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{
"metadata": {
"accession": "IPR001313",
"entry_id": null,
"type": "repeat",
"go_terms": [
{
"identifier": "GO:0003723",
"name": "RNA binding",
"category": {
"code": "F",
"name": "molecular_function"
}
}
],
"source_database": "interpro",
"member_databases": {
"pfam": {
"PF22493": "NOP9-like PUF repeat domain",
"PF00806": "Pumilio-family RNA binding repeat"
},
"profile": {
"PS50302": "Pumilio RNA-binding repeat profile"
},
"smart": {
"SM00025": "Pumilio-like repeats"
}
},
"integrated": null,
"hierarchy": {
"accession": "IPR001313",
"name": "Pumilio RNA-binding repeat",
"type": "Repeat",
"children": []
},
"name": {
"name": "Pumilio RNA-binding repeat",
"short": "Pumilio_RNA-bd_rpt"
},
"description": [
{
"text": "<p>Members of the Pumilio family of proteins (Puf) regulate translation and mRNA stability in a wide variety of eukaryotic organisms including mammals, flies, worms, slime mold, and yeast [[cite:PUB00018238]]. Pumilio family members are characterised by the presence of eight tandem copies of an imperfectly repeated 36 amino acids sequence motif, the Pumilio repeat, surrounded by a short N- and C-terminal conserved region. The eight repeats and the N- and C-terminal regions form the Pumilio homology domain (PUM-HD). The PUM-HD domain is a sequence-specific RNA binding domain. The Puf family of proteins are mainly post-transcriptional regulators. Several Puf members have been shown to bind specific RNA sequences mainly found in the 3' UTR of mRNA and repress their translation [[cite:PUB00018239], [cite:PUB00094378]]. Frequently, Puf proteins function asymmetrically to create protein gradients, thus causing asymmetric cell division and regulating cell fate specification [[cite:PUB00018240]].</p>\n\n<p>Crystal structure of Pumilio repeats has been solved [[cite:PUB00018241]]. The PUM repeat with the N- and C-terminal regions pack together to form a right-handed superhelix that approximates a half doughnut structurally similar to the Armadillo (ARM) repeat proteins, beta-catenin and\nkaryopherin alpha. The RNA binds the concave surface of the molecule, where\neach of the protein's eight repeats makes contacts with a different RNA base\nvia three amino acid side chains at conserved positions [[cite:PUB00018242]].</p>\n\n<p>This entry represents the Pumilio repeat.</p>",
"llm": false,
"checked": false,
"updated": false
}
],
"wikipedia": null,
"literature": {
"PUB00018238": {
"PMID": 10662662,
"ISBN": null,
"volume": "10",
"issue": "2",
"year": 2000,
"title": "Translational repression: a duet of Nanos and Pumilio.",
"URL": null,
"raw_pages": "R81-3",
"medline_journal": "Curr Biol",
"ISO_journal": "Curr. Biol.",
"authors": [
"Parisi M",
"Lin H."
],
"DOI_URL": "http://dx.doi.org/10.1016/S0960-9822(00)00283-9"
},
"PUB00018239": {
"PMID": 14584586,
"ISBN": null,
"volume": "55",
"issue": "7",
"year": 2003,
"title": "The PUF family of RNA-binding proteins: does evolutionarily conserved structure equal conserved function?",
"URL": null,
"raw_pages": "359-66",
"medline_journal": "IUBMB Life",
"ISO_journal": "IUBMB Life",
"authors": [
"Spassov DS",
"Jurecic R."
],
"DOI_URL": "http://dx.doi.org/10.1080/15216540310001603093"
},
"PUB00018242": {
"PMID": 12202039,
"ISBN": null,
"volume": "110",
"issue": "4",
"year": 2002,
"title": "Modular recognition of RNA by a human pumilio-homology domain.",
"URL": null,
"raw_pages": "501-12",
"medline_journal": "Cell",
"ISO_journal": "Cell",
"authors": [
"Wang X",
"McLachlan J",
"Zamore PD",
"Hall TM."
],
"DOI_URL": "http://dx.doi.org/10.1016/S0092-8674(02)00873-5"
},
"PUB00018240": {
"PMID": 1459455,
"ISBN": null,
"volume": "6",
"issue": "12A",
"year": 1992,
"title": "Pumilio is essential for function but not for distribution of the Drosophila abdominal determinant Nanos.",
"URL": null,
"raw_pages": "2312-26",
"medline_journal": "Genes Dev",
"ISO_journal": "Genes Dev.",
"authors": [
"Barker DD",
"Wang C",
"Moore J",
"Dickinson LK",
"Lehmann R."
],
"DOI_URL": "http://www.genesdev.org/cgi/content/abstract/6/12A/2312"
},
"PUB00018241": {
"PMID": 11336708,
"ISBN": null,
"volume": "7",
"issue": "4",
"year": 2001,
"title": "Crystal structure of a Pumilio homology domain.",
"URL": null,
"raw_pages": "855-65",
"medline_journal": "Mol Cell",
"ISO_journal": "Mol. Cell",
"authors": [
"Wang X",
"Zamore PD",
"Hall TM."
],
"DOI_URL": "http://dx.doi.org/10.1016/S1097-2765(01)00229-5"
},
"PUB00094378": {
"PMID": 29385744,
"ISBN": null,
"volume": "19",
"issue": "2",
"year": 2018,
"title": "The PUF Protein Family: Overview on PUF RNA Targets, Biological Functions, and Post Transcriptional Regulation.",
"URL": null,
"raw_pages": null,
"medline_journal": "Int J Mol Sci",
"ISO_journal": "Int J Mol Sci",
"authors": [
"Wang M",
"Oge L",
"Perez-Garcia MD",
"Hamama L",
"Sakr S."
],
"DOI_URL": null
},
"PUB00050752": {
"PMID": 18328718,
"ISBN": null,
"volume": "16",
"issue": "4",
"year": 2008,
"title": "Structures of human Pumilio with noncognate RNAs reveal molecular mechanisms for binding promiscuity.",
"URL": null,
"raw_pages": "549-57",
"medline_journal": "Structure",
"ISO_journal": "Structure",
"authors": [
"Gupta YK",
"Nair DT",
"Wharton RP",
"Aggarwal AK."
],
"DOI_URL": "http://dx.doi.org/10.1016/j.str.2008.01.006"
},
"PUB00050806": {
"PMID": 18327269,
"ISBN": null,
"volume": "15",
"issue": "4",
"year": 2008,
"title": "Basis of altered RNA-binding specificity by PUF proteins revealed by crystal structures of yeast Puf4p.",
"URL": null,
"raw_pages": "397-402",
"medline_journal": "Nat Struct Mol Biol",
"ISO_journal": "Nat. Struct. Mol. Biol.",
"authors": [
"Miller MT",
"Higgin JJ",
"Hall TM."
],
"DOI_URL": "http://dx.doi.org/10.1038/nsmb.1390"
},
"PUB00052211": {
"PMID": 19540345,
"ISBN": null,
"volume": null,
"issue": null,
"year": 2009,
"title": "Structure and RNA binding of the mouse Pumilio-2 Puf Domain.",
"URL": null,
"raw_pages": null,
"medline_journal": "J Struct Biol",
"ISO_journal": "J. Struct. Biol.",
"authors": [
"Jenkins HT",
"Baker-Wilding R",
"Edwards TA."
],
"DOI_URL": null
},
"PUB00057141": {
"PMID": 21653694,
"ISBN": null,
"volume": "286",
"issue": "30",
"year": 2011,
"title": "Specific and modular binding code for cytosine recognition in Pumilio/FBF (PUF) RNA-binding domains.",
"URL": null,
"raw_pages": "26732-42",
"medline_journal": "J Biol Chem",
"ISO_journal": "J. Biol. Chem.",
"authors": [
"Dong S",
"Wang Y",
"Cassidy-Amstutz C",
"Lu G",
"Bigler R",
"Jezyk MR",
"Li C",
"Hall TM",
"Wang Z."
],
"DOI_URL": "http://dx.doi.org/10.1074/jbc.M111.244889"
}
},
"set_info": null,
"overlaps_with": [
{
"accession": "IPR011989",
"name": "Armadillo-like helical",
"type": "homologous_superfamily"
},
{
"accession": "IPR016024",
"name": "Armadillo-type fold",
"type": "homologous_superfamily"
}
],
"counters": {
"subfamilies": 0,
"domain_architectures": 551,
"interactions": 1,
"matches": 194208,
"pathways": 4,
"proteins": 34346,
"proteomes": 3602,
"sets": 0,
"structural_models": {
"alphafold": 29405,
"bfvd": 0
},
"structures": 78,
"taxa": 10282
},
"entry_annotations": {
"alignment:seed": 120,
"alignment:full": 3592
},
"cross_references": {
"prositedoc": {
"displayName": "PROSITE Doc",
"description": "PROSITE is a database of protein families and domains.",
"rank": 18,
"accessions": [
{
"accession": "PDOC50302",
"url": "http://prosite.expasy.org/PDOC50302"
}
]
}
},
"is_llm": false,
"is_reviewed_llm": false,
"is_updated_llm": false,
"representative_structure": {
"accession": "5kla",
"name": "Crystal structure of the drosophila Pumilio RNA-binding domain in complex with hunchback RNA"
}
}
}
