NUD16_XENLA
ID NUD16_XENLA Reviewed; 212 AA.
AC Q6TEC1; Q3KQG8; Q569R2; Q6AX51;
DT 22-JUL-2008, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 89.
DE RecName: Full=U8 snoRNA-decapping enzyme;
DE EC=3.6.1.62 {ECO:0000269|PubMed:15053875, ECO:0000269|PubMed:17567574, ECO:0000269|PubMed:18820299};
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=U8 snoRNA-binding protein X29;
DE AltName: Full=m7GpppN-mRNA hydrolase;
GN Name=nudt16;
OS Xenopus laevis (African clawed frog).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia;
OC Batrachia; Anura; Pipoidea; Pipidae; Xenopodinae; Xenopus; Xenopus.
OX NCBI_TaxID=8355;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], PARTIAL PROTEIN SEQUENCE, FUNCTION, CATALYTIC
RP ACTIVITY, RNA-BINDING, COFACTOR, SUBCELLULAR LOCATION, MUTAGENESIS OF
RP 92-GLU-GLU-93, TISSUE SPECIFICITY, AND IDENTIFICATION BY MASS SPECTROMETRY.
RC TISSUE=Liver, and Ovary;
RX PubMed=15053875; DOI=10.1016/s1097-2765(04)00127-3;
RA Ghosh T., Peterson B., Tomasevic N., Peculis B.A.;
RT "Xenopus U8 snoRNA binding protein is a conserved nuclear decapping
RT enzyme.";
RL Mol. Cell 13:817-828(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Brain, Eye, Fat body, and Testis;
RG NIH - Xenopus Gene Collection (XGC) project;
RL Submitted (MAY-2007) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP FUNCTION, AND RNA-BINDING.
RX PubMed=10585477; DOI=10.1074/jbc.274.50.35914;
RA Tomasevic N., Peculis B.;
RT "Identification of a U8 snoRNA-specific binding protein.";
RL J. Biol. Chem. 274:35914-35920(1999).
RN [4]
RP FUNCTION AS A DECAPPING ENZYME, BIOPHYSICOCHEMICAL PROPERTIES, CATALYTIC
RP ACTIVITY, COFACTOR SUBUNIT, RNA-BINDING, AND MUTAGENESIS OF GLU-89 AND
RP GLU-150.
RX PubMed=17567574; DOI=10.1074/jbc.m704179200;
RA Peculis B.A., Reynolds K., Cleland M.;
RT "Metal determines efficiency and substrate specificity of the nuclear NUDIX
RT decapping proteins X29 and H29K (Nudt16).";
RL J. Biol. Chem. 282:24792-24805(2007).
RN [5]
RP FUNCTION AS A DECAPPING ENZYME, CATALYTIC ACTIVITY, SUBUNIT, AND
RP RNA-BINDING.
RX PubMed=18820299; DOI=10.1093/nar/gkn605;
RA Taylor M.J., Peculis B.A.;
RT "Evolutionary conservation supports ancient origin for Nudt16, a nuclear-
RT localized, RNA-binding, RNA-decapping enzyme.";
RL Nucleic Acids Res. 36:6021-6034(2008).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) IN COMPLEXES WITH MANGANESE; GTP AND
RP M7G-NUCLEOTIDES, AND SUBUNIT.
RX PubMed=16472752; DOI=10.1016/j.str.2005.11.010;
RA Scarsdale J.N., Peculis B.A., Wright H.T.;
RT "Crystal structures of U8 snoRNA decapping nudix hydrolase, X29, and its
RT metal and cap complexes.";
RL Structure 14:331-343(2006).
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
CC (PubMed:15053875, PubMed:10585477, PubMed:17567574, PubMed:18820299).
CC Acts also as a phosphatase; hydrolyzes the non-canonical purine
CC nucleotides inosine diphosphate (IDP) and deoxyinosine diphosphate
CC (dITP) as well as guanosine diphosphate (GDP), deoxyguanosine
CC diphosphate (dGDP), xanthine diphosphate (XDP), inosine triphosphate
CC (ITP) and deoxyinosine triphosphate (ITP) to their respective
CC monophosphate derivatives and does not distinguish between the
CC deoxy- and ribose forms. The order of activity with different
CC substrates is IDP > dIDP >> GDP = dGDP > XDP = ITP = dITP. Binds
CC strongly to GTP, ITP and XTP. Participates in the hydrolysis of
CC dIDP/IDP and probably excludes non-canonical purines from RNA and DNA
CC precursor pools, thus preventing their incorporation into RNA and DNA
CC and avoiding chromosomal lesions (By similarity).Exhibits decapping
CC activity towards NAD-capped RNAs and FAD-capped RNAs (By similarity).
CC Exhibits decapping activity towards dpCoA-capped RNAs in vitro (By
CC similarity). {ECO:0000250|UniProtKB:Q6P3D0,
CC ECO:0000250|UniProtKB:Q96DE0, ECO:0000269|PubMed:10585477,
CC ECO:0000269|PubMed:15053875, ECO:0000269|PubMed:17567574,
CC ECO:0000269|PubMed:18820299}.
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:0000269|PubMed:15053875,
CC ECO:0000269|PubMed:17567574, ECO:0000269|PubMed:18820299};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:67485;
CC Evidence={ECO:0000269|PubMed:15053875, ECO:0000269|PubMed:17567574,
CC ECO:0000269|PubMed:18820299};
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:0000269|PubMed:15053875, ECO:0000269|PubMed:17567574};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:15053875, ECO:0000269|PubMed:17567574};
CC Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Evidence={ECO:0000269|PubMed:15053875, ECO:0000269|PubMed:17567574};
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:0000269|PubMed:15053875,
CC ECO:0000269|PubMed:17567574};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 8.5-9. {ECO:0000269|PubMed:17567574};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:16472752,
CC ECO:0000269|PubMed:18820299}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:15053875}. Nucleus,
CC nucleolus {ECO:0000269|PubMed:15053875}. Nucleus, nucleoplasm
CC {ECO:0000269|PubMed:15053875}. Cytoplasm
CC {ECO:0000250|UniProtKB:Q96DE0}. Note=Predominantly localized in
CC nucleolus, and in a minor proportion in distinct foci in the
CC nucleoplasm. {ECO:0000269|PubMed:15053875}.
CC -!- TISSUE SPECIFICITY: Detected in ovary, and at very low levels in
CC epithelial cells (at protein level). {ECO:0000269|PubMed:15053875}.
CC -!- SIMILARITY: Belongs to the Nudix hydrolase family. NUDT16 subfamily.
CC {ECO:0000305}.
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DR EMBL; AY423379; AAR36909.1; -; mRNA.
DR EMBL; BC079757; AAH79757.1; -; mRNA.
DR EMBL; BC092340; AAH92340.1; -; mRNA.
DR EMBL; BC106213; AAI06214.1; -; mRNA.
DR EMBL; BC124911; AAI24912.1; -; mRNA.
DR EMBL; BC141719; AAI41720.1; -; mRNA.
DR RefSeq; NP_001084713.1; NM_001091244.1.
DR PDB; 1U20; X-ray; 2.10 A; A/B=1-212.
DR PDB; 2A8P; X-ray; 2.70 A; A/B=1-212.
DR PDB; 2A8Q; X-ray; 2.60 A; A/B=1-212.
DR PDB; 2A8R; X-ray; 2.45 A; A/B=1-212.
DR PDB; 2A8S; X-ray; 2.45 A; A/B=1-212.
DR PDB; 2A8T; X-ray; 2.10 A; A/B=1-212.
DR PDBsum; 1U20; -.
DR PDBsum; 2A8P; -.
DR PDBsum; 2A8Q; -.
DR PDBsum; 2A8R; -.
DR PDBsum; 2A8S; -.
DR PDBsum; 2A8T; -.
DR AlphaFoldDB; Q6TEC1; -.
DR SMR; Q6TEC1; -.
DR DIP; DIP-29033N; -.
DR MaxQB; Q6TEC1; -.
DR DNASU; 414677; -.
DR GeneID; 414677; -.
DR KEGG; xla:414677; -.
DR CTD; 414677; -.
DR Xenbase; XB-GENE-6252278; nudt16.L.
DR OMA; HVMLYCD; -.
DR OrthoDB; 1385294at2759; -.
DR BRENDA; 3.6.1.62; 6725.
DR EvolutionaryTrace; Q6TEC1; -.
DR Proteomes; UP000186698; Chromosome 8L.
DR Bgee; 414677; Expressed in internal ear and 19 other tissues.
DR GO; GO:0005737; C:cytoplasm; ISS:UniProtKB.
DR GO; GO:0005730; C:nucleolus; IDA:UniProtKB.
DR GO; GO:0005654; C:nucleoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0050897; F:cobalt ion binding; IDA: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; IDA:UniProtKB.
DR GO; GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
DR GO; GO:0030145; F:manganese ion binding; IDA: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:0042803; F:protein homodimerization activity; IDA:UniProtKB.
DR GO; GO:0110152; F:RNA NAD-cap (NAD-forming) hydrolase activity; IEA:RHEA.
DR GO; GO:0030515; F:snoRNA binding; IDA: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; IDA:UniProtKB.
DR GO; GO:0090068; P:positive regulation of cell cycle process; ISS:UniProtKB.
DR GO; GO:0016077; P:sno(s)RNA catabolic process; IDA: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 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Direct protein sequencing; Hydrolase; Magnesium;
KW Manganese; Metal-binding; Nucleotide metabolism; Nucleotide-binding;
KW Nucleus; Reference proteome; RNA-binding.
FT CHAIN 1..212
FT /note="U8 snoRNA-decapping enzyme"
FT /id="PRO_0000344987"
FT DOMAIN 39..187
FT /note="Nudix hydrolase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00794"
FT REGION 1..23
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 74..95
FT /note="Nudix box"
FT BINDING 37
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:16472752"
FT BINDING 63
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:16472752"
FT BINDING 70
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q96DE0"
FT BINDING 72
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:16472752"
FT BINDING 89
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:16472752"
FT BINDING 89
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="3"
FT /evidence="ECO:0000269|PubMed:16472752"
FT BINDING 93
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:16472752"
FT BINDING 93
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="3"
FT /evidence="ECO:0000269|PubMed:16472752"
FT BINDING 150
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="3"
FT /evidence="ECO:0000269|PubMed:16472752"
FT BINDING 150
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="4"
FT /evidence="ECO:0000269|PubMed:16472752"
FT BINDING 180
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:16472752"
FT BINDING 184
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:16472752"
FT MUTAGEN 88
FT /note="R->L: Loss of activity; no effect on RNA-binding."
FT MUTAGEN 89
FT /note="E->Q: Loss of activity; no effect on RNA-binding."
FT /evidence="ECO:0000269|PubMed:17567574"
FT MUTAGEN 92..93
FT /note="EE->KK: Strongly reduced activity; no effect on RNA-
FT binding."
FT /evidence="ECO:0000269|PubMed:15053875"
FT MUTAGEN 92
FT /note="E->Q: Reduced activity; no effect on RNA-binding."
FT MUTAGEN 93
FT /note="E->Q: Strongly reduced activity; no effect on RNA-
FT binding."
FT MUTAGEN 150
FT /note="E->Q: Loss of activity; no effect on RNA-binding."
FT /evidence="ECO:0000269|PubMed:17567574"
FT STRAND 18..20
FT /evidence="ECO:0007829|PDB:1U20"
FT HELIX 23..27
FT /evidence="ECO:0007829|PDB:1U20"
FT STRAND 33..43
FT /evidence="ECO:0007829|PDB:1U20"
FT TURN 49..51
FT /evidence="ECO:0007829|PDB:1U20"
FT STRAND 56..63
FT /evidence="ECO:0007829|PDB:1U20"
FT STRAND 71..75
FT /evidence="ECO:0007829|PDB:1U20"
FT TURN 77..79
FT /evidence="ECO:0007829|PDB:1U20"
FT HELIX 82..94
FT /evidence="ECO:0007829|PDB:1U20"
FT HELIX 96..100
FT /evidence="ECO:0007829|PDB:1U20"
FT HELIX 105..107
FT /evidence="ECO:0007829|PDB:1U20"
FT STRAND 108..114
FT /evidence="ECO:0007829|PDB:1U20"
FT STRAND 116..118
FT /evidence="ECO:0007829|PDB:2A8T"
FT STRAND 120..128
FT /evidence="ECO:0007829|PDB:1U20"
FT HELIX 131..141
FT /evidence="ECO:0007829|PDB:1U20"
FT TURN 148..150
FT /evidence="ECO:0007829|PDB:1U20"
FT STRAND 151..156
FT /evidence="ECO:0007829|PDB:1U20"
FT HELIX 169..172
FT /evidence="ECO:0007829|PDB:1U20"
FT HELIX 181..191
FT /evidence="ECO:0007829|PDB:1U20"
FT HELIX 197..208
FT /evidence="ECO:0007829|PDB:1U20"
SQ SEQUENCE 212 AA; 24350 MW; 6E73DC50B7F49AB1 CRC64;
MAESRSPDRG AKEDKPRPRN ISREESLQLE GYKHACHALL HAPSQAKLFD RVPIRRVLLM
MMRFDGRLGF PGGFVDTRDI SLEEGLKREL EEELGPALAT VEVTEDDYRS SQVREHPQKC
VTHFYIKELK LEEIERIEAE AVNAKDHGLE VMGLIRVPLY TLRDRVGGLP AFLCNNFIGN
SKSQLLYALR SLKLLREDQI QEVLKASHRL QY
