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95  structures 1441  species 0  interactions 3285  sequences 108  architectures

Family: Tyr-DNA_phospho (PF06087)

Summary: Tyrosyl-DNA phosphodiesterase

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Tyrosyl-DNA phosphodiesterase Provide feedback

Covalent intermediates between topoisomerase I and DNA can become dead-end complexes that lead to cell death. Tyrosyl-DNA phosphodiesterase can hydrolyse the bond between topoisomerase I and DNA [1].

Literature references

  1. Pouliot JJ, Yao KC, Robertson CA, Nash HA; , Science 1999;286:552-555.: Yeast gene for a Tyr-DNA phosphodiesterase that repairs topoisomerase I complexes. PUBMED:10521354 EPMC:10521354


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR010347

Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is a DNA repair enzyme that can remove a variety of covalent adducts from DNA through hydrolysis of a 3'-phosphodiester bond, giving rise to DNA with a free 3' phosphate [ PUBMED:12023295 , PUBMED:19505854 ].

Mutations in human TDP1 gene cause spinocerebellar ataxia, autosomal recessive, with axonal neuropathy (SCAN1), which is a clinically and genetically heterogeneous group of cerebellar disorders [ PUBMED:16141202 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan PLD (CL0479), which has the following description:

This superfamily includes proteins that are related to Phospholiase D.

The clan contains the following 11 members:

DNase_II FAM83 MIT_C PLDc PLDc_2 PLDc_3 PP_kinase_C PP_kinase_C_1 RE_NgoFVII Regulator_TrmB Tyr-DNA_phospho

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(111)
Full
(3285)
Representative proteomes UniProt
(5192)
RP15
(610)
RP35
(1489)
RP55
(2496)
RP75
(3360)
Jalview View  View  View  View  View  View  View 
HTML View  View           
PP/heatmap 1 View           

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(111)
Full
(3285)
Representative proteomes UniProt
(5192)
RP15
(610)
RP35
(1489)
RP55
(2496)
RP75
(3360)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(111)
Full
(3285)
Representative proteomes UniProt
(5192)
RP15
(610)
RP35
(1489)
RP55
(2496)
RP75
(3360)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_8155 (release 9.0)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD
Number in seed: 111
Number in full: 3285
Average length of the domain: 341 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 64 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.0 22.0
Trusted cut-off 22.1 22.2
Noise cut-off 21.9 21.9
Model length: 450
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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The tree shows the occurrence of this domain across different species. More...

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Tyr-DNA_phospho domain has been found. There are 95 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A077Z2Q7 View 3D Structure Click here
A0A0D2GQW4 View 3D Structure Click here
A0A0D2H0G1 View 3D Structure Click here
A0A0K0EKK2 View 3D Structure Click here
A0A0N4UDY8 View 3D Structure Click here
A0A0R0IF24 View 3D Structure Click here
A0A0R0K355 View 3D Structure Click here
A0A175VYS8 View 3D Structure Click here
A0A175W768 View 3D Structure Click here
A0A1C1CQR4 View 3D Structure Click here
A0A1C1CZE6 View 3D Structure Click here
A0A1X7YF09 View 3D Structure Click here
A0A2K6W2L3 View 3D Structure Click here
A0A3P7FG15 View 3D Structure Click here
A0A3Q0KVE4 View 3D Structure Click here
A4I9E7 View 3D Structure Click here
C0NXE2 View 3D Structure Click here
C0NZT4 View 3D Structure Click here
C0PDG6 View 3D Structure Click here
C1GXK2 View 3D Structure Click here
C1H6Q9 View 3D Structure Click here
F8W5U2 View 3D Structure Click here
I1JUA1 View 3D Structure Click here
K7KTG1 View 3D Structure Click here
P38319 View 3D Structure Click here
Q0JDH5 View 3D Structure Click here
Q4CRV9 View 3D Structure Click here
Q4DE23 View 3D Structure Click here
Q4G056 View 3D Structure Click here
Q556S0 View 3D Structure Click here
Q55BL9 View 3D Structure Click here
Q586D1 View 3D Structure Click here
Q7XHY3 View 3D Structure Click here
Q84MA4 View 3D Structure Click here
Q8BJ37 View 3D Structure Click here
Q8H1D9 View 3D Structure Click here
Q9NUW8 View 3D Structure Click here
Q9TXV7 View 3D Structure Click here
Q9USG9 View 3D Structure Click here
Q9VQM4 View 3D Structure Click here