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427  structures 801  species 1  interaction 17429  sequences 92  architectures

Family: PUF (PF00806)

Summary: Pumilio-family RNA binding repeat

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Pumilio-family RNA binding repeat Provide feedback

Puf repeats (aka PUM-HD, Pumilio homology domain) are necessary and sufficient for sequence specific RNA binding in fly Pumilio and worm FBF-1 and FBF-2. Both proteins function as translational repressors in early embryonic development by binding sequences in the 3' UTR of target mRNAs (e.g. the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA). Other proteins that contain Puf domains are also plausible RNA binding proteins. P47135 for instance, appears to also contain a single RRM domain by HMM analysis. Puf domains usually occur as a tandem repeat of 8 domains. The Pfam model does not necessarily recognise all 8 repeats in all sequences; some sequences appear to have 5 or 6 repeats on initial analysis, but further analysis suggests the presence of additional divergent repeats. Structures of PUF repeat proteins show they consist of a two helix structure [3,4].

Literature references

  1. Zhang B, Gallegos M, Puoti A, Durkin E, Fields S, Kimble J, Wickens MP. , Nature 1997;390:477-484.: A conserved RNA-binding protein that regulates sexual fates in the C. elegans hermaphrodite germ line. PUBMED:9393998 EPMC:9393998

  2. Zamore PD, Williamson JR, Lehmann R. , RNA 1997;3:1421-1433.: The Pumilio protein binds RNA through a conserved domain that defines a new class of RNA-binding proteins. PUBMED:9404893 EPMC:9404893

  3. Edwards TA, Pyle SE, Wharton RP, Aggarwal AK; , Cell 2001;105:281-289.: Structure of Pumilio reveals similarity between RNA and peptide binding motifs. PUBMED:11336677 EPMC:11336677

  4. Wang X, Zamore PD, Hall TM; , Mol Cell 2001;7:855-865.: Crystal structure of a Pumilio homology domain. PUBMED:11336708 EPMC:11336708


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001313

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 [PUBMED:10662662]. 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. Several Puf members have been shown to bind specific RNA sequences mainly found in the 3' UTR of mRNA and repress their translation [PUBMED:14584586]. Frequently, Puf proteins function asymmetrically to create protein gradients, thus causing asymmetric cell division and regulating cell fate specification [PUBMED:1459455].

Crystal structure of Pumilio repeats has been solved [PUBMED:11336708]. 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 karyopherin alpha. The RNA binds the concave surface of the molecule, where each of the protein's eight repeats makes contacts with a different RNA base via three amino acid side chains at conserved positions [PUBMED:12202039].

This entry represents the Pumilio repeat.

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, 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
(50)
Full
(17429)
Representative proteomes UniProt
(24637)
NCBI
(45846)
Meta
(23)
RP15
(3781)
RP35
(8993)
RP55
(13485)
RP75
(16774)
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PP/heatmap 1                

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(50)
Full
(17429)
Representative proteomes UniProt
(24637)
NCBI
(45846)
Meta
(23)
RP15
(3781)
RP35
(8993)
RP55
(13485)
RP75
(16774)
Alignment:
Format:
Order:
Sequence:
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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
(50)
Full
(17429)
Representative proteomes UniProt
(24637)
NCBI
(45846)
Meta
(23)
RP15
(3781)
RP35
(8993)
RP55
(13485)
RP75
(16774)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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: [1]
Previous IDs: none
Type: Repeat
Author: Eddy SR
Number in seed: 50
Number in full: 17429
Average length of the domain: 33.60 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 20.03 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.2 18.6
Trusted cut-off 21.2 18.6
Noise cut-off 21.1 18.5
Model length: 35
Family (HMM) version: 18
Download: download the raw HMM for this family

Species distribution

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Interactions

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

PUF

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 PUF domain has been found. There are 427 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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