NUDT16 nudix hydrolase 16 [Homo sapiens (human)] - Gene

Summary

Official Symbol: NUDT16provided by HGNC
Official Full Name: nudix hydrolase 16provided by HGNC
Primary source: HGNC:HGNC:26442
See related: Ensembl:ENSG00000198585 MIM:617381; AllianceGenome:HGNC:26442
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary: Enables several functions, including RNA binding activity; metal ion binding activity; and pyrophosphatase activity. Involved in RNA metabolic process and positive regulation of cell cycle process. Located in cytoplasm; nucleolus; and nucleoplasm. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in fat (RPKM 14.5), kidney (RPKM 13.4) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3q22.1

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (131381671..131388830)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (134125463..134132622)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (131100515..131107674)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

NUDT16 regulates CtIP PARylation to dictate homologous recombination repair.
Title: NUDT16 regulates CtIP PARylation to dictate homologous recombination repair.
Transcriptomic profile investigations highlight a putative role for NUDT16 in sepsis.
Title: Transcriptomic profile investigations highlight a putative role for NUDT16 in sepsis.
CAG RNAs induce DNA damage and apoptosis by silencing NUDT16 expression in polyglutamine degeneration.
Title: CAG RNAs induce DNA damage and apoptosis by silencing NUDT16 expression in polyglutamine degeneration.
Nudix Hydrolase NUDT16 Regulates 53BP1 Protein by Reversing 53BP1 ADP-Ribosylation.
Title: Nudix Hydrolase NUDT16 Regulates 53BP1 Protein by Reversing 53BP1 ADP-Ribosylation.
Mammalian Nudix proteins cleave nucleotide metabolite caps on RNAs.
Title: Mammalian Nudix proteins cleave nucleotide metabolite caps on RNAs.
hNudt16 hydrolysis of dinucleotide cap analogs and short capped oligonucleotides displayed a broader spectrum specificity than is currently known.
Title: Hydrolytic activity of human Nudt16 enzyme on dinucleotide cap analogs and short capped oligonucleotides.
data suggest the existence in T-ALL of a disrupted RNA decapping pathway, mediated by the DNA methylation-associated loss of NUDT16, which contributes to the natural history of the disease by stabilizing transforming factors, such as is the case of the leukemogenic protein C-MYC
Title: Epigenetic loss of the RNA decapping enzyme NUDT16 mediates C-MYC activation in T-cell acute lymphoblastic leukemia.
This study details structural and regulatory mechanisms explaining how substrates are selected for hydrolysis by human NUDT16.
Title: Structural Basis for the Specificity of Human NUDT16 and Its Regulation by Inosine Monophosphate.
The RNA decapping enzyme NUDT16 selectively degrades 5'-TOP mRNAs during Rift Valley fever virus infection and this decay is triggered in response to mTOR attenuation via the translational repressor 4EBP1/2 axis.
Title: Virus-induced translational arrest through 4EBP1/2-dependent decay of 5'-TOP mRNAs restricts viral infection.
hNUDT16 can also actively cleave the mGDP cap from mRNAs in the presence of Mg(2)(+) or Mn(2)(+).
Title: hNUDT16: a universal decapping enzyme for small nucleolar RNA and cytoplasmic mRNA.

Submit: New GeneRIF Correction See all GeneRIFs (14)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-77345 (e-PCR)
- UniSTS:55642

SHGC-35112 (e-PCR)
- UniSTS:37981

RH102345 (e-PCR)
- UniSTS:96679

SHGC-77347 (e-PCR)
- UniSTS:69812

RH48866 (e-PCR)
- UniSTS:9661

RH79085 (e-PCR)
- UniSTS:73154

RH68746 (e-PCR)
- UniSTS:35274

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity	IDA Inferred from Direct Assay more info	PubMed
enables IDP phosphatase activity	IDA Inferred from Direct Assay more info	PubMed
enables RNA NAD-cap (NMN-forming) hydrolase activity	IEA Inferred from Electronic Annotation more info
enables chloride ion binding	IDA Inferred from Direct Assay more info	PubMed
enables cobalt ion binding	IDA Inferred from Direct Assay more info	PubMed
enables dIDP phosphatase activity	IEA Inferred from Electronic Annotation more info
enables dITP diphosphatase activity	ISS Inferred from Sequence or Structural Similarity more info
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables mRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables magnesium ion binding	IDA Inferred from Direct Assay more info	PubMed
enables manganese ion binding	IDA Inferred from Direct Assay more info	PubMed
enables metalloexopeptidase activity	IDA Inferred from Direct Assay more info	PubMed
enables nucleotide binding	IEA Inferred from Electronic Annotation more info
enables phosphodiesterase decapping endonuclease activity	IBA Inferred from Biological aspect of Ancestor more info
enables phosphodiesterase decapping endonuclease activity	IDA Inferred from Direct Assay more info	PubMed
enables protein homodimerization activity	IDA Inferred from Direct Assay more info	PubMed
enables snoRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables snoRNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in NAD-cap decapping	IDA Inferred from Direct Assay more info	PubMed
involved_in dITP catabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in mRNA catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in mRNA catabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of rRNA processing	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of cell cycle process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in sno(s)RNA catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in sno(s)RNA catabolic process	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	HDA more info	PubMed
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: U8 snoRNA-decapping enzyme

Names: IDP phosphatase; IDPase; U8 snoRNA-binding protein H29K; inosine diphosphate phosphatase; m7GpppN-mRNA hydrolase; nucleoside diphosphate-linked moiety X motif 16; nudix (nucleoside diphosphate linked moiety X)-type motif 16; nudix motif 16; testicular tissue protein Li 129

NP_001165376.1

EC 3.6.1.62

EC 3.6.1.64

NP_001165377.1

EC 3.6.1.62

EC 3.6.1.64

NP_689608.2

EC 3.6.1.62

EC 3.6.1.64

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001171905.2 → NP_001165376.1 U8 snoRNA-decapping enzyme isoform 3

Status: VALIDATED

Description

Transcript Variant: This variant (3) has multiple differences, compared to variant 1. The encoded isoform (3) is shorter at the N-terminus and has a distinct C-terminus, compared to isoform 1.

Source sequence(s)

AC010210, BP199028

Consensus CDS

CCDS54641.1

UniProtKB/TrEMBL

B4DIZ6

Related

ENSP00000440230.1, ENST00000537561.5

Conserved Domains (1) summary

cl00447
Location:7 → 36

Nudix_Hydrolase; Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ ...
NM_001171906.2 → NP_001165377.1 U8 snoRNA-decapping enzyme isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1).

Source sequence(s)

AC010210, AK304650, BP219080

Consensus CDS

CCDS54640.1

UniProtKB/Swiss-Prot

Q96DE0

Related

ENSP00000422375.1, ENST00000502852.1

Conserved Domains (1) summary

cl00447
Location:53 → 82

Nudix_Hydrolase; Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ ...
NM_152395.3 → NP_689608.2 U8 snoRNA-decapping enzyme isoform 2

See identical proteins and their annotated locations for NP_689608.2

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 3' UTR and 3' coding region, compared to variant 1. The encoded isoform (2) is shorter and has a distinct C-terminus compared to isoform 1.

Source sequence(s)

AC010210, CB121755

Consensus CDS

CCDS3070.2

UniProtKB/Swiss-Prot

B4E3B4, E9PED4, F5GYJ1, Q96DE0, Q96N82

UniProtKB/TrEMBL

A0A140VJQ3

Related

ENSP00000429274.2, ENST00000521288.2

Conserved Domains (2) summary

PRK05379
Location:53 → 131

PRK05379; bifunctional nicotinamide-nucleotide adenylyltransferase/Nudix hydroxylase

cl00447
Location:53 → 82

Nudix_Hydrolase; Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ ...

RNA

NR_033268.2 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (4) has multiple differences, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC010210, AK295852, DC343245