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Protein

U8 snoRNA-decapping enzyme

Gene

nudt16

Organism
Xenopus laevis (African clawed frog)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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).By similarity4 Publications

Catalytic activityi

5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] + H2O = N(7)-methylguanosine 5'-diphosphate + 5'-phospho-[mRNA].3 Publications
IDP + H2O = IMP + phosphate.By similarity
dIDP + H2O = dIMP + phosphate.By similarity

Cofactori

Mg2+2 Publications, Mn2+2 Publications, Co2+2 PublicationsNote: 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).2 Publications

pH dependencei

Optimum pH is 8.5-9.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei37 – 371Substrate1 Publication
Binding sitei63 – 631Substrate1 Publication
Binding sitei70 – 701Substrate; via amide nitrogenBy similarity
Metal bindingi72 – 721Magnesium or manganese 1; via carbonyl oxygen1 Publication
Metal bindingi89 – 891Magnesium or manganese 21 Publication
Metal bindingi89 – 891Magnesium or manganese 31 Publication
Metal bindingi93 – 931Magnesium or manganese 11 Publication
Metal bindingi93 – 931Magnesium or manganese 31 Publication
Metal bindingi150 – 1501Magnesium or manganese 31 Publication
Metal bindingi150 – 1501Magnesium or manganese 41 Publication
Binding sitei180 – 1801Substrate1 Publication
Binding sitei184 – 1841Substrate1 Publication

GO - Molecular functioni

  • cobalt ion binding Source: UniProtKB
  • dITP diphosphatase activity Source: UniProtKB
  • GTP binding Source: UniProtKB
  • ITP binding Source: UniProtKB
  • m7G(5')pppN diphosphatase activity Source: UniProtKB
  • magnesium ion binding Source: UniProtKB
  • manganese ion binding Source: UniProtKB
  • metalloexopeptidase activity Source: UniProtKB
  • mRNA binding Source: UniProtKB
  • nucleotide phosphatase activity, acting on free nucleotides Source: UniProtKB
  • protein homodimerization activity Source: UniProtKB
  • snoRNA binding Source: UniProtKB
  • XTP binding Source: UniProtKB

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Nucleotide metabolism

Keywords - Ligandi

Magnesium, Manganese, Metal-binding, Nucleotide-binding, RNA-binding

Enzyme and pathway databases

BRENDAi3.6.1.62. 6725.

Names & Taxonomyi

Protein namesi
Recommended name:
U8 snoRNA-decapping enzyme (EC:3.6.1.623 Publications)
Alternative name(s):
IDP phosphatase (EC:3.6.1.64By similarity)
Short name:
IDPase
Inosine diphosphate phosphatase
Nucleoside diphosphate-linked moiety X motif 16
Short name:
Nudix motif 16
U8 snoRNA-binding protein X29
m7GpppN-mRNA hydrolase
Gene namesi
Name:nudt16
OrganismiXenopus laevis (African clawed frog)
Taxonomic identifieri8355 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiAmphibiaBatrachiaAnuraPipoideaPipidaeXenopodinaeXenopusXenopus

Organism-specific databases

XenbaseiXB-GENE-6252278. nudt16.

Subcellular locationi

  • Nucleus 1 Publication
  • Nucleusnucleolus 1 Publication
  • Nucleusnucleoplasm 1 Publication
  • Cytoplasm By similarity

  • Note: Predominantly localized in nucleolus, and in a minor proportion in distinct foci in the nucleoplasm.1 Publication

GO - Cellular componenti

  • cytoplasm Source: UniProtKB
  • nucleolus Source: UniProtKB
  • nucleoplasm Source: UniProtKB-SubCell
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi88 – 881R → L: Loss of activity; no effect on RNA-binding.
Mutagenesisi89 – 891E → Q: Loss of activity; no effect on RNA-binding. 1 Publication
Mutagenesisi92 – 932EE → KK: Strongly reduced activity; no effect on RNA-binding. 1 Publication
Mutagenesisi92 – 921E → Q: Reduced activity; no effect on RNA-binding.
Mutagenesisi93 – 931E → Q: Strongly reduced activity; no effect on RNA-binding.
Mutagenesisi150 – 1501E → Q: Loss of activity; no effect on RNA-binding. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 212212U8 snoRNA-decapping enzymePRO_0000344987Add
BLAST

Expressioni

Tissue specificityi

Detected in ovary, and at very low levels in epithelial cells (at protein level).1 Publication

Interactioni

Subunit structurei

Homodimer.2 Publications

GO - Molecular functioni

  • protein homodimerization activity Source: UniProtKB

Protein-protein interaction databases

DIPiDIP-29033N.

Structurei

Secondary structure

1
212
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi18 – 203Combined sources
Helixi23 – 275Combined sources
Beta strandi33 – 4311Combined sources
Turni49 – 513Combined sources
Beta strandi56 – 638Combined sources
Beta strandi71 – 755Combined sources
Turni77 – 793Combined sources
Helixi82 – 9413Combined sources
Helixi96 – 1005Combined sources
Helixi105 – 1073Combined sources
Beta strandi108 – 1147Combined sources
Beta strandi116 – 1183Combined sources
Beta strandi120 – 1289Combined sources
Helixi131 – 14111Combined sources
Turni148 – 1503Combined sources
Beta strandi151 – 1566Combined sources
Helixi169 – 1724Combined sources
Helixi181 – 19111Combined sources
Helixi197 – 20812Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1U20X-ray2.10A/B1-212[»]
2A8PX-ray2.70A/B1-212[»]
2A8QX-ray2.60A/B1-212[»]
2A8RX-ray2.45A/B1-212[»]
2A8SX-ray2.45A/B1-212[»]
2A8TX-ray2.10A/B1-212[»]
ProteinModelPortaliQ6TEC1.
SMRiQ6TEC1. Positions 14-209.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ6TEC1.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini39 – 187149Nudix hydrolasePROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi74 – 9522Nudix boxAdd
BLAST

Sequence similaritiesi

Contains 1 nudix hydrolase domain.PROSITE-ProRule annotation

Phylogenomic databases

HOVERGENiHBG067297.
KOiK16855.

Family and domain databases

Gene3Di3.90.79.10. 1 hit.
InterProiIPR000086. NUDIX_hydrolase_dom.
IPR015797. NUDIX_hydrolase_dom-like.
[Graphical view]
PfamiPF00293. NUDIX. 1 hit.
[Graphical view]
SUPFAMiSSF55811. SSF55811. 1 hit.
PROSITEiPS51462. NUDIX. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q6TEC1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAESRSPDRG AKEDKPRPRN ISREESLQLE GYKHACHALL HAPSQAKLFD
60 70 80 90 100
RVPIRRVLLM MMRFDGRLGF PGGFVDTRDI SLEEGLKREL EEELGPALAT
110 120 130 140 150
VEVTEDDYRS SQVREHPQKC VTHFYIKELK LEEIERIEAE AVNAKDHGLE
160 170 180 190 200
VMGLIRVPLY TLRDRVGGLP AFLCNNFIGN SKSQLLYALR SLKLLREDQI
210
QEVLKASHRL QY
Length:212
Mass (Da):24,350
Last modified:July 5, 2004 - v1
Checksum:i6E73DC50B7F49AB1
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY423379 mRNA. Translation: AAR36909.1.
BC079757 mRNA. Translation: AAH79757.1.
BC092340 mRNA. Translation: AAH92340.1.
BC106213 mRNA. Translation: AAI06214.1.
BC124911 mRNA. Translation: AAI24912.1.
BC141719 mRNA. Translation: AAI41720.1.
RefSeqiNP_001084713.1. NM_001091244.1.
UniGeneiXl.46732.

Genome annotation databases

GeneIDi414677.
KEGGixla:414677.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY423379 mRNA. Translation: AAR36909.1.
BC079757 mRNA. Translation: AAH79757.1.
BC092340 mRNA. Translation: AAH92340.1.
BC106213 mRNA. Translation: AAI06214.1.
BC124911 mRNA. Translation: AAI24912.1.
BC141719 mRNA. Translation: AAI41720.1.
RefSeqiNP_001084713.1. NM_001091244.1.
UniGeneiXl.46732.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1U20X-ray2.10A/B1-212[»]
2A8PX-ray2.70A/B1-212[»]
2A8QX-ray2.60A/B1-212[»]
2A8RX-ray2.45A/B1-212[»]
2A8SX-ray2.45A/B1-212[»]
2A8TX-ray2.10A/B1-212[»]
ProteinModelPortaliQ6TEC1.
SMRiQ6TEC1. Positions 14-209.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-29033N.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi414677.
KEGGixla:414677.

Organism-specific databases

CTDi131870.
XenbaseiXB-GENE-6252278. nudt16.

Phylogenomic databases

HOVERGENiHBG067297.
KOiK16855.

Enzyme and pathway databases

BRENDAi3.6.1.62. 6725.

Miscellaneous databases

EvolutionaryTraceiQ6TEC1.

Family and domain databases

Gene3Di3.90.79.10. 1 hit.
InterProiIPR000086. NUDIX_hydrolase_dom.
IPR015797. NUDIX_hydrolase_dom-like.
[Graphical view]
PfamiPF00293. NUDIX. 1 hit.
[Graphical view]
SUPFAMiSSF55811. SSF55811. 1 hit.
PROSITEiPS51462. NUDIX. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Xenopus U8 snoRNA binding protein is a conserved nuclear decapping enzyme."
    Ghosh T., Peterson B., Tomasevic N., Peculis B.A.
    Mol. Cell 13:817-828(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], PARTIAL PROTEIN SEQUENCE, FUNCTION, CATALYTIC ACTIVITY, RNA-BINDING, COFACTOR, SUBCELLULAR LOCATION, MUTAGENESIS OF 92-GLU-GLU-93, TISSUE SPECIFICITY, IDENTIFICATION BY MASS SPECTROMETRY.
    Tissue: Liver and Ovary.
  2. NIH - Xenopus Gene Collection (XGC) project
    Submitted (MAY-2007) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Brain, Eye, Fat body and Testis.
  3. "Identification of a U8 snoRNA-specific binding protein."
    Tomasevic N., Peculis B.
    J. Biol. Chem. 274:35914-35920(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, RNA-BINDING.
  4. "Metal determines efficiency and substrate specificity of the nuclear NUDIX decapping proteins X29 and H29K (Nudt16)."
    Peculis B.A., Reynolds K., Cleland M.
    J. Biol. Chem. 282:24792-24805(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS A DECAPPING ENZYME, BIOPHYSICOCHEMICAL PROPERTIES, CATALYTIC ACTIVITY, COFACTOR SUBUNIT, RNA-BINDING, MUTAGENESIS OF GLU-89 AND GLU-150.
  5. "Evolutionary conservation supports ancient origin for Nudt16, a nuclear-localized, RNA-binding, RNA-decapping enzyme."
    Taylor M.J., Peculis B.A.
    Nucleic Acids Res. 36:6021-6034(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS A DECAPPING ENZYME, CATALYTIC ACTIVITY, SUBUNIT, RNA-BINDING.
  6. "Crystal structures of U8 snoRNA decapping nudix hydrolase, X29, and its metal and cap complexes."
    Scarsdale J.N., Peculis B.A., Wright H.T.
    Structure 14:331-343(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) IN COMPLEXES WITH MANGANESE; GTP AND M7G-NUCLEOTIDES, SUBUNIT.

Entry informationi

Entry nameiNUD16_XENLA
AccessioniPrimary (citable) accession number: Q6TEC1
Secondary accession number(s): Q3KQG8, Q569R2, Q6AX51
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 22, 2008
Last sequence update: July 5, 2004
Last modified: December 9, 2015
This is version 65 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Direct protein sequencing

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.