Summary: Pirin
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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
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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
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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
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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
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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
SCOOP: | AraC_binding Cupin_1 Cupin_2 Cupin_3 |
Similarity to PfamA using HHSearch: | Cupin_2 |
External database links
SCOP: | 1j1l |
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 65 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 AIM24 AraC_binding AraC_binding_2 AraC_N ARD Asp_Arg_Hydrox AUDH_Cupin Auxin_BP CDO_I CENP-C_C cNMP_binding CsiD Cupin_1 Cupin_2 Cupin_3 Cupin_4 Cupin_5 Cupin_6 Cupin_7 Cupin_8 DIOX_N DMSP_lyase dTDP_sugar_isom DUF1479 DUF1971 DUF386 DUF4437 DUF4867 DUF5070 Ectoine_synth ERG2_Sigma1R EutQ FdtA FTO_NTD GPI HgmA HutD JmjC JmjN KduI Lyx_isomer MannoseP_isomer Ofd1_CTDD Oxygenase-NA PCO_ADO PhyH Pirin Pirin_C Pirin_C_2 PMI_typeI Popeye Pox_C4_C10 Ppnp TauD Tet_JBP Ureidogly_lyase VIT VIT_2Alignments
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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics 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.
Seed (37) |
Full (11646) |
Representative proteomes | UniProt (48351) |
NCBI (67015) |
Meta (1845) |
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RP15 (1173) |
RP35 (4697) |
RP55 (11179) |
RP75 (20893) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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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.
Seed (37) |
Full (11646) |
Representative proteomes | UniProt (48351) |
NCBI (67015) |
Meta (1845) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (1173) |
RP35 (4697) |
RP55 (11179) |
RP75 (20893) |
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Raw Stockholm | |||||||||
Gzipped |
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
Seed source: | COG1741 |
Previous IDs: | DUF209; |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Mian N |
Number in seed: | 37 |
Number in full: | 11646 |
Average length of the domain: | 107.30 aa |
Average identity of full alignment: | 34 % |
Average coverage of the sequence by the domain: | 37.59 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 108 | ||||||||||||
Family (HMM) version: | 17 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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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Interactions
There is 1 interaction for this family. More...
Pirin_CStructures
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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