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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)DescriptionActionsGraphical viewLength
Binding sitei37Substrate1 Publication1
Binding sitei63Substrate1 Publication1
Binding sitei70Substrate; via amide nitrogenBy similarity1
Metal bindingi72Magnesium or manganese 1; via carbonyl oxygen1 Publication1
Metal bindingi89Magnesium or manganese 21 Publication1
Metal bindingi89Magnesium or manganese 31 Publication1
Metal bindingi93Magnesium or manganese 11 Publication1
Metal bindingi93Magnesium or manganese 31 Publication1
Metal bindingi150Magnesium or manganese 31 Publication1
Metal bindingi150Magnesium or manganese 41 Publication1
Binding sitei180Substrate1 Publication1
Binding sitei184Substrate1 Publication1

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)DescriptionActionsGraphical viewLength
Mutagenesisi88R → L: Loss of activity; no effect on RNA-binding. 1
Mutagenesisi89E → Q: Loss of activity; no effect on RNA-binding. 1 Publication1
Mutagenesisi92 – 93EE → KK: Strongly reduced activity; no effect on RNA-binding. 1 Publication2
Mutagenesisi92E → Q: Reduced activity; no effect on RNA-binding. 1
Mutagenesisi93E → Q: Strongly reduced activity; no effect on RNA-binding. 1
Mutagenesisi150E → Q: Loss of activity; no effect on RNA-binding. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003449871 – 212U8 snoRNA-decapping enzymeAdd BLAST212

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

1212
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi18 – 20Combined sources3
Helixi23 – 27Combined sources5
Beta strandi33 – 43Combined sources11
Turni49 – 51Combined sources3
Beta strandi56 – 63Combined sources8
Beta strandi71 – 75Combined sources5
Turni77 – 79Combined sources3
Helixi82 – 94Combined sources13
Helixi96 – 100Combined sources5
Helixi105 – 107Combined sources3
Beta strandi108 – 114Combined sources7
Beta strandi116 – 118Combined sources3
Beta strandi120 – 128Combined sources9
Helixi131 – 141Combined sources11
Turni148 – 150Combined sources3
Beta strandi151 – 156Combined sources6
Helixi169 – 172Combined sources4
Helixi181 – 191Combined sources11
Helixi197 – 208Combined sources12

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ6TEC1.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini39 – 187Nudix hydrolasePROSITE-ProRule annotationAdd BLAST149

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi74 – 95Nudix boxAdd BLAST22

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
PDB 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.
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...

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: November 2, 2016
This is version 68 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.