Tdp1 tyrosyl-DNA phosphodiesterase 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Tdp1provided by MGI
Official Full Name: tyrosyl-DNA phosphodiesterase 1provided by MGI
Primary source: MGI:MGI:1920036
See related: Ensembl:ENSMUSG00000021177 AllianceGenome:MGI:1920036
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: SCAN1; Gm40556; MLZ-501; 2810481F14Rik; 4921509N21Rik; E430034L06Rik
Summary: Predicted to enable 3'-tyrosyl-DNA phosphodiesterase activity; double-stranded DNA binding activity; and single-stranded DNA binding activity. Acts upstream of or within single strand break repair. Located in nucleus. Is expressed in ovary and testis. Used to study spinocerebellar ataxia type 1 with axonal neuropathy. Human ortholog(s) of this gene implicated in spinocerebellar ataxia type 1 with axonal neuropathy. Orthologous to human TDP1 (tyrosyl-DNA phosphodiesterase 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Broad expression in testis adult (RPKM 14.7), CNS E14 (RPKM 6.9) and 22 other tissues See more
Orthologs: human all
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Genomic context

Location:: 12; 12 E

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	12	NC_000078.7 (99850767..99921482)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	12	NC_000078.6 (99884515..99955223)

Chromosome 12 - NC_000078.7 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: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Promising New Inhibitors of Tyrosyl-DNA Phosphodiesterase I (Tdp 1) Combining 4-Arylcoumarin and Monoterpenoid Moieties as Components of Complex Antitumor Therapy.
Title: Promising New Inhibitors of Tyrosyl-DNA Phosphodiesterase I (Tdp 1) Combining 4-Arylcoumarin and Monoterpenoid Moieties as Components of Complex Antitumor Therapy.
These findings provide evidence for TDP1 as a novel mitochondrial enzyme.
Title: Role of tyrosyl-DNA phosphodiesterase (TDP1) in mitochondria.
The interaction with Lig3alpha is promoted by serine 81 that is located within a putative S/TQ site in the N-terminus domain of TDP1.
Title: TDP1 serine 81 promotes interaction with DNA ligase IIIalpha and facilitates cell survival following DNA damage.
Tdp1(-/-) fibroblasts exhibited deficiencies in processing 3'-phosphotyrosyl single-strand breaks and 3'-phosphoglycolate double-strand breaks, but not 3'-phosphoglycolate single-strand breaks.
Title: In vitro complementation of Tdp1 deficiency indicates a stabilized enzyme-DNA adduct from tyrosyl but not glycolate lesions as a consequence of the SCAN1 mutation.
Data indicate that TDP1 is required for neural homeostasis and reveal a widespread requisite for TDP1 function in response to acutely elevated levels of DNA topoisomerase I (Top1)-associated DNA strand breaks.
Title: TDP1 facilitates chromosomal single-strand break repair in neurons and is neuroprotective in vivo.
This study provides a direct demonstration that Tdp1 repairs Topo I covalent lesions in vivo and suggests that spinocerebellar ataxia with axonal neuropathy (SCAN1) arises from the recessive neomorphic mutation H493R.
Title: Spinocerebellar ataxia with axonal neuropathy: consequence of a Tdp1 recessive neomorphic mutation?

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Gene trapped (3) 1 citation
Endonuclease-mediated (2)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AW493413 (e-PCR)
- UniSTS:180445

AI838772 (e-PCR)
- UniSTS:180447

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables 3'-tyrosyl-DNA phosphodiesterase activity	IBA Inferred from Biological aspect of Ancestor more info
enables 3'-tyrosyl-DNA phosphodiesterase activity	ISO Inferred from Sequence Orthology more info
enables double-stranded DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables double-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables exonuclease activity	IEA Inferred from Electronic Annotation more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables nuclease activity	IEA Inferred from Electronic Annotation more info
enables phosphoric diester hydrolase activity	IEA Inferred from Electronic Annotation more info
enables single-stranded DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables single-stranded DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA damage response	IEA Inferred from Electronic Annotation more info
involved_in DNA repair	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within DNA repair	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in DNA repair	ISO Inferred from Sequence Orthology more info
involved_in double-strand break repair	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within single strand break repair	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in single strand break repair	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
NOT located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in intracellular membrane-bounded organelle	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: tyrosyl-DNA phosphodiesterase 1

Names: protein expressed in male leptotene and zygotene spermatocytes 501; tyr-DNA phosphodiesterase 1; tyrosyl-DNA phodphodiesterase 1

NP_001366001.1

EC 3.1.4.-

NP_082630.2

EC 3.1.4.-

XP_030102366.1

EC 3.1.4.-

XP_030102367.1

EC 3.1.4.-

XP_036013044.1

EC 3.1.4.-

XP_036013045.1

EC 3.1.4.-

XP_036013046.1

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.

mRNA and Protein(s)

NM_001379072.1 → NP_001366001.1 tyrosyl-DNA phosphodiesterase 1 isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AC160931, CT010436

UniProtKB/Swiss-Prot

Q8BJ37, Q8VE39

Conserved Domains (1) summary

pfam06087
Location:167 → 548

Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase
NM_028354.5 → NP_082630.2 tyrosyl-DNA phosphodiesterase 1 isoform 2

See identical proteins and their annotated locations for NP_082630.2

Status: VALIDATED

Source sequence(s)

AC160931, CT010436

Consensus CDS

CCDS26105.2

UniProtKB/Swiss-Prot

Q8BJ37, Q8VE39

UniProtKB/TrEMBL

B8JJC1

Related

ENSMUSP00000118656.2, ENSMUST00000153627.8

Conserved Domains (1) summary

pfam06087
Location:167 → 580

Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000078.7 Reference GRCm39 C57BL/6J

Range

99850767..99921482

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036157151.1 → XP_036013044.1 tyrosyl-DNA phosphodiesterase 1 isoform X3

UniProtKB/Swiss-Prot

Q8BJ37, Q8VE39

Conserved Domains (1) summary

pfam06087
Location:171 → 584

Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase
XM_030246506.2 → XP_030102366.1 tyrosyl-DNA phosphodiesterase 1 isoform X1

UniProtKB/Swiss-Prot

Q8BJ37, Q8VE39

Conserved Domains (1) summary

pfam06087
Location:171 → 554

Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase
XM_036157152.1 → XP_036013045.1 tyrosyl-DNA phosphodiesterase 1 isoform X4

UniProtKB/Swiss-Prot

Q8BJ37, Q8VE39

UniProtKB/TrEMBL

B8JJC1

Conserved Domains (1) summary

pfam06087
Location:167 → 580

Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase
XM_030246507.2 → XP_030102367.1 tyrosyl-DNA phosphodiesterase 1 isoform X2

UniProtKB/Swiss-Prot

Q8BJ37, Q8VE39

Conserved Domains (1) summary

pfam06087
Location:199 → 612

Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase
XM_036157153.1 → XP_036013046.1 tyrosyl-DNA phosphodiesterase 1 isoform X5

UniProtKB/Swiss-Prot

Q8BJ37, Q8VE39

Conserved Domains (1) summary

pfam06087
Location:167 → 548

Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase