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674  structures 1559  species 0  interactions 65868  sequences 195  architectures

Family: PUF (PF00806)

Summary: Pumilio-family RNA binding repeat

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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.

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

  5. Wang M, Oge L, Perez-Garcia MD, Hamama L, Sakr S;, International Journal of Molecular Sciences 2018;19(2).: The PUF Protein Family: Overview on PUF RNA Targets, Biological Functions, and Post Transcriptional Regulation. PUBMED:29385744 EPMC:29385744


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. 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 [ PUBMED:14584586 , PUBMED:29385744 ]. 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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Pfam Clan

This family is a member of clan TPR (CL0020), which has the following description:

Tetratricopeptide-like repeats are found in a numerous and diverse proteins involved in such functions as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding.

The clan contains the following 252 members:

14-3-3 AAR2 Aconitase_B_N Adaptin_N Alkyl_sulf_dimr ANAPC3 ANAPC5 ANAPC8 Apc1_MidN APC_rep API5 Aquarius_N Arm Arm_2 Arm_3 Arm_vescicular Atx10homo_assoc B56 BAF250_C BRO1 BTAD CAS_CSE1 ChAPs CHIP_TPR_N CID CLASP_N Clathrin Clathrin-link Clathrin_H_link Clathrin_propel Cnd1 Cnd1_N Cnd3 CNOT1_CAF1_bind CNOT1_HEAT_N CNOT1_TTP_bind Coatomer_E Cohesin_HEAT Cohesin_load ComR_TPR COPI_C CPL CRM1_C CRM1_repeat CRM1_repeat_3 Cse1 CTK3 CTNNBL Cullin DHR-2_Lobe_A DHR-2_Lobe_C DIL DNA-PKcs_N DNA_alkylation DNAPKcs_CC1-2 DNAPKcs_CC3 DNAPKcs_CC5 Dopey_N Drf_FH3 Drf_GBD DUF1822 DUF2019 DUF2225 DUF3385 DUF3458_C DUF3730 DUF3856 DUF4042 DUF4704 DUF5071 DUF5106 DUF5588 DUF5691 DUF6340 DUF6377 DUF6584 DUF924 E_motif EAD11 eIF-3c_N ELMO_ARM EST1 EST1_DNA_bind FA_FANCE FANCF FANCI_HD1 FANCI_HD2 FANCI_S1 FANCI_S1-cap FANCI_S2 FANCI_S3 FANCI_S4 FAT Fes1 Fis1_TPR_C Fis1_TPR_N Focadhesin Foie-gras_1 GET4 GLE1 GUN4_N HAT HEAT HEAT_2 HEAT_EZ HEAT_PBS HEAT_UF HemY_N HMW1C_N HPS6_C HrpB1_HrpK HSM3_C HSM3_N Hyccin IBB IBN_N IFRD Iml2-TPR_39 Importin_rep Importin_rep_2 Importin_rep_3 Importin_rep_4 Importin_rep_5 Importin_rep_6 Insc_C Ints3_N KAP Kinetochor_Ybp2 Laa1_Sip1_HTR5 Leuk-A4-hydro_C LRV LRV_FeS MA3 Mad3_BUB1_I MAP3K_TRAF_bd MIF4G MIF4G_like MIF4G_like_2 MIX MMS19_C Mo25 MRP-S27 Mtf2 MUN NatA_aux_su Neurobeachin Neurochondrin Nic96 Nipped-B_C Not1 Nro1 NSF Paf67 ParcG PAT1 PC_rep PDS5 Peptidase_M9_N PHAT PI3Ka PknG_TPR PPP5 PPR PPR_1 PPR_2 PPR_3 PPR_long PPTA Proteasom_PSMB PUF PUL RAI16-like Rapsyn_N Rcd1 RIH_assoc RINT1_TIP1 RIX1 RNPP_C RPM2 RPN6_N RPN7 RYDR_ITPR Sel1 SHNi-TPR SIL1 SLT_L SNAP SPO22 SRP_TPR_like ST7 STAG Suf SusD-like SusD-like_2 SusD-like_3 SusD_RagB SYCP2_ARLD SYMPK_PTA1_N TAF1_subA TAF6_C TAL_effector TAP42 TAtT Tcf25 TIP120 TOM20_plant TPR-S TPR_1 TPR_10 TPR_11 TPR_12 TPR_14 TPR_15 TPR_16 TPR_17 TPR_18 TPR_19 TPR_2 TPR_20 TPR_21 TPR_22 TPR_3 TPR_4 TPR_5 TPR_6 TPR_7 TPR_8 TPR_9 TPR_MalT Tra1_ring TRF TTC7_N Type_III_YscG UNC45-central Upf2 Uso1_p115_head V-ATPase_H_C V-ATPase_H_N Vac14_Fab1_bd Vitellogenin_N Vps16_C Vps35 Vps39_1 VPS53_C W2 Wap1 WSLR Wzy_C_2 Xpo1 YcaO_C YfiO Zmiz1_N

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 and the UniProtKB 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
(1109)
Full
(65868)
Representative proteomes UniProt
(101595)
RP15
(10777)
RP35
(27921)
RP55
(49801)
RP75
(68858)
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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
(1109)
Full
(65868)
Representative proteomes UniProt
(101595)
RP15
(10777)
RP35
(27921)
RP55
(49801)
RP75
(68858)
Alignment:
Format:
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Sequence:
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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
(1109)
Full
(65868)
Representative proteomes UniProt
(101595)
RP15
(10777)
RP35
(27921)
RP55
(49801)
RP75
(68858)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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
Sequence Ontology: SO:0001068
Author: Eddy SR , Hirsh L
Number in seed: 1109
Number in full: 65868
Average length of the domain: 33.20 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 24.70 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.3 5.1
Trusted cut-off 26.3 5.7
Noise cut-off 26.2 -1000000.0
Model length: 35
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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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 674 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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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0N7KIR5 View 3D Structure Click here
A0A0P0VRF7 View 3D Structure Click here
A0A0P0W7A7 View 3D Structure Click here
A0A0P0WKY6 View 3D Structure Click here
A0A0P0XJ32 View 3D Structure Click here
A0A0R0F940 View 3D Structure Click here
A0A0R0G2S0 View 3D Structure Click here
A0A0R0K6R0 View 3D Structure Click here
A0A0R4IWL6 View 3D Structure Click here
A0A1D6EEV5 View 3D Structure Click here
A0A1D6EPD4 View 3D Structure Click here
A0A1D6FVZ8 View 3D Structure Click here
A0A1D6HPP4 View 3D Structure Click here
A0A1D6HTC9 View 3D Structure Click here
A0A1D6I3B8 View 3D Structure Click here
A0A1D6IUN0 View 3D Structure Click here
A0A1D6J492 View 3D Structure Click here
A0A1D6JSI5 View 3D Structure Click here
A0A1D6KCY5 View 3D Structure Click here
A0A1D6KJF9 View 3D Structure Click here
A0A1D6LHT6 View 3D Structure Click here
A0A1D6PXT6 View 3D Structure Click here
A0A1D8PFN4 View 3D Structure Click here
A0A1D8PHC4 View 3D Structure Click here
A0A1D8PJ46 View 3D Structure Click here
A0A1D8PMA5 View 3D Structure Click here
A0A1D8PNF9 View 3D Structure Click here
A0A368UHG3 View 3D Structure Click here
A4HSP8 View 3D Structure Click here
A4HY12 View 3D Structure Click here
A4HYX9 View 3D Structure Click here
A4HYY0 View 3D Structure Click here
A4HZH4 View 3D Structure Click here
A4I7Z0 View 3D Structure Click here
A4I8Y0 View 3D Structure Click here
A4ICY3 View 3D Structure Click here
B4FBB8 View 3D Structure Click here
B7F8F5 View 3D Structure Click here
C0PCJ5 View 3D Structure Click here
C0PGL0 View 3D Structure Click here