..237
FT /evidence="ECO:0007829|PDB:5BUD"
FT HELIX 239..241
FT /evidence="ECO:0007829|PDB:5BUD"
FT STRAND 242..249
FT /evidence="ECO:0007829|PDB:5BUD"
FT HELIX 254..274
FT /evidence="ECO:0007829|PDB:5BUD"
FT STRAND 278..284
FT /evidence="ECO:0007829|PDB:5BUD"
FT STRAND 289..297
FT /evidence="ECO:0007829|PDB:5BUD"
FT HELIX 298..300
FT /evidence="ECO:0007829|PDB:5BUD"
FT HELIX 301..306
FT /evidence="ECO:0007829|PDB:5BUD"
FT HELIX 309..311
FT /evidence="ECO:0007829|PDB:5BTH"
FT TURN 315..317
FT /evidence="ECO:0007829|PDB:5BUD"
FT HELIX 321..338
FT /evidence="ECO:0007829|PDB:5BUD"
FT STRAND 348..353
FT /evidence="ECO:0007829|PDB:5BUD"
FT TURN 354..357
FT /evidence="ECO:0007829|PDB:5BUD"
FT STRAND 358..363
FT /evidence="ECO:0007829|PDB:5BUD"
FT HELIX 366..373
FT /evidence="ECO:0007829|PDB:5BUD"
FT TURN 374..376
FT /evidence="ECO:0007829|PDB:5BUD"
FT HELIX 380..388
FT /evidence="ECO:0007829|PDB:5BUD"
SQ SEQUENCE 391 AA; 45689 MW; 385566A27A162EB6 CRC64;
MAKSLPLNSR SKTTALKQPR ELFSYARDID GKYVYDDPEN SLSYYYLPDS TIDTGIDLQG
GYSKFKKIPD EQNLADFNSL LKAIIKYETS EGKKISSDII TFREIMTKIL SLPYNLTDPI
DLYVVPFDGQ LFIKSDDELD MKRRKEQEVR MKQTNTVERY DYMKRCEYVG YKFETIATIP
KPWSQVSRSQ IENRNKKVVN NYEQYLSVIR TGIGNVKLVL AGEIDCCWDY LPDEQNKKLN
HYVELKTSRI IENNSQVVSF EQKLFKAWCQ CFLMGVTKII YGFRDNNLIL KNVELFNTEE
IPILIKNNPL TNAATEKKIN CTNALKWYGA VVDWLNTTVD KKDETKSYRL KYDPVRKSFT
LSETESETNE KLRNGELLTP EFTEWRQSLK K
