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Protein

U8 snoRNA-decapping enzyme

Gene

NUDT16

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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. 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 (PubMed:20385596, PubMed:26121039). The order of activity with different substrates is IDP > dIDP >> GDP = dGDP > XDP = ITP = dITP (PubMed:20385596). 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 (PubMed:20385596).7 Publications

Catalytic activityi

5'-(N7-methylguanosine 5'-triphospho)-[mRNA] + H2O = N7-methylguanosine 5'-diphosphate + 5'-phospho-[mRNA].5 Publications
IDP + H2O = IMP + phosphate.2 Publications
dIDP + H2O = dIMP + phosphate.2 Publications

Cofactori

Mg2+3 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

Enzyme regulationi

The phosphatase activity is inhibited by the product IMP.1 Publication

Kineticsi

kcat is 0.931 sec(-1) with IDP. kcat is 0.966 sec(-1) with dIDP. kcat is 0.518 sec(-1) with GDP. kcat is 0.492 sec(-1) with dGDP. kcat is 2.6 sec(-1) with XDP. kcat is 3.06 sec(-1) with ITP. kcat is 3.2 sec(-1) with dITP. The catalytic efficiency for IDP is at least 1.3-fold higher than for dIDP, 9.6-fold higher than for GDP and dGDP, 100-fold higher than for XDP, ITP and dITP.1 Publication
  1. KM=0.062 µM for IDP (at 37 degrees Celsius)1 Publication
  2. KM=0.088 µM for dIDP (at 37 degrees Celsius)1 Publication
  3. KM=0.330 µM for GDP (at 37 degrees Celsius)1 Publication
  4. KM=0.319 mM for dGDP (at 37 degrees Celsius)1 Publication
  5. KM=15.7 mM for XDP (at 37 degrees Celsius)1 Publication
  6. KM=22.1 mM for ITP (at 37 degrees Celsius)1 Publication
  7. KM=24.1 mM for dITP (at 37 degrees Celsius)1 Publication

    pH dependencei

    Gradually increased from pH 6.5 to 8.5 in its IDP hydrolyzing activity.1 Publication

    Temperature dependencei

    Exhibited a temperature-dependent increase in its IDP hydrolyzing activity up to 60 degrees Celsius.1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei24Substrate1 Publication1
    Binding sitei50Substrate1 Publication1
    Binding sitei57Substrate; via amide nitrogen1 Publication1
    Metal bindingi59Magnesium or manganese 1; via carbonyl oxygen1 Publication1
    Metal bindingi76Magnesium or manganese 21 Publication1
    Metal bindingi76Magnesium or manganese 3By similarity1
    Metal bindingi80Magnesium or manganese 11 Publication1
    Metal bindingi80Magnesium or manganese 3By similarity1
    Metal bindingi136Magnesium or manganese 3By similarity1
    Metal bindingi136Magnesium or manganese 4By similarity1
    Binding sitei170Substrate1 Publication1

    GO - Molecular functioni

    • cobalt ion binding Source: UniProtKB
    • dIDP diphosphatase activity Source: Reactome
    • dITP diphosphatase activity Source: UniProtKB
    • GTP binding Source: UniProtKB
    • identical protein binding Source: IntAct
    • IDP phosphatase activity Source: Reactome
    • 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

    • adenosine to inosine editing Source: UniProtKB
    • dITP catabolic process Source: UniProtKB
    • IDP catabolic process Source: UniProtKB
    • mRNA catabolic process Source: UniProtKB
    • negative regulation of rRNA processing Source: UniProtKB
    • nucleobase-containing small molecule catabolic process Source: Reactome
    • positive regulation of cell cycle process Source: UniProtKB
    • positive regulation of cell proliferation Source: UniProtKB
    • positive regulation of double-strand break repair Source: UniProtKB
    • snoRNA catabolic process Source: UniProtKB
    • XDP catabolic process Source: UniProtKB

    Keywordsi

    Molecular functionHydrolase, RNA-binding
    Biological processNucleotide metabolism
    LigandMagnesium, Manganese, Metal-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-17869
    BRENDAi3.6.1.62 2681
    3.6.1.64 2681
    ReactomeiR-HSA-2393930 Phosphate bond hydrolysis by NUDT proteins

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    U8 snoRNA-decapping enzyme (EC:3.6.1.625 Publications)
    Alternative name(s):
    IDP phosphatase (EC:3.6.1.642 Publications)
    Short name:
    IDPase
    Inosine diphosphate phosphatase
    Nucleoside diphosphate-linked moiety X motif 16
    Short name:
    Nudix motif 16
    Nudix hydrolase 16
    U8 snoRNA-binding protein H29K1 Publication
    m7GpppN-mRNA hydrolase
    Gene namesi
    Name:NUDT16
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    Proteomesi
    • UP000005640 Componenti: Chromosome 3

    Organism-specific databases

    EuPathDBiHostDB:ENSG00000198585.11
    HGNCiHGNC:26442 NUDT16
    MIMi617381 gene
    neXtProtiNX_Q96DE0

    Subcellular locationi

    Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

    Keywords - Cellular componenti

    Cytoplasm, Nucleus

    Pathology & Biotechi

    Organism-specific databases

    DisGeNETi131870
    OpenTargetsiENSG00000198585
    PharmGKBiPA134955224

    Polymorphism and mutation databases

    BioMutaiNUDT16
    DMDMi68565926

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00000571171 – 195U8 snoRNA-decapping enzymeAdd BLAST195

    Proteomic databases

    EPDiQ96DE0
    MaxQBiQ96DE0
    PaxDbiQ96DE0
    PeptideAtlasiQ96DE0
    PRIDEiQ96DE0
    ProteomicsDBi76283
    TopDownProteomicsiQ96DE0-1 [Q96DE0-1]

    PTM databases

    iPTMnetiQ96DE0
    PhosphoSitePlusiQ96DE0

    Expressioni

    Tissue specificityi

    Expressed strongly in lung, kidney, adrenal gland, testis, heart and brain.1 Publication

    Gene expression databases

    BgeeiENSG00000198585
    CleanExiHS_NUDT16
    GenevisibleiQ96DE0 HS

    Organism-specific databases

    HPAiHPA060452
    HPA062492

    Interactioni

    Subunit structurei

    Homodimer.3 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    itself2EBI-5464685,EBI-5464685

    GO - Molecular functioni

    • identical protein binding Source: IntAct
    • protein homodimerization activity Source: UniProtKB

    Protein-protein interaction databases

    BioGridi126295, 13 interactors
    IntActiQ96DE0, 1 interactor
    MINTiQ96DE0
    STRINGi9606.ENSP00000422375

    Structurei

    Secondary structure

    1195
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi5 – 7Combined sources3
    Helixi9 – 13Combined sources5
    Beta strandi20 – 35Combined sources16
    Turni36 – 38Combined sources3
    Beta strandi39 – 50Combined sources12
    Beta strandi58 – 61Combined sources4
    Turni64 – 66Combined sources3
    Helixi69 – 81Combined sources13
    Helixi83 – 87Combined sources5
    Helixi92 – 94Combined sources3
    Beta strandi95 – 100Combined sources6
    Beta strandi102 – 114Combined sources13
    Helixi117 – 126Combined sources10
    Helixi127 – 129Combined sources3
    Turni134 – 136Combined sources3
    Beta strandi137 – 142Combined sources6
    Helixi155 – 158Combined sources4
    Helixi167 – 177Combined sources11
    Turni178 – 181Combined sources4

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2XSQX-ray1.72A1-195[»]
    3COUX-ray1.80A1-195[»]
    3MGMX-ray1.80A/B1-195[»]
    ProteinModelPortaliQ96DE0
    SMRiQ96DE0
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ96DE0

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini18 – 173Nudix hydrolasePROSITE-ProRule annotationAdd BLAST156

    Motif

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Motifi61 – 82Nudix boxAdd BLAST22

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG410IYGP Eukaryota
    ENOG4111QA1 LUCA
    GeneTreeiENSGT00390000016224
    HOGENOMiHOG000007083
    HOVERGENiHBG067297
    InParanoidiQ96DE0
    KOiK16855
    OMAiFYAKCLT
    OrthoDBiEOG091G0XY4
    PhylomeDBiQ96DE0

    Family and domain databases

    InterProiView protein in InterPro
    IPR015797 NUDIX_hydrolase-like_dom_sf
    IPR000086 NUDIX_hydrolase_dom
    PfamiView protein in Pfam
    PF00293 NUDIX, 1 hit
    SUPFAMiSSF55811 SSF55811, 1 hit
    PROSITEiView protein in PROSITE
    PS51462 NUDIX, 1 hit

    Sequences (4)i

    Sequence statusi: Complete.

    This entry describes 4 isoformsi produced by alternative splicing. AlignAdd to basket

    Isoform 1 (identifier: Q96DE0-1) [UniParc]FASTAAdd to basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

            10         20         30         40         50
    MAGARRLELG EALALGSGWR HACHALLYAP DPGMLFGRIP LRYAILMQMR
    60 70 80 90 100
    FDGRLGFPGG FVDTQDRSLE DGLNRELREE LGEAAAAFRV ERTDYRSSHV
    110 120 130 140 150
    GSGPRVVAHF YAKRLTLEEL LAVEAGATRA KDHGLEVLGL VRVPLYTLRD
    160 170 180 190
    GVGGLPTFLE NSFIGSAREQ LLEALQDLGL LQSGSISGLK IPAHH
    Length:195
    Mass (Da):21,273
    Last modified:July 5, 2005 - v2
    Checksum:i4AC7EA679D1D7468
    GO
    Isoform 2 (identifier: Q96DE0-2) [UniParc]FASTAAdd to basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-33: Missing.
         138-195: LGLVRVPLYT...ISGLKIPAHH → GPAWDSVPFP...MSLCCSLLTV

    Note: No experimental confirmation available.
    Show »
    Length:194
    Mass (Da):21,816
    Checksum:iF41E209A5248D017
    GO
    Isoform 3 (identifier: Q96DE0-3) [UniParc]FASTAAdd to basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-46: Missing.
         174-195: ALQDLGLLQSGSISGLKIPAHH → AALHGPMKTEMRTLVLGREGRTWECFLIGSER

    Note: No experimental confirmation available.Curated
    Show »
    Length:159
    Mass (Da):17,676
    Checksum:iA73EF509993E7BB5
    GO
    Isoform 4 (identifier: Q96DE0-4) [UniParc]FASTAAdd to basket

    The sequence of this isoform differs from the canonical sequence as follows:
         138-195: LGLVRVPLYT...ISGLKIPAHH → GPAWDSVPFP...MSLCCSLLTV

    Show »
    Length:227
    Mass (Da):25,259
    Checksum:iFCD1CBE3CCC3F086
    GO

    Sequence cautioni

    The sequence BAB71024 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti22A → V in AAH31215 (PubMed:15489334).Curated1
    Isoform 3 (identifier: Q96DE0-3)
    Sequence conflicti128Missing in BP199028 (PubMed:16344560).Curated1

    Alternative sequence

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Alternative sequenceiVSP_0454491 – 46Missing in isoform 3. 1 PublicationAdd BLAST46
    Alternative sequenceiVSP_0454501 – 33Missing in isoform 2. 1 PublicationAdd BLAST33
    Alternative sequenceiVSP_045451138 – 195LGLVR…IPAHH → GPAWDSVPFPISSSPKAFSP PRKHPWRKVFAPLTLPSPQL SWWSWDRDHLYSELVLPTWA FCKGLSHPLPGEILSRTHSS MSLCCSLLTV in isoform 2 and isoform 4. 1 PublicationAdd BLAST58
    Alternative sequenceiVSP_045452174 – 195ALQDL…IPAHH → AALHGPMKTEMRTLVLGREG RTWECFLIGSER in isoform 3. 1 PublicationAdd BLAST22

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AK055827 mRNA Translation: BAB71024.1 Different initiation.
    AK304650 mRNA Translation: BAG65426.1
    BP199028 mRNA No translation available.
    AC010210 Genomic DNA No translation available.
    BC009546 mRNA Translation: AAH09546.1
    BC031215 mRNA Translation: AAH31215.2
    CCDSiCCDS3070.2 [Q96DE0-1]
    CCDS54640.1 [Q96DE0-4]
    CCDS54641.1 [Q96DE0-3]
    RefSeqiNP_001165376.1, NM_001171905.1 [Q96DE0-3]
    NP_001165377.1, NM_001171906.1 [Q96DE0-4]
    NP_689608.2, NM_152395.2 [Q96DE0-1]
    UniGeneiHs.282050

    Genome annotation databases

    EnsembliENST00000502852; ENSP00000422375; ENSG00000198585 [Q96DE0-4]
    ENST00000521288; ENSP00000429274; ENSG00000198585 [Q96DE0-1]
    ENST00000537561; ENSP00000440230; ENSG00000198585 [Q96DE0-3]
    GeneIDi131870
    KEGGihsa:131870
    UCSCiuc003eog.3 human [Q96DE0-1]

    Keywords - Coding sequence diversityi

    Alternative splicing

    Similar proteinsi

    Entry informationi

    Entry nameiNUD16_HUMAN
    AccessioniPrimary (citable) accession number: Q96DE0
    Secondary accession number(s): B4E3B4
    , E9PED4, F5GYJ1, Q96N82
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 5, 2005
    Last sequence update: July 5, 2005
    Last modified: June 20, 2018
    This is version 136 of the entry and version 2 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program
    DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Human chromosome 3
      Human chromosome 3: entries, gene names and cross-references to MIM
    2. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families

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