NUD16_BOVIN
ID NUD16_BOVIN Reviewed; 195 AA.
AC A1A4Q9;
DT 22-JUL-2008, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 1.
DT 03-AUG-2022, entry version 93.
DE RecName: Full=U8 snoRNA-decapping enzyme;
DE EC=3.6.1.62 {ECO:0000250|UniProtKB:Q96DE0};
DE AltName: Full=IDP phosphatase;
DE Short=IDPase;
DE EC=3.6.1.64 {ECO:0000250|UniProtKB:Q96DE0};
DE AltName: Full=Inosine diphosphate phosphatase;
DE AltName: Full=Nucleoside diphosphate-linked moiety X motif 16;
DE Short=Nudix motif 16;
DE AltName: Full=m7GpppN-mRNA hydrolase;
GN Name=NUDT16;
OS Bos taurus (Bovine).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Laurasiatheria; Artiodactyla; Ruminantia; Pecora; Bovidae;
OC Bovinae; Bos.
OX NCBI_TaxID=9913;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=Hereford; TISSUE=Fetal cerebellum;
RG NIH - Mammalian Gene Collection (MGC) project;
RL Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: RNA-binding and decapping enzyme that catalyzes the cleavage
CC of the cap structure of snoRNAs and mRNAs in a metal-dependent manner.
CC Part of the U8 snoRNP complex that is required for the accumulation of
CC mature 5.8S and 28S rRNA. Has diphosphatase activity and removes m7G
CC and/or m227G caps from U8 snoRNA and leaves a 5'monophosphate on the
CC RNA. Catalyzes also the cleavage of the cap structure on mRNAs. Does
CC not hydrolyze cap analog structures like 7-methylguanosine nucleoside
CC triphosphate (m7GpppG). Also hydrolysis m7G- and m227G U3-capped RNAs
CC but with less efficiencies. Has broad substrate specificity with
CC manganese or cobalt as cofactor and can act on various RNA species.
CC Binds to the U8 snoRNA; metal is not required for RNA-binding. May play
CC a role in the regulation of snoRNAs and mRNAs degradation. Acts also as
CC a phosphatase; hydrolyzes the non-canonical purine nucleotides inosine
CC diphosphate (IDP) and deoxyinosine diphosphate (dITP) as well as
CC guanosine diphosphate (GDP), deoxyguanosine diphosphate (dGDP),
CC xanthine diphosphate (XDP), inosine triphosphate (ITP) and deoxyinosine
CC triphosphate (ITP) to their respective monophosphate derivatives and
CC does not distinguish between the deoxy- and ribose forms. The order of
CC activity with different substrates is IDP > dIDP >> GDP = dGDP > XDP =
CC ITP = dITP. Binds strongly to GTP, ITP and XTP. Participates in the
CC hydrolysis of dIDP/IDP and probably excludes non-canonical purines from
CC RNA and DNA precursor pools, thus preventing their incorporation into
CC RNA and DNA and avoiding chromosomal lesions (By similarity). Exhibits
CC decapping activity towards NAD-capped RNAs and FAD-capped RNAs (By
CC similarity). Exhibits decapping activity towards NAD-capped RNAs and
CC FAD-capped RNAs (By similarity). Exhibits decapping activity towards
CC dpCoA-capped RNAs in vitro (By similarity).
CC {ECO:0000250|UniProtKB:Q6P3D0, ECO:0000250|UniProtKB:Q96DE0}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside
CC in mRNA + H2O = a 5'-end phospho-ribonucleoside in mRNA + 2 H(+) +
CC N(7)-methyl-GDP; Xref=Rhea:RHEA:67484, Rhea:RHEA-COMP:15692,
CC Rhea:RHEA-COMP:17167, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:63714, ChEBI:CHEBI:138282, ChEBI:CHEBI:156461;
CC EC=3.6.1.62; Evidence={ECO:0000250|UniProtKB:Q96DE0};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:67485;
CC Evidence={ECO:0000250|UniProtKB:Q96DE0};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + IDP = H(+) + IMP + phosphate; Xref=Rhea:RHEA:35207,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:58053, ChEBI:CHEBI:58280; EC=3.6.1.64;
CC Evidence={ECO:0000250|UniProtKB:Q96DE0};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:35208;
CC Evidence={ECO:0000250|UniProtKB:Q96DE0};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=dIDP + H2O = dIMP + H(+) + phosphate; Xref=Rhea:RHEA:35211,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:61194, ChEBI:CHEBI:62286; EC=3.6.1.64;
CC Evidence={ECO:0000250|UniProtKB:Q96DE0};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:35212;
CC Evidence={ECO:0000250|UniProtKB:Q96DE0};
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:Q96DE0};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:60881;
CC Evidence={ECO:0000250|UniProtKB:Q96DE0};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 5'-end FAD-phospho-ribonucleoside in mRNA + H2O = a 5'-end
CC phospho-adenosine-phospho-ribonucleoside in mRNA + FMN + 2 H(+);
CC Xref=Rhea:RHEA:67588, Rhea:RHEA-COMP:15719, Rhea:RHEA-COMP:17275,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:58210,
CC ChEBI:CHEBI:144051, ChEBI:CHEBI:172372;
CC Evidence={ECO:0000250|UniProtKB:Q96DE0};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:67589;
CC Evidence={ECO:0000250|UniProtKB:Q96DE0};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 5'-end CoA-ribonucleoside in mRNA + H2O = (R)-4'-
CC phosphopantetheine + a 5'-end phospho-adenosine-phospho-
CC ribonucleoside in mRNA + 2 H(+); Xref=Rhea:RHEA:67592, Rhea:RHEA-
CC COMP:15719, Rhea:RHEA-COMP:17276, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:61723, ChEBI:CHEBI:144051,
CC ChEBI:CHEBI:172371; Evidence={ECO:0000250|UniProtKB:Q6P3D0};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:67593;
CC Evidence={ECO:0000250|UniProtKB:Q6P3D0};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000250|UniProtKB:Q96DE0};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000250|UniProtKB:Q96DE0};
CC Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Evidence={ECO:0000250|UniProtKB:Q96DE0};
CC Note=Binds 3 or 4 divalent metal cations. Acts specifically on U8
CC snoRNA with magnesium as cofactor. Has broad substrate specificity with
CC bound manganese or cobalt (in vitro). {ECO:0000250|UniProtKB:Q96DE0};
CC -!- SUBUNIT: Homodimer. {ECO:0000250|UniProtKB:Q96DE0}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:Q96DE0}. Nucleus,
CC nucleolus {ECO:0000250|UniProtKB:Q6TEC1}. Nucleus, nucleoplasm
CC {ECO:0000250|UniProtKB:Q6TEC1}. Cytoplasm
CC {ECO:0000250|UniProtKB:Q96DE0}. Note=Localized predominantly in the
CC cytoplasm. Localized in nucleolus, and in a minor proportion in
CC distinct foci in the nucleoplasm. {ECO:0000250|UniProtKB:Q6TEC1,
CC ECO:0000250|UniProtKB:Q96DE0}.
CC -!- SIMILARITY: Belongs to the Nudix hydrolase family. NUDT16 subfamily.
CC {ECO:0000305}.
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DR EMBL; BC126814; AAI26815.1; -; mRNA.
DR RefSeq; XP_005202022.1; XM_005201965.2.
DR AlphaFoldDB; A1A4Q9; -.
DR SMR; A1A4Q9; -.
DR STRING; 9913.ENSBTAP00000024966; -.
DR PaxDb; A1A4Q9; -.
DR PRIDE; A1A4Q9; -.
DR Ensembl; ENSBTAT00000053197; ENSBTAP00000049112; ENSBTAG00000018749.
DR GeneID; 512320; -.
DR CTD; 131870; -.
DR VEuPathDB; HostDB:ENSBTAG00000018749; -.
DR VGNC; VGNC:32330; NUDT16.
DR eggNOG; ENOG502TAG2; Eukaryota.
DR GeneTree; ENSGT00390000016224; -.
DR HOGENOM; CLU_110418_0_1_1; -.
DR InParanoid; A1A4Q9; -.
DR OMA; HVMLYCD; -.
DR Reactome; R-BTA-2393930; Phosphate bond hydrolysis by NUDT proteins.
DR Proteomes; UP000009136; Chromosome 1.
DR Bgee; ENSBTAG00000018749; Expressed in anterior segment of eyeball and 107 other tissues.
DR ExpressionAtlas; A1A4Q9; baseline and differential.
DR GO; GO:0005737; C:cytoplasm; ISS:UniProtKB.
DR GO; GO:0005730; C:nucleolus; ISS:UniProtKB.
DR GO; GO:0005654; C:nucleoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; ISS:UniProtKB.
DR GO; GO:0050897; F:cobalt ion binding; ISS:UniProtKB.
DR GO; GO:0097383; F:dIDP diphosphatase activity; IEA:RHEA.
DR GO; GO:0035870; F:dITP diphosphatase activity; ISS:UniProtKB.
DR GO; GO:0005525; F:GTP binding; ISS:UniProtKB.
DR GO; GO:1990003; F:inosine-diphosphatase activity; IEA:UniProtKB-EC.
DR GO; GO:1901641; F:ITP binding; ISS:UniProtKB.
DR GO; GO:0050072; F:m7G(5')pppN diphosphatase activity; ISS:UniProtKB.
DR GO; GO:0000287; F:magnesium ion binding; ISS:UniProtKB.
DR GO; GO:0030145; F:manganese ion binding; ISS:UniProtKB.
DR GO; GO:0008235; F:metalloexopeptidase activity; ISS:UniProtKB.
DR GO; GO:0003729; F:mRNA binding; ISS:UniProtKB.
DR GO; GO:0098519; F:nucleotide phosphatase activity, acting on free nucleotides; ISS:UniProtKB.
DR GO; GO:1990174; F:phosphodiesterase decapping endonuclease activity; IBA:GO_Central.
DR GO; GO:0042803; F:protein homodimerization activity; ISS:UniProtKB.
DR GO; GO:0110152; F:RNA NAD-cap (NAD-forming) hydrolase activity; IEA:RHEA.
DR GO; GO:0030515; F:snoRNA binding; ISS:UniProtKB.
DR GO; GO:1901640; F:XTP binding; ISS:UniProtKB.
DR GO; GO:0006382; P:adenosine to inosine editing; ISS:UniProtKB.
DR GO; GO:0035863; P:dITP catabolic process; ISS:UniProtKB.
DR GO; GO:0046709; P:IDP catabolic process; ISS:UniProtKB.
DR GO; GO:0006402; P:mRNA catabolic process; ISS:UniProtKB.
DR GO; GO:0110155; P:NAD-cap decapping; ISS:UniProtKB.
DR GO; GO:2000233; P:negative regulation of rRNA processing; ISS:UniProtKB.
DR GO; GO:0090068; P:positive regulation of cell cycle process; ISS:UniProtKB.
DR GO; GO:0016077; P:sno(s)RNA catabolic process; ISS:UniProtKB.
DR InterPro; IPR015797; NUDIX_hydrolase-like_dom_sf.
DR InterPro; IPR000086; NUDIX_hydrolase_dom.
DR Pfam; PF00293; NUDIX; 1.
DR SUPFAM; SSF55811; SSF55811; 1.
DR PROSITE; PS51462; NUDIX; 1.
PE 2: Evidence at transcript level;
KW Cytoplasm; Hydrolase; Magnesium; Manganese; Metal-binding;
KW Nucleotide metabolism; Nucleotide-binding; Nucleus; Reference proteome;
KW RNA-binding.
FT CHAIN 1..195
FT /note="U8 snoRNA-decapping enzyme"
FT /id="PRO_0000344986"
FT DOMAIN 18..168
FT /note="Nudix hydrolase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00794"
FT MOTIF 61..82
FT /note="Nudix box"
FT BINDING 24
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q6TEC1"
FT BINDING 50
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q6TEC1"
FT BINDING 57
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q96DE0"
FT BINDING 59
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q96DE0"
FT BINDING 76
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q96DE0"
FT BINDING 76
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:Q6TEC1"
FT BINDING 80
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q96DE0"
FT BINDING 80
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:Q6TEC1"
FT BINDING 99
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="4"
FT /evidence="ECO:0000250|UniProtKB:Q96DE0"
FT BINDING 166
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q6TEC1"
FT BINDING 170
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q6TEC1"
FT BINDING 173
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="4"
FT /evidence="ECO:0000250|UniProtKB:Q96DE0"
SQ SEQUENCE 195 AA; 21399 MW; F17578006C73466D CRC64;
MAGMRRLELS EALHLGPGWR HACHALLYAP DPGLLFGRIP LRYAVLMQMR FDGRLGFPGG
FVDLRDGSLE DGLNRELGEE LGEAAGAFRV ERADYRSSHA GSRPRVVAHF YTKLLTLEQL
TAVEMGAPRA RDHGLEVLGL VRVPLYTLRD GVGGLPAFLE NTFIGNAREQ LLEAVQNLGL
LEPGSFARLK ISTPP
