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360  structures 324  species 1  interaction 6866  sequences 49  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


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001313

The drosophila pumilio gene codes for an unusual protein that binds through the Puf domain that usually occurs as a tandem repeat of eight domains. The FBF-2 protein of Caenorhabditis elegans also has a Puf domain. Both proteins function as translational repressors in early embryonic development by binding sequences in the 3' UTR of target mRNAs [PUBMED:9393998, PUBMED:9404893]. The same type of repetitive domain has been found in in a number of other proteins from all eukaryotic kingdoms. The Puf proteins characterised to date have been reported to bind to 3'-untranslated region (UTR) sequences encompassing a so-called UGUR tetranucleotide motif and thereby to repress gene expression by affecting mRNA translation or stability.

In Saccharomyces cerevisiae (Baker's yeast), five proteins, termed Puf1p to Puf5p, bear six to eight Puf repeats [PUBMED:15024427]. Puf3p binds nearly exclusively to cytoplasmic mRNAs that encode mitochondrial proteins; Puf1p and Puf2p interact preferentially with mRNAs encoding membrane-associated proteins; Puf4p preferentially binds mRNAs encoding nucleolar ribosomal RNA-processing factors; and Puf5p is associated with mRNAs encoding chromatin modifiers and components of the spindle pole body. This suggests the existence of an extensive network of RNA-protein interactions that coordinate the post-transcriptional fate of large sets of cytotopically and functionally related RNAs through each stage of its lifecycle.

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
(6866)
Representative proteomes NCBI
(7032)
Meta
(23)
RP15
(1426)
RP35
(2555)
RP55
(3719)
RP75
(4462)
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Format an alignment

  Seed
(50)
Full
(6866)
Representative proteomes NCBI
(7032)
Meta
(23)
RP15
(1426)
RP35
(2555)
RP55
(3719)
RP75
(4462)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(6866)
Representative proteomes NCBI
(7032)
Meta
(23)
RP15
(1426)
RP35
(2555)
RP55
(3719)
RP75
(4462)
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: [1]
Previous IDs: none
Type: Repeat
Author: Eddy SR
Number in seed: 50
Number in full: 6866
Average length of the domain: 33.70 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 20.65 %

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 21.2 18.6
Trusted cut-off 21.2 18.6
Noise cut-off 21.1 18.5
Model length: 35
Family (HMM) version: 14
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 360 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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