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5  structures 2388  species 1  interaction 4965  sequences 18  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


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003829

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].

This entry represents the Pirin N-terminal domain.

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 Cupin (CL0029), which has the following description:

This clan represents the conserved barrel domain of the 'cupin' superfamily [1] ('cupa' is the Latin term for a small barrel). The cupin fold is found in a wide variety of enzymes, but notably contains the non-enzymatic seed storage proteins also.

The clan contains the following 53 members:

2OG-Fe_Oxy_2 2OG-FeII_Oxy 2OG-FeII_Oxy_2 2OG-FeII_Oxy_3 2OG-FeII_Oxy_4 2OG-FeII_Oxy_5 3-HAO AraC_binding AraC_binding_2 AraC_N ARD Asp_Arg_Hydrox Auxin_BP CDO_I CENP-C_C CsiD Cupin_1 Cupin_2 Cupin_3 Cupin_4 Cupin_5 Cupin_6 Cupin_7 Cupin_8 dTDP_sugar_isom DUF1255 DUF1479 DUF1498 DUF1637 DUF1971 DUF386 DUF4437 Ectoine_synth EutQ FdtA FTO_NTD GPI HgmA HutD JmjC KduI MannoseP_isomer Ofd1_CTDD Oxygenase-NA PhyH Pirin Pirin_C PMI_typeI Pox_C4_C10 TauD Tet_JBP VIT VIT_2

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics 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
(52)
Full
(4965)
Representative proteomes NCBI
(3896)
Meta
(1851)
RP15
(450)
RP35
(941)
RP55
(1293)
RP75
(1562)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(52)
Full
(4965)
Representative proteomes NCBI
(3896)
Meta
(1851)
RP15
(450)
RP35
(941)
RP55
(1293)
RP75
(1562)
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
(52)
Full
(4965)
Representative proteomes NCBI
(3896)
Meta
(1851)
RP15
(450)
RP35
(941)
RP55
(1293)
RP75
(1562)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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: COG1741
Previous IDs: DUF209;
Type: Family
Author: Mian N, Bateman A, Moxon SJ, Yeats C
Number in seed: 52
Number in full: 4965
Average length of the domain: 109.40 aa
Average identity of full alignment: 35 %
Average coverage of the sequence by the domain: 40.71 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.1 26.1
Trusted cut-off 26.5 26.1
Noise cut-off 25.9 26.0
Model length: 107
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

Pirin_C

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 Pirin domain has been found. There are 5 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 seqence.

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