Summary: CAF1 family ribonuclease
Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.
The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.
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
-
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
-
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
-
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
SCOOP: | DNA_pol_A_exo1 R3H zf-CCCH |
Similarity to PfamA using HHSearch: | RNase_T |
External database links
SCOP: | 1uoc |
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...
Loading domain graphics...
Pfam Clan
This family is a member of clan RNase_H (CL0219), which has the following description:
This clan includes a diverse set of nucleases that share a similar structure to Ribonuclease H.
The clan contains the following 64 members:
Arena_ncap_C CAF1 DDE_1 DDE_2 DDE_3 DDE_5 DDE_Tnp_1 DDE_Tnp_1_2 DDE_Tnp_1_3 DDE_Tnp_1_4 DDE_Tnp_1_5 DDE_Tnp_1_6 DDE_Tnp_1_7 DDE_Tnp_2 DDE_Tnp_4 DDE_Tnp_IS1 DDE_Tnp_IS1595 DDE_Tnp_IS240 DDE_Tnp_IS66 DDE_Tnp_ISAZ013 DDE_Tnp_ISL3 Dimer_Tnp_Tn5 DNA_pol_A_exo1 DNA_pol_B_exo1 DNA_pol_B_exo2 DNA_pol_P_Exo DUF1258 DUF2779 DUF3882 DUF4152 DUF5051 DUF99 Endonuclease_5 KDZ Maelstrom MULE NurA OrfB_IS605 Piwi Plant_tran Plavaka Pox_A22 RNase_H RNase_H_2 RNase_HII RNase_T RNaseH_like RT_RNaseH RT_RNaseH_2 RuvC RuvC_1 rve rve_2 rve_3 RVT_3 Taq-exonuc Terminase_3C Terminase_6C Transposase_1 Transposase_21 Transposase_mut UPF0236 UvrC_HhH_N Ydc2-catalytAlignments
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) |
||||
Jalview | |||||||
HTML | |||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
Format an alignment
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 | |||||||
Gzipped |
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
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
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: |
|
||||||||||||
Model length: | 322 | ||||||||||||
Family (HMM) version: | 22 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
Sunburst controls
HideWeight segments by...
Change the size of the sunburst
Colour assignments
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
Selections
Align selected sequences to HMM
Generate a FASTA-format file
Clear selection
This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...
Tree controls
HideThe tree shows the occurrence of this domain across different species. More...
Loading...
Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
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.
Loading structure mapping...