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31  structures 1426  species 0  interactions 7634  sequences 97  architectures

Family: CAF1 (PF04857)

Summary: CAF1 family ribonuclease

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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.

CAF1 family ribonuclease Provide feedback

The major pathways of mRNA turnover in eukaryotes initiate with shortening of the polyA tail. CAF1 P39008 encodes a critical component of the major cytoplasmic deadenylase in yeast. Both Caf1p is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent polyA-specific exonuclease activity. Some members of this family include and inserted RNA binding domain PF01424. This family of proteins is related to other exonucleases PF00929 (Bateman A pers. obs.). The crystal structure of Saccharomyces cerevisiae Pop2 (P39008) has been resolved at 2.3 Angstrom resolution [3].

Literature references

  1. Tucker M, Valencia-Sanchez MA, Staples RR, Chen J, Denis CL, Parker R; , Cell 2001;104:377-386.: The transcription factor associated Ccr4 and Caf1 proteins are components of the major cytoplasmic mRNA deadenylase in Saccharomyces cerevisiae. PUBMED:11239395 EPMC:11239395

  2. Korner CG, Wormington M, Muckenthaler M, Schneider S, Dehlin E, Wahle E; , EMBO J 1998;17:5427-5437.: The deadenylating nuclease (DAN) is involved in poly(A) tail removal during the meiotic maturation of Xenopus oocytes. PUBMED:9736620 EPMC:9736620

  3. Thore S, Mauxion F, Seraphin B, Suck D; , EMBO Rep 2003;4:1150-1155.: X-ray structure and activity of the yeast Pop2 protein: a nuclease subunit of the mRNA deadenylase complex. PUBMED:14618157 EPMC:14618157


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006941

The major pathways of mRNA turnover in eukaryotes initiate with shortening of the poly(A) tail. CAF1 (also known as CCR4-associated factor 1) is an RNase of the DEDD superfamily, and a subunit of the CCR4-NOT complex that mediates 3' to 5' mRNA deadenylation [ PUBMED:15215893 , PUBMED:15769875 ]. In yeast, CAF1 ( SWISSPROT ) is also known as POP2, and encodes a critical component of the major cytoplasmic deadenylase [ PUBMED:11410650 , PUBMED:11239395 ]. It is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. CAF1 copurifies with a CCR4-dependent poly(A)-specific exonuclease activity. The crystal structure of Saccharomyces cerevisiae POP2 has been resolved [ PUBMED:14618157 ].

Some members of this family contain a single-stranded nucleic acid binding domain, R3H, such as poly(A)-specific ribonuclease (PARN), which also contains an RRM domain [ PUBMED:23388391 ]. PARN is only conserved in vertebrates and may be important in regulated deadenylation such as early developmentand DNA damage response [ PUBMED:15247430 , PUBMED:20379136 ].

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 and the UniProtKB sequence database. More...

View options

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
(139)
Full
(7634)
Representative proteomes UniProt
(13266)
RP15
(1377)
RP35
(3461)
RP55
(6046)
RP75
(8178)
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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
(139)
Full
(7634)
Representative proteomes UniProt
(13266)
RP15
(1377)
RP35
(3461)
RP55
(6046)
RP75
(8178)
Alignment:
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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
(139)
Full
(7634)
Representative proteomes UniProt
(13266)
RP15
(1377)
RP35
(3461)
RP55
(6046)
RP75
(8178)
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: Pfam-B_1567 (release 7.5)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 139
Number in full: 7634
Average length of the domain: 190.10 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 60.86 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 24.2 24.2
Trusted cut-off 24.2 24.2
Noise cut-off 24.1 24.1
Model length: 322
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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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 CAF1 domain has been found. There are 31 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
A0A096UWG8 View 3D Structure Click here
A0A0G2JZE8 View 3D Structure Click here
A0A0G2JZE8 View 3D Structure Click here
A0A0G2K6N8 View 3D Structure Click here
A0A0P0X2X3 View 3D Structure Click here
A0A0P0XR79 View 3D Structure Click here
A0A0R0HDH6 View 3D Structure Click here
A0A1D6E505 View 3D Structure Click here
A0A1D6F7T7 View 3D Structure Click here
A0A1D6F9L9 View 3D Structure Click here
A0A1D6JIJ1 View 3D Structure Click here
A0A1D6K8T2 View 3D Structure Click here
A0A1D6KJ93 View 3D Structure Click here
A0A1D6KNT8 View 3D Structure Click here
A0A1D6PPV8 View 3D Structure Click here
A0A1D6PPW1 View 3D Structure Click here
A0A1D6Q1N2 View 3D Structure Click here
A4I022 View 3D Structure Click here
A4I022 View 3D Structure Click here
A4I0A0 View 3D Structure Click here
A4IBC6 View 3D Structure Click here
A4IC91 View 3D Structure Click here
A8E5K6 View 3D Structure Click here
A8E5K6 View 3D Structure Click here
B2RXZ1 View 3D Structure Click here
B3DMA5 View 3D Structure Click here
B3DMA5 View 3D Structure Click here
B4FDJ4 View 3D Structure Click here
B4FG48 View 3D Structure Click here
B4FG48 View 3D Structure Click here
B4FK83 View 3D Structure Click here
B8A5U4 View 3D Structure Click here
B8A5U4 View 3D Structure Click here
B9FTH1 View 3D Structure Click here
C0PAU8 View 3D Structure Click here
C0PFF8 View 3D Structure Click here
C7J0V5 View 3D Structure Click here
I1JQ66 View 3D Structure Click here
I1JU83 View 3D Structure Click here
I1K8P4 View 3D Structure Click here
I1KGU2 View 3D Structure Click here
I1KGU2 View 3D Structure Click here
I1KVK6 View 3D Structure Click here
I1KVK6 View 3D Structure Click here
I1LKN4 View 3D Structure Click here
I1LRJ8 View 3D Structure Click here
I1LTY5 View 3D Structure Click here
I1M4A3 View 3D Structure Click here
I1NAS4 View 3D Structure Click here
K7LAC5 View 3D Structure Click here
K7LAL5 View 3D Structure Click here
K7MQH1 View 3D Structure Click here
K7U8Y1 View 3D Structure Click here
K7UPB7 View 3D Structure Click here
O64773 View 3D Structure Click here
O74856 View 3D Structure Click here
O74856 View 3D Structure Click here
O94386 View 3D Structure Click here
O95453 View 3D Structure Click here
P39008 View 3D Structure Click here
Q08BM8 View 3D Structure Click here
Q08BM8 View 3D Structure Click here
Q0DWT7 View 3D Structure Click here
Q0J5E9 View 3D Structure Click here
Q17345 View 3D Structure Click here
Q21412 View 3D Structure Click here
Q4CSP5 View 3D Structure Click here
Q4D3V7 View 3D Structure Click here
Q4DE88 View 3D Structure Click here
Q4DE88 View 3D Structure Click here
Q4DFY0 View 3D Structure Click here
Q4DH18 View 3D Structure Click here
Q4DQB5 View 3D Structure Click here
Q4DQB5 View 3D Structure Click here
Q4DW62 View 3D Structure Click here
Q4DYM4 View 3D Structure Click here
Q54NG7 View 3D Structure Click here
Q54NG7 View 3D Structure Click here
Q54PZ4 View 3D Structure Click here
Q54PZ4 View 3D Structure Click here
Q5U2U9 View 3D Structure Click here
Q5U2U9 View 3D Structure Click here
Q5VPG5 View 3D Structure Click here
Q5Z5E6 View 3D Structure Click here
Q60809 View 3D Structure Click here
Q60809 View 3D Structure Click here
Q6EQ06 View 3D Structure Click here
Q6EQ06 View 3D Structure Click here
Q6Z9G7 View 3D Structure Click here
Q7XPU5 View 3D Structure Click here
Q7ZU92 View 3D Structure Click here
Q86I34 View 3D Structure Click here
Q8IL36 View 3D Structure Click here
Q8NA58 View 3D Structure Click here
Q8S804 View 3D Structure Click here
Q8VDG3 View 3D Structure Click here
Q8W4C3 View 3D Structure Click here
Q96GM8 View 3D Structure Click here
Q96GM8 View 3D Structure Click here
Q9C6M9 View 3D Structure Click here
Q9D2E2 View 3D Structure Click here
Q9D2E2 View 3D Structure Click here
Q9D8X5 View 3D Structure Click here
Q9D8X5 View 3D Structure Click here
Q9FMS6 View 3D Structure Click here
Q9LEU4 View 3D Structure Click here
Q9LG26 View 3D Structure Click here
Q9LXM2 View 3D Structure Click here
Q9LXM4 View 3D Structure Click here
Q9LXM4 View 3D Structure Click here
Q9NA76 View 3D Structure Click here
Q9NA76 View 3D Structure Click here
Q9S9P2 View 3D Structure Click here
Q9S9P2 View 3D Structure Click here
Q9SAI2 View 3D Structure Click here
Q9SAI2 View 3D Structure Click here
Q9SFX6 View 3D Structure Click here
Q9SHJ0 View 3D Structure Click here
Q9SHJ0 View 3D Structure Click here
Q9SKZ2 View 3D Structure Click here
Q9SKZ2 View 3D Structure Click here
Q9UFF9 View 3D Structure Click here
Q9UFF9 View 3D Structure Click here
Q9UIV1 View 3D Structure Click here
Q9UIV1 View 3D Structure Click here
X2JCC3 View 3D Structure Click here
X2JCC3 View 3D Structure Click here