TDP2 tyrosyl-DNA phosphodiesterase 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: TDP2provided by HGNC
Official Full Name: tyrosyl-DNA phosphodiesterase 2provided by HGNC
Primary source: HGNC:HGNC:17768
See related: Ensembl:ENSG00000111802 MIM:605764; AllianceGenome:HGNC:17768
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: EAP2; AD022; EAPII; TTRAP; hTDP2; dJ30M3.3
Summary: This gene encodes a member of a superfamily of divalent cation-dependent phosphodiesterases. The encoded protein associates with CD40, tumor necrosis factor (TNF) receptor-75 and TNF receptor associated factors (TRAFs), and inhibits nuclear factor-kappa-B activation. This protein has sequence and structural similarities with APE1 endonuclease, which is involved in both DNA repair and the activation of transcription factors. [provided by RefSeq, Jul 2008]
Expression: Broad expression in small intestine (RPKM 97.5), colon (RPKM 87.6) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 6p22.3

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (24649979..24666899, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (24520363..24537292, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (24650207..24667127, complement)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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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?

Inactivating TDP2 missense mutation in siblings with congenital abnormalities reminiscent of fanconi anemia.
Title: Inactivating TDP2 missense mutation in siblings with congenital abnormalities reminiscent of fanconi anemia.
A novel non-sense mutation in TDP2 causes spinocerebellar ataxia autosomal recessive 23 accompanied by bilateral upward gaze; report of a case and review of the literature.
Title: A novel non-sense mutation in TDP2 causes spinocerebellar ataxia autosomal recessive 23 accompanied by bilateral upward gaze; report of a case and review of the literature.
DNA and RNA Cleavage Complexes and Repair Pathway for TOP3B RNA- and DNA-Protein Crosslinks.
Title: DNA and RNA Cleavage Complexes and Repair Pathway for TOP3B RNA- and DNA-Protein Crosslinks.
Characterization of a novel loss-of-function variant in TDP2 in two adult patients with spinocerebellar ataxia autosomal recessive 23 (SCAR23).
Title: Characterization of a novel loss-of-function variant in TDP2 in two adult patients with spinocerebellar ataxia autosomal recessive 23 (SCAR23).
Untangling trapped topoisomerases with tyrosyl-DNA phosphodiesterases.
Title: Untangling trapped topoisomerases with tyrosyl-DNA phosphodiesterases.
Tyrosyl-DNA phosphodiesterase 2 (TDP2) repairs topoisomerase 1 DNA-protein crosslinks and 3'-blocking lesions in the absence of tyrosyl-DNA phosphodiesterase 1 (TDP1).
Title: Tyrosyl-DNA phosphodiesterase 2 (TDP2) repairs topoisomerase 1 DNA-protein crosslinks and 3'-blocking lesions in the absence of tyrosyl-DNA phosphodiesterase 1 (TDP1).
Effects of TDP2/VPg Unlinkase Activity on Picornavirus Infections Downstream of Virus Translation.
Title: Effects of TDP2/VPg Unlinkase Activity on Picornavirus Infections Downstream of Virus Translation.
TDP2 suppresses genomic instability induced by androgens in the epithelial cells of prostate glands.
Title: TDP2 suppresses genomic instability induced by androgens in the epithelial cells of prostate glands.
Ubiquitin stimulated reversal of topoisomerase 2 DNA-protein crosslinks by TDP2.
Title: Ubiquitin stimulated reversal of topoisomerase 2 DNA-protein crosslinks by TDP2.
This article reviews TDP1 and TDP2 in the context of mitochondrial DNA repair. [review]
Title: Mammalian Tyrosyl-DNA Phosphodiesterases in the Context of Mitochondrial DNA Repair.

Submit: New GeneRIF Correction See all GeneRIFs (38)

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

Associated conditions

Description	Tests
Spinocerebellar ataxia, autosomal recessive 23 MedGen: C4750914 OMIM: 616949 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
integrase	gag-pol	TTRAP and HIV-1 IN interact in vivo and in vitro. The interaction involves the first 180 amino acids of TTRAP	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

G19612 (e-PCR)
- UniSTS:357

A001T03 (e-PCR)
- UniSTS:358

RH36217 (e-PCR)
- UniSTS:56728

RH93934 (e-PCR)
- UniSTS:92916

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables 5'-tyrosyl-DNA phosphodiesterase activity	IBA Inferred from Biological aspect of Ancestor more info
enables 5'-tyrosyl-DNA phosphodiesterase activity	IDA Inferred from Direct Assay more info	PubMed
enables 5'-tyrosyl-DNA phosphodiesterase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables magnesium ion binding	IDA Inferred from Direct Assay more info	PubMed
enables magnesium ion binding	TAS Traceable Author Statement more info	PubMed
enables manganese ion binding	IDA Inferred from Direct Assay more info	PubMed
enables nuclease activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables single-stranded DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables single-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription corepressor activity	TAS Traceable Author Statement more info	PubMed
enables tyrosyl-RNA phosphodiesterase activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in cell surface receptor signaling pathway	TAS Traceable Author Statement more info	PubMed
involved_in double-strand break repair	IBA Inferred from Biological aspect of Ancestor more info
involved_in double-strand break repair	IDA Inferred from Direct Assay more info	PubMed
involved_in double-strand break repair	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in neuron development	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in PML body	IBA Inferred from Biological aspect of Ancestor more info
located_in PML body	IDA Inferred from Direct Assay more info	PubMed
located_in aggresome	IDA Inferred from Direct Assay more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear body	IDA Inferred from Direct Assay more info
located_in nucleolus	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: tyrosyl-DNA phosphodiesterase 2

Names: 5'-Tyr-DNA phosphodiesterase; 5'-tyrosyl-DNA phosphodiesterase; ETS1-associated protein 2; ETS1-associated protein II; TRAF and TNF receptor-associated protein; VPg unlinkase; epididymis secretory sperm binding protein; tyr-DNA phosphodiesterase 2; tyrosyl-RNA phosphodiesterase

NP_057698.2

EC 3.1.4.-

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.

Genomic

NG_052787.1 RefSeqGene

Range

4989..21909

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_016614.3 → NP_057698.2 tyrosyl-DNA phosphodiesterase 2

See identical proteins and their annotated locations for NP_057698.2

Status: REVIEWED

Source sequence(s)

AL031775

Consensus CDS

CCDS4557.1

UniProtKB/Swiss-Prot

B4DKL8, B4DQ95, O95551, Q2TBE2, Q5JYM0, Q7Z6U5, Q9NUK5, Q9NYY9

UniProtKB/TrEMBL

A0A384MDM5

Related

ENSP00000367440.4, ENST00000378198.9

Conserved Domains (2) summary

cd09080
Location:114 → 358

TDP2; Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains

cd14344
Location:27 → 63

UBA_TYDP2; UBA-like domain found in tyrosyl-DNA phosphodiesterase 2 (TDP2) and similar proteins