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22  structures 5685  species 0  interactions 13497  sequences 65  architectures

Family: Pirin (PF02678)

Summary: Pirin

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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.

Pirin Provide feedback

This family consists of Pirin proteins from both eukaryotes and prokaryotes. The function of Pirin is unknown but the gene coding for this protein is known to be expressed in all tissues in the human body although it is expressed most strongly in the liver and heart. Pirin is known to be a nuclear protein, exclusively localised within the nucleoplasma and predominantly concentrated within dot-like subnuclear structures [1]. A tomato homologue of human Pirin has been found to be induced during programmed cell death [2]. Human Pirin interacts with Bcl-3 and NFI [3] and hence is probably involved in the regulation of DNA transcription and replication. It appears to be an Fe(II)-containing member of the Cupin superfamily.

Literature references

  1. Wendler WM, Kremmer E, Forster R, Winnacker EL; , J Biol Chem 1997;272:8482-8489.: Identification of pirin, a novel highly conserved nuclear protein. PUBMED:9079676 EPMC:9079676

  2. Orzaez D, de Jong AJ, Woltering EJ; , Plant Mol Biol 2001;46:459-468.: A tomato homologue of the human protein PIRIN is induced during programmed cell death. PUBMED:11485202 EPMC:11485202

  3. Dechend R, Hirano F, Lehmann K, Heissmeyer V, Ansieau S, Wulczyn FG, Scheidereit C, Leutz A; , Oncogene 1999;18:3316-3323.: The Bcl-3 oncoprotein acts as a bridging factor between NF-kappaB/Rel and nuclear co-regulators. PUBMED:10362352 EPMC:10362352

  4. Pang H, Bartlam M, Zeng Q, Miyatake H, Hisano T, Miki K, Wong LL, Gao GF, Rao Z; , J Biol Chem 2004;279:1491-1498.: Crystal structure of human pirin: an iron-binding nuclear protein and transcription cofactor. PUBMED:14573596 EPMC:14573596

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003829

This entry represents the Pirin N-terminal domain.

Eukaryotic pirins are highly conserved nuclear proteins that may function as transcriptional regulators with a role in apoptosis [ PUBMED:21514450 , PUBMED:11485202 ]. Prokaryotic homologues have also been identified. Both bacterial and human pirins have been shown to possess quercetinase activity [ PUBMED:15951572 ], although this is not universally true for all family members - YhaK ( SWISSPROT ), for example, displays no such enzymatic activity [ PUBMED:18561187 ].

Pirin is composed of two structurally similar domains arranged face to face. Although the two domains are similar, the C-terminal domain of pirin differs from the N-terminal domain as it does not contain a metal binding site and its sequence does not contain the conserved metal-coordinating residues [ PUBMED:14573596 ].

Pirin is considered a member of the cupin superfamily on the basis of primary sequence and structural similarity. The presence of a metal binding site in the N-terminal beta-barrel of pirin, may be significant in its interaction with Bcl-3 and nuclear factor I (NFI) and role in regulating NF-kappaB transcription factor activity [ PUBMED:14573596 ].

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: COG1741
Previous IDs: DUF209;
Type: Family
Sequence Ontology: SO:0100021
Author: Mian N , Bateman A , Moxon SJ , Yeats C
Number in seed: 37
Number in full: 13497
Average length of the domain: 107.00 aa
Average identity of full alignment: 35 %
Average coverage of the sequence by the domain: 37.29 %

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 26.1 26.1
Trusted cut-off 26.2 26.1
Noise cut-off 26.0 26.0
Model length: 108
Family (HMM) version: 18
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 Pirin domain has been found. There are 22 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
A0A0R0EY21 View 3D Structure Click here
A0A0R0J157 View 3D Structure Click here
A0A0R0KN26 View 3D Structure Click here
A0A1D6FJU3 View 3D Structure Click here
A0A1D6LBR8 View 3D Structure Click here
A0A1D6P132 View 3D Structure Click here
A0A1D8PDN9 View 3D Structure Click here
A0A1D8PDP2 View 3D Structure Click here
B4FDB3 View 3D Structure Click here
B4FMB9 View 3D Structure Click here
C0P2Q1 View 3D Structure Click here
C7G074 View 3D Structure Click here
F1QLW3 View 3D Structure Click here
I1JJF8 View 3D Structure Click here
I1KYF4 View 3D Structure Click here
I1M6K5 View 3D Structure Click here
I1N5F6 View 3D Structure Click here
O00625 View 3D Structure Click here
P42624 View 3D Structure Click here
P46852 View 3D Structure Click here
P9WI85 View 3D Structure Click here
Q0J0T5 View 3D Structure Click here
Q0J657 View 3D Structure Click here
Q54EK6 View 3D Structure Click here
Q54I01 View 3D Structure Click here
Q54QI5 View 3D Structure Click here
Q54TP1 View 3D Structure Click here
Q54UE5 View 3D Structure Click here
Q54UE9 View 3D Structure Click here
Q54UY3 View 3D Structure Click here
Q557H8 View 3D Structure Click here
Q5AA21 View 3D Structure Click here
Q5AA23 View 3D Structure Click here
Q5M827 View 3D Structure Click here
Q75LB9 View 3D Structure Click here
Q9D711 View 3D Structure Click here
Q9LPS9 View 3D Structure Click here
Q9LX45 View 3D Structure Click here
Q9LX49 View 3D Structure Click here
Q9ZW82 View 3D Structure Click here