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162  structures 1062  species 0  interactions 2866  sequences 238  architectures

Family: PARP_reg (PF02877)

Summary: Poly(ADP-ribose) polymerase, regulatory domain

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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.

Poly(ADP-ribose) polymerase, regulatory domain Provide feedback

Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active [2].

Literature references

  1. Ruf A, Mennissier de Murcia J, de Murcia G, Schulz GE; , Proc Natl Acad Sci U S A 1996;93:7481-7485.: Structure of the catalytic fragment of poly(AD-ribose) polymerase from chicken. PUBMED:8755499 EPMC:8755499

  2. Simonin F, Hofferer L, Panzeter PL, Muller S, de Murcia G, Althaus FR; , J Biol Chem 1993;268:13454-13461.: The carboxyl-terminal domain of human poly(ADP-ribose) polymerase. Overproduction in Escherichia coli, large scale purification, and characterization. PUBMED:8390463 EPMC:8390463

  3. Ruf A, de Murcia G, Schulz GE; , Biochemistry 1998;37:3893-3900.: Inhibitor and NAD+ binding to poly(ADP-ribose) polymerase as derived from crystal structures and homology modeling. PUBMED:9521710 EPMC:9521710


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004102

Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The regulatory domain of the polymerase is almost always associated with the C-terminal catalytic domain (see INTERPRO ).

This domain consists of a duplication of two helix-loop-helix structural repeats [ PUBMED:9521710 ].

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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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
(162)
Full
(2866)
Representative proteomes UniProt
(5199)
RP15
(647)
RP35
(1391)
RP55
(2394)
RP75
(3098)
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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
(162)
Full
(2866)
Representative proteomes UniProt
(5199)
RP15
(647)
RP35
(1391)
RP55
(2394)
RP75
(3098)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(162)
Full
(2866)
Representative proteomes UniProt
(5199)
RP15
(647)
RP35
(1391)
RP55
(2394)
RP75
(3098)
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: Bateman A
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Griffiths-Jones SR
Number in seed: 162
Number in full: 2866
Average length of the domain: 130.90 aa
Average identity of full alignment: 32 %
Average coverage of the sequence by the domain: 17.01 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.8 26.8
Trusted cut-off 26.9 26.8
Noise cut-off 26.5 26.7
Model length: 136
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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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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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 PARP_reg domain has been found. There are 162 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
A0A0R0EYR1 View 3D Structure Click here
A0A0R0HN12 View 3D Structure Click here
A0A1D6FI97 View 3D Structure Click here
A0A1D6H9V4 View 3D Structure Click here
F1QLV3 View 3D Structure Click here
F1QSK1 View 3D Structure Click here
G3V749 View 3D Structure Click here
I1JP21 View 3D Structure Click here
K7K5Y1 View 3D Structure Click here
K7LQ69 View 3D Structure Click here
K7US99 View 3D Structure Click here
O50017 View 3D Structure Click here
O88554 View 3D Structure Click here
P09874 View 3D Structure Click here
P11103 View 3D Structure Click here
P27008 View 3D Structure Click here
P35875 View 3D Structure Click here
Q09525 View 3D Structure Click here
Q0E0Q3 View 3D Structure Click here
Q0JMY1 View 3D Structure Click here
Q11207 View 3D Structure Click here
Q3ULW8 View 3D Structure Click here
Q4D1I2 View 3D Structure Click here
Q4DB33 View 3D Structure Click here
Q54E42 View 3D Structure Click here
Q54HY5 View 3D Structure Click here
Q54X55 View 3D Structure Click here
Q54XI2 View 3D Structure Click here
Q55GU8 View 3D Structure Click here
Q5RHR0 View 3D Structure Click here
Q5U2U3 View 3D Structure Click here
Q5Z8Q9 View 3D Structure Click here
Q7EYV7 View 3D Structure Click here
Q8I7C6 View 3D Structure Click here
Q9FK91 View 3D Structure Click here
Q9N4H4 View 3D Structure Click here
Q9SWB4 View 3D Structure Click here
Q9TXQ1 View 3D Structure Click here
Q9UGN5 View 3D Structure Click here
Q9Y6F1 View 3D Structure Click here
Q9ZP54 View 3D Structure Click here
Q9ZSV1 View 3D Structure Click here