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40  structures 1250  species 0  interactions 3738  sequences 176  architectures

Family: zf-PARP (PF00645)

Summary: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region

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Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region Provide feedback

Poly(ADP-ribose) polymerase is an important regulatory component of the cellular response to DNA damage. The amino-terminal region of Poly(ADP-ribose) polymerase consists of two PARP-type zinc fingers. This region acts as a DNA nick sensor.

Literature references

  1. de Murcia G, Menissier de Murcia J; , Trends Biochem Sci 1994;19:172-176.: Poly(ADP-ribose) polymerase: a molecular nick-sensor. PUBMED:8016868 EPMC:8016868

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001510

Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [ PUBMED:10529348 , PUBMED:15963892 , PUBMED:15718139 , PUBMED:17210253 , PUBMED:12665246 ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few [ PUBMED:11179890 ]. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.

This entry represents PARP (Poly(ADP) polymerase) type zinc finger domains.

NAD(+) ADP-ribosyltransferase( EC ) [ PUBMED:3118181 , PUBMED:8016868 ] is a eukaryotic enzyme that catalyses the covalent attachment of ADP-ribose units from NAD(+) to various nuclear acceptor proteins. This post-translational modification of nuclear proteins is dependent on DNA. It appears to be involved in the regulation of various important cellular processes such as differentiation, proliferation and tumour transformation as well as in the regulation of the molecular events involved in the recovery of the cell from DNA damage. Structurally, NAD(+) ADP-ribosyltransferase consists of three distinct domains: an N-terminal zinc-dependent DNA-binding domain, a central automodification domain and a C-terminal NAD-binding domain. The DNA-binding region contains a pair of PARP-type zinc finger domains which have been shown to bind DNA in a zinc-dependent manner. The PARP-type zinc finger domains seem to bind specifically to single-stranded DNA and to act as a DNA nick sensor. DNA ligase III [ PUBMED:7760816 ] contains, in its N-terminal section, a single copy of a zinc finger highly similar to those of PARP.

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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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...

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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.

Representative proteomes UniProt
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Representative proteomes UniProt

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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.

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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...


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: Prosite
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 182
Number in full: 3738
Average length of the domain: 81.4 aa
Average identity of full alignment: 33 %
Average coverage of the sequence by the domain: 14.9 %

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 39.3 39.3
Trusted cut-off 39.4 39.3
Noise cut-off 39.2 39.1
Model length: 82
Family (HMM) version: 21
Download: download the raw HMM for this family

Species distribution

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Colour assignments

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


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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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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 zf-PARP domain has been found. There are 40 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
A0A044UHL6 View 3D Structure Click here
A0A096MKE9 View 3D Structure Click here
A0A0D2GQ76 View 3D Structure Click here
A0A0H5S926 View 3D Structure Click here
A0A0K0E108 View 3D Structure Click here
A0A0P0V7Y6 View 3D Structure Click here
A0A0R0EYR1 View 3D Structure Click here
A0A175VYW3 View 3D Structure Click here
A0A1C1CFF5 View 3D Structure Click here
A0A1D6ND74 View 3D Structure Click here
A0A2K6VDT1 View 3D Structure Click here
A0A3P7DEL1 View 3D Structure Click here
A0A3P7DHH2 View 3D Structure Click here
A0A3Q0KLJ1 View 3D Structure Click here
A0A5S6PTT8 View 3D Structure Click here
A4I1B6 View 3D Structure Click here
A4ICK1 View 3D Structure Click here
C1H8S1 View 3D Structure Click here
F1QJL4 View 3D Structure Click here
I1JP21 View 3D Structure Click here
K7LUT0 View 3D Structure Click here
O13706 View 3D Structure Click here
P09874 View 3D Structure Click here
P11103 View 3D Structure Click here
P18493 View 3D Structure Click here
P26446 View 3D Structure Click here
P27008 View 3D Structure Click here
P35875 View 3D Structure Click here
P49916 View 3D Structure Click here
P97386 View 3D Structure Click here
Q21275 View 3D Structure Click here
Q38AV1 View 3D Structure Click here
Q4E4B2 View 3D Structure Click here
Q4E4N3 View 3D Structure Click here
Q54E19 View 3D Structure Click here
Q54X55 View 3D Structure Click here
Q54XI2 View 3D Structure Click here
Q5RHR0 View 3D Structure Click here
Q7EYV7 View 3D Structure Click here
Q84JE8 View 3D Structure Click here