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DUS2 dihydrouridine synthase 2 [ Homo sapiens (human) ]

Gene ID: 54920, updated on 2-Nov-2024

Summary

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Official Symbol
DUS2provided by HGNC
Official Full Name
dihydrouridine synthase 2provided by HGNC
Primary source
HGNC:HGNC:26014
See related
Ensembl:ENSG00000167264 MIM:609707; AllianceGenome:HGNC:26014
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SMM1; DUS2L; URLC8
Summary
This gene encodes a cytoplasmic protein that catalyzes the conversion of uridine residues to dihydrouridine in the D-loop of tRNA. The resulting modified bases confer enhanced regional flexibility to tRNA. The encoded protein may increase the rate of translation by inhibiting an interferon-induced protein kinase. This gene has been implicated in pulmonary carcinogenesis. Alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Nov 2012]
Expression
Broad expression in testis (RPKM 12.7), lymph node (RPKM 5.7) and 24 other tissues See more
Orthologs
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Genomic context

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See DUS2 in Genome Data Viewer
Location:
16q22.1
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (68023284..68079320)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (73819064..73875073)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (68057187..68113223)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:68055836-68056586 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:68056587-68057337 Neighboring gene RNA, U6 small nuclear 359, pseudogene Neighboring gene DEAD-box helicase 28 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:68078446-68078635 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11003 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11004 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11005 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7638 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7639 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11006 Neighboring gene Sharpr-MPRA regulatory region 7518 Neighboring gene nuclear factor of activated T cells 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7640 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:68197467-68198334 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68221558-68222058 Neighboring gene small nucleolar RNA SNORA48 Neighboring gene ribosomal protein S12 pseudogene 27

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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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Related articles in PubMed

  1. Characterization of gene expression regulated by American ginseng and ginsenoside Rg3 in human colorectal cancer cells. Luo X, et al. Int J Oncol, 2008 May. PMID 18425323, Free PMC Article
  2. Crystallization and preliminary X-ray crystallographic analysis of the catalytic domain of human dihydrouridine synthase. Griffiths S, et al. Acta Crystallogr Sect F Struct Biol Cryst Commun, 2012 Mar 1. PMID 22442237, Free PMC Article
  3. From bacterial to human dihydrouridine synthase: automated structure determination. Whelan F, et al. Acta Crystallogr D Biol Crystallogr, 2015 Jul. PMID 26143927, Free PMC Article
  4. Molecular basis for transfer RNA recognition by the double-stranded RNA-binding domain of human dihydrouridine synthase 2. Bou-Nader C, et al. Nucleic Acids Res, 2019 Apr 8. PMID 30605527, Free PMC Article
  5. Sequence- and Structure-Specific tRNA Dihydrouridylation by hDUS2. Ji J, et al. ACS Cent Sci, 2024 Apr 24. PMID 38680565, Free PMC Article

See all (31) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. we establish that while hDus2 dsRBD retains a conventional dsRNA recognition capability, the presence of an N-terminal extension appended to the canonical domain provides additional residues for binding tRNA in a structure-specific mode of action.
    Title: Molecular basis for transfer RNA recognition by the double-stranded RNA-binding domain of human dihydrouridine synthase 2.
  2. Here, the X-ray crystal structure of a construct of hDus2 encompassing the catalytic and tRNA-recognition domains (residues 1-340) determined at 1.9 A resolution is presented.
    Title: From bacterial to human dihydrouridine synthase: automated structure determination.
  3. This is the first reported case of a tRNA-modifying enzyme (dihydrouridine synthase 2) carrying a dsRNA binding domain used to bind tRNAs.
    Title: An extended dsRBD is required for post-transcriptional modification in human tRNAs.
  4. crystals belonged to space group P2(1) and contained a single molecule of HsDus2L in the asymmetric unit
    Title: Crystallization and preliminary X-ray crystallographic analysis of the catalytic domain of human dihydrouridine synthase.
  5. Observational study of gene-disease association. (HuGE Navigator)
    Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
  6. hDUS2 interacts with protein kinase PKR through its dsRNA binding/dimerization domain and inhibits its kinase activity.
    Title: Interaction of human tRNA-dihydrouridine synthase-2 with interferon-induced protein kinase PKR.
Submit: New GeneRIF Correction

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)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Potential readthrough

Included gene: NFATC3

Homology

Clone Names

  • FLJ20399

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables FMN binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables NADPH binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables double-stranded RNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables flavin adenine dinucleotide binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein kinase inhibitor activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables tRNA binding IEA
Inferred from Electronic Annotation
more info
  
enables tRNA dihydrouridine synthase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables tRNA dihydrouridine synthase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables tRNA-dihydrouridine20 synthase activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in antiviral innate immune response IPI
Inferred from Physical Interaction
more info
 PubMed 
involved_in tRNA dihydrouridine synthesis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in tRNA dihydrouridine synthesis IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
  
located_in mitochondrion HTP PubMed 

General protein information

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Preferred Names
tRNA-dihydrouridine(20) synthase [NAD(P)+]-like
Names
SMM1 homolog
dihydrouridine synthase 2-like, SMM1 homolog
tRNA-dihydrouridine(20) synthase (NAD(P)(+))
up-regulated in lung cancer protein 8
NP_001258691.1
NP_001258692.1
NP_060273.1

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)

  1. NM_001271762.2 → NP_001258691.1  tRNA-dihydrouridine(20) synthase [NAD(P)+]-like isoform 1

    See identical proteins and their annotated locations for NP_001258691.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    AC130462, AK000406, BC006527
    Consensus CDS
    CCDS10859.1
    UniProtKB/Swiss-Prot
    A8K3G3, Q4H4D9, Q9NX74
    UniProtKB/TrEMBL
    B4DKP8
    Related
    ENSP00000351769.6, ENST00000358896.10
    Conserved Domains (2) summary
    cd00048
    Location:369 → 433
    DSRM; Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, ...
    cd02801
    Location:13 → 252
    DUS_like_FMN; Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also ...

  2. NM_001271763.2 → NP_001258692.1  tRNA-dihydrouridine(20) synthase [NAD(P)+]-like isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks two alternate exons, resulting in the loss of an in-frame segment in the coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AC130462, AK000406, AK296663, BC006527
    Consensus CDS
    CCDS61970.1
    UniProtKB/TrEMBL
    B4DKP8, E7EUN9
    Related
    ENSP00000409498.1, ENST00000432752.5
    Conserved Domains (3) summary
    COG0042
    Location:10 → 279
    DusA; tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]
    cd00048
    Location:334 → 398
    DSRM; Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, ...
    cd02801
    Location:13 → 217
    DUS_like_FMN; Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also ...

  3. NM_017803.5 → NP_060273.1  tRNA-dihydrouridine(20) synthase [NAD(P)+]-like isoform 1

    See identical proteins and their annotated locations for NP_060273.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC130462, AK000406, BC006527
    Consensus CDS
    CCDS10859.1
    UniProtKB/Swiss-Prot
    A8K3G3, Q4H4D9, Q9NX74
    UniProtKB/TrEMBL
    B4DKP8
    Related
    ENSP00000455229.1, ENST00000565263.6
    Conserved Domains (2) summary
    cd00048
    Location:369 → 433
    DSRM; Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, ...
    cd02801
    Location:13 → 252
    DUS_like_FMN; Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also ...

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    68023284..68079320
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    73819064..73875073
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NX74.1 GenPept UniProtKB/Swiss-Prot:Q9NX74

Gene LinkOut

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