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U8 snoRNA-decapping enzyme (EC 3.6.1.62) (IDP phosphatase) (IDPase) (EC 3.6.1.64) (Inosine diphosphate phosphatase) (Nucleoside diphosphate-linked moiety X motif 16) (Nudix motif 16) (U8 snoRNA-binding protein X29) (m7GpppN-mRNA hydrolase)

 NUD16_XENLA             Reviewed;         212 AA.
Q6TEC1; Q3KQG8; Q569R2; Q6AX51;
22-JUL-2008, integrated into UniProtKB/Swiss-Prot.
05-JUL-2004, sequence version 1.
22-NOV-2017, entry version 73.
RecName: Full=U8 snoRNA-decapping enzyme;
EC=3.6.1.62 {ECO:0000269|PubMed:15053875, ECO:0000269|PubMed:17567574, ECO:0000269|PubMed:18820299};
AltName: Full=IDP phosphatase;
Short=IDPase;
EC=3.6.1.64 {ECO:0000250|UniProtKB:Q96DE0};
AltName: Full=Inosine diphosphate phosphatase;
AltName: Full=Nucleoside diphosphate-linked moiety X motif 16;
Short=Nudix motif 16;
AltName: Full=U8 snoRNA-binding protein X29;
AltName: Full=m7GpppN-mRNA hydrolase;
Name=nudt16;
Xenopus laevis (African clawed frog).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Amphibia; Batrachia; Anura; Pipoidea; Pipidae; Xenopodinae; Xenopus;
Xenopus.
NCBI_TaxID=8355;
[1]
NUCLEOTIDE SEQUENCE [MRNA], PARTIAL PROTEIN SEQUENCE, FUNCTION,
CATALYTIC ACTIVITY, RNA-BINDING, COFACTOR, SUBCELLULAR LOCATION,
MUTAGENESIS OF 92-GLU-GLU-93, TISSUE SPECIFICITY, AND IDENTIFICATION
BY MASS SPECTROMETRY.
TISSUE=Liver, and Ovary;
PubMed=15053875; DOI=10.1016/S1097-2765(04)00127-3;
Ghosh T., Peterson B., Tomasevic N., Peculis B.A.;
"Xenopus U8 snoRNA binding protein is a conserved nuclear decapping
enzyme.";
Mol. Cell 13:817-828(2004).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
TISSUE=Brain, Eye, Fat body, and Testis;
NIH - Xenopus Gene Collection (XGC) project;
Submitted (MAY-2007) to the EMBL/GenBank/DDBJ databases.
[3]
FUNCTION, AND RNA-BINDING.
PubMed=10585477; DOI=10.1074/jbc.274.50.35914;
Tomasevic N., Peculis B.;
"Identification of a U8 snoRNA-specific binding protein.";
J. Biol. Chem. 274:35914-35920(1999).
[4]
FUNCTION AS A DECAPPING ENZYME, BIOPHYSICOCHEMICAL PROPERTIES,
CATALYTIC ACTIVITY, COFACTOR SUBUNIT, RNA-BINDING, AND MUTAGENESIS OF
GLU-89 AND GLU-150.
PubMed=17567574; DOI=10.1074/jbc.M704179200;
Peculis B.A., Reynolds K., Cleland M.;
"Metal determines efficiency and substrate specificity of the nuclear
NUDIX decapping proteins X29 and H29K (Nudt16).";
J. Biol. Chem. 282:24792-24805(2007).
[5]
FUNCTION AS A DECAPPING ENZYME, CATALYTIC ACTIVITY, SUBUNIT, AND
RNA-BINDING.
PubMed=18820299; DOI=10.1093/nar/gkn605;
Taylor M.J., Peculis B.A.;
"Evolutionary conservation supports ancient origin for Nudt16, a
nuclear-localized, RNA-binding, RNA-decapping enzyme.";
Nucleic Acids Res. 36:6021-6034(2008).
[6]
X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) IN COMPLEXES WITH MANGANESE; GTP
AND M7G-NUCLEOTIDES, AND SUBUNIT.
PubMed=16472752; DOI=10.1016/j.str.2005.11.010;
Scarsdale J.N., Peculis B.A., Wright H.T.;
"Crystal structures of U8 snoRNA decapping nudix hydrolase, X29, and
its metal and cap complexes.";
Structure 14:331-343(2006).
-!- FUNCTION: RNA-binding and decapping enzyme that catalyzes the
cleavage of the cap structure of snoRNAs and mRNAs in a metal-
dependent manner. Part of the U8 snoRNP complex that is required
for the accumulation of mature 5.8S and 28S rRNA. Has
diphosphatase activity and removes m7G and/or m227G caps from U8
snoRNA and leaves a 5'monophosphate on the RNA. Catalyzes also the
cleavage of the cap structure on mRNAs. Does not hydrolyze cap
analog structures like 7-methylguanosine nucleoside triphosphate
(m7GpppG). Also hydrolysis m7G- and m227G U3-capped RNAs but with
less efficiencies. Has broad substrate specificity with manganese
or cobalt as cofactor and can act on various RNA species. Binds to
the U8 snoRNA; metal is not required for RNA-binding. May play a
role in the regulation of snoRNAs and mRNAs degradation
(PubMed:15053875, PubMed:10585477, PubMed:17567574,
PubMed:18820299). Acts also as a phosphatase; hydrolyzes the non-
canonical purine nucleotides inosine diphosphate (IDP) and
deoxyinosine diphosphate (dITP) as well as guanosine diphosphate
(GDP), deoxyguanosine diphosphate (dGDP), xanthine diphosphate
(XDP), inosine triphosphate (ITP) and deoxyinosine triphosphate
(ITP) to their respective monophosphate derivatives and does not
distinguish between the deoxy- and ribose forms. The order of
activity with different substrates is IDP > dIDP >> GDP = dGDP >
XDP = ITP = dITP. Binds strongly to GTP, ITP and XTP. Participates
in the hydrolysis of dIDP/IDP and probably excludes non-canonical
purines from RNA and DNA precursor pools, thus preventing their
incorporation into RNA and DNA and avoiding chromosomal lesions
(By similarity). {ECO:0000250|UniProtKB:Q96DE0,
ECO:0000269|PubMed:10585477, ECO:0000269|PubMed:15053875,
ECO:0000269|PubMed:17567574, ECO:0000269|PubMed:18820299}.
-!- CATALYTIC ACTIVITY: 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA]
+ H(2)O = N(7)-methylguanosine 5'-diphosphate + 5'-phospho-[mRNA].
{ECO:0000269|PubMed:15053875, ECO:0000269|PubMed:17567574,
ECO:0000269|PubMed:18820299}.
-!- CATALYTIC ACTIVITY: IDP + H(2)O = IMP + phosphate.
{ECO:0000250|UniProtKB:Q96DE0}.
-!- CATALYTIC ACTIVITY: dIDP + H(2)O = dIMP + phosphate.
{ECO:0000250|UniProtKB:Q96DE0}.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000269|PubMed:15053875,
ECO:0000269|PubMed:17567574};
Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
Evidence={ECO:0000269|PubMed:15053875,
ECO:0000269|PubMed:17567574};
Name=Co(2+); Xref=ChEBI:CHEBI:48828;
Evidence={ECO:0000269|PubMed:15053875,
ECO:0000269|PubMed:17567574};
Note=Binds 3 or 4 divalent metal cations. Acts specifically on U8
snoRNA with magnesium as cofactor. Has broad substrate specificity
with bound manganese or cobalt (in vitro).
{ECO:0000269|PubMed:15053875, ECO:0000269|PubMed:17567574};
-!- BIOPHYSICOCHEMICAL PROPERTIES:
pH dependence:
Optimum pH is 8.5-9. {ECO:0000269|PubMed:17567574};
-!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:16472752,
ECO:0000269|PubMed:18820299}.
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:15053875}.
Nucleus, nucleolus {ECO:0000269|PubMed:15053875}. Nucleus,
nucleoplasm {ECO:0000269|PubMed:15053875}. Cytoplasm
{ECO:0000250|UniProtKB:Q96DE0}. Note=Predominantly localized in
nucleolus, and in a minor proportion in distinct foci in the
nucleoplasm. {ECO:0000269|PubMed:15053875}.
-!- TISSUE SPECIFICITY: Detected in ovary, and at very low levels in
epithelial cells (at protein level).
{ECO:0000269|PubMed:15053875}.
-!- SIMILARITY: Belongs to the Nudix hydrolase family. NUDT16
subfamily. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; AY423379; AAR36909.1; -; mRNA.
EMBL; BC079757; AAH79757.1; -; mRNA.
EMBL; BC092340; AAH92340.1; -; mRNA.
EMBL; BC106213; AAI06214.1; -; mRNA.
EMBL; BC124911; AAI24912.1; -; mRNA.
EMBL; BC141719; AAI41720.1; -; mRNA.
RefSeq; NP_001084713.1; NM_001091244.1.
UniGene; Xl.46732; -.
PDB; 1U20; X-ray; 2.10 A; A/B=1-212.
PDB; 2A8P; X-ray; 2.70 A; A/B=1-212.
PDB; 2A8Q; X-ray; 2.60 A; A/B=1-212.
PDB; 2A8R; X-ray; 2.45 A; A/B=1-212.
PDB; 2A8S; X-ray; 2.45 A; A/B=1-212.
PDB; 2A8T; X-ray; 2.10 A; A/B=1-212.
PDBsum; 1U20; -.
PDBsum; 2A8P; -.
PDBsum; 2A8Q; -.
PDBsum; 2A8R; -.
PDBsum; 2A8S; -.
PDBsum; 2A8T; -.
ProteinModelPortal; Q6TEC1; -.
SMR; Q6TEC1; -.
DIP; DIP-29033N; -.
MaxQB; Q6TEC1; -.
GeneID; 414677; -.
KEGG; xla:414677; -.
CTD; 414677; -.
Xenbase; XB-GENE-6252278; nudt16.
HOVERGEN; HBG067297; -.
KO; K16855; -.
BRENDA; 3.6.1.62; 6725.
EvolutionaryTrace; Q6TEC1; -.
GO; GO:0005737; C:cytoplasm; ISS:UniProtKB.
GO; GO:0005730; C:nucleolus; IDA:UniProtKB.
GO; GO:0005654; C:nucleoplasm; IEA:UniProtKB-SubCell.
GO; GO:0005634; C:nucleus; IDA:UniProtKB.
GO; GO:0050897; F:cobalt ion binding; IDA:UniProtKB.
GO; GO:0035870; F:dITP diphosphatase activity; ISS:UniProtKB.
GO; GO:0005525; F:GTP binding; ISS:UniProtKB.
GO; GO:1901641; F:ITP binding; ISS:UniProtKB.
GO; GO:0050072; F:m7G(5')pppN diphosphatase activity; IDA:UniProtKB.
GO; GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
GO; GO:0030145; F:manganese ion binding; IDA:UniProtKB.
GO; GO:0008235; F:metalloexopeptidase activity; ISS:UniProtKB.
GO; GO:0003729; F:mRNA binding; ISS:UniProtKB.
GO; GO:0098519; F:nucleotide phosphatase activity, acting on free nucleotides; ISS:UniProtKB.
GO; GO:0042803; F:protein homodimerization activity; IDA:UniProtKB.
GO; GO:0030515; F:snoRNA binding; IDA:UniProtKB.
GO; GO:1901640; F:XTP binding; ISS:UniProtKB.
GO; GO:0006382; P:adenosine to inosine editing; ISS:UniProtKB.
GO; GO:0035863; P:dITP catabolic process; ISS:UniProtKB.
GO; GO:0046709; P:IDP catabolic process; ISS:UniProtKB.
GO; GO:0006402; P:mRNA catabolic process; ISS:UniProtKB.
GO; GO:2000233; P:negative regulation of rRNA processing; IDA:UniProtKB.
GO; GO:0090068; P:positive regulation of cell cycle process; ISS:UniProtKB.
GO; GO:0008284; P:positive regulation of cell proliferation; ISS:UniProtKB.
GO; GO:2000781; P:positive regulation of double-strand break repair; ISS:UniProtKB.
GO; GO:0016077; P:snoRNA catabolic process; IDA:UniProtKB.
GO; GO:1901639; P:XDP catabolic process; ISS:UniProtKB.
InterPro; IPR015797; NUDIX_hydrolase-like_dom_sf.
InterPro; IPR000086; NUDIX_hydrolase_dom.
Pfam; PF00293; NUDIX; 1.
SUPFAM; SSF55811; SSF55811; 1.
PROSITE; PS51462; NUDIX; 1.
1: Evidence at protein level;
3D-structure; Cytoplasm; Direct protein sequencing; Hydrolase;
Magnesium; Manganese; Metal-binding; Nucleotide metabolism;
Nucleotide-binding; Nucleus; RNA-binding.
CHAIN 1 212 U8 snoRNA-decapping enzyme.
/FTId=PRO_0000344987.
DOMAIN 39 187 Nudix hydrolase. {ECO:0000255|PROSITE-
ProRule:PRU00794}.
MOTIF 74 95 Nudix box.
METAL 72 72 Magnesium or manganese 1; via carbonyl
oxygen. {ECO:0000269|PubMed:16472752}.
METAL 89 89 Magnesium or manganese 2.
{ECO:0000269|PubMed:16472752}.
METAL 89 89 Magnesium or manganese 3.
{ECO:0000269|PubMed:16472752}.
METAL 93 93 Magnesium or manganese 1.
{ECO:0000269|PubMed:16472752}.
METAL 93 93 Magnesium or manganese 3.
{ECO:0000269|PubMed:16472752}.
METAL 150 150 Magnesium or manganese 3.
{ECO:0000269|PubMed:16472752}.
METAL 150 150 Magnesium or manganese 4.
{ECO:0000269|PubMed:16472752}.
BINDING 37 37 Substrate. {ECO:0000269|PubMed:16472752}.
BINDING 63 63 Substrate. {ECO:0000269|PubMed:16472752}.
BINDING 70 70 Substrate; via amide nitrogen.
{ECO:0000250|UniProtKB:Q96DE0}.
BINDING 180 180 Substrate. {ECO:0000269|PubMed:16472752}.
BINDING 184 184 Substrate. {ECO:0000269|PubMed:16472752}.
MUTAGEN 88 88 R->L: Loss of activity; no effect on RNA-
binding.
MUTAGEN 89 89 E->Q: Loss of activity; no effect on RNA-
binding. {ECO:0000269|PubMed:17567574}.
MUTAGEN 92 93 EE->KK: Strongly reduced activity; no
effect on RNA-binding.
{ECO:0000269|PubMed:15053875}.
MUTAGEN 92 92 E->Q: Reduced activity; no effect on RNA-
binding.
MUTAGEN 93 93 E->Q: Strongly reduced activity; no
effect on RNA-binding.
MUTAGEN 150 150 E->Q: Loss of activity; no effect on RNA-
binding. {ECO:0000269|PubMed:17567574}.
STRAND 18 20 {ECO:0000244|PDB:1U20}.
HELIX 23 27 {ECO:0000244|PDB:1U20}.
STRAND 33 43 {ECO:0000244|PDB:1U20}.
TURN 49 51 {ECO:0000244|PDB:1U20}.
STRAND 56 63 {ECO:0000244|PDB:1U20}.
STRAND 71 75 {ECO:0000244|PDB:1U20}.
TURN 77 79 {ECO:0000244|PDB:1U20}.
HELIX 82 94 {ECO:0000244|PDB:1U20}.
HELIX 96 100 {ECO:0000244|PDB:1U20}.
HELIX 105 107 {ECO:0000244|PDB:1U20}.
STRAND 108 114 {ECO:0000244|PDB:1U20}.
STRAND 116 118 {ECO:0000244|PDB:2A8T}.
STRAND 120 128 {ECO:0000244|PDB:1U20}.
HELIX 131 141 {ECO:0000244|PDB:1U20}.
TURN 148 150 {ECO:0000244|PDB:1U20}.
STRAND 151 156 {ECO:0000244|PDB:1U20}.
HELIX 169 172 {ECO:0000244|PDB:1U20}.
HELIX 181 191 {ECO:0000244|PDB:1U20}.
HELIX 197 208 {ECO:0000244|PDB:1U20}.
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


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